diff --git a/_r_e_a_d_m_e_8md.html b/_r_e_a_d_m_e_8md.html index 8acd5a414..31aa97ade 100644 --- a/_r_e_a_d_m_e_8md.html +++ b/_r_e_a_d_m_e_8md.html @@ -102,7 +102,7 @@ diff --git a/annotated.html b/annotated.html index 70c120782..447336230 100644 --- a/annotated.html +++ b/annotated.html @@ -147,7 +147,7 @@ diff --git a/barray-bones_8hpp.html b/barray-bones_8hpp.html index 97b56920a..9d1d21bf5 100644 --- a/barray-bones_8hpp.html +++ b/barray-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/barray-bones_8hpp_source.html b/barray-bones_8hpp_source.html index eb1db405e..b8931122e 100644 --- a/barray-bones_8hpp_source.html +++ b/barray-bones_8hpp_source.html @@ -328,7 +328,7 @@ diff --git a/barray-iterator_8hpp.html b/barray-iterator_8hpp.html index 926cb15e2..8aa926a8c 100644 --- a/barray-iterator_8hpp.html +++ b/barray-iterator_8hpp.html @@ -112,7 +112,7 @@ diff --git a/barray-iterator_8hpp_source.html b/barray-iterator_8hpp_source.html index d9e27f6e6..c66707358 100644 --- a/barray-iterator_8hpp_source.html +++ b/barray-iterator_8hpp_source.html @@ -148,7 +148,7 @@ diff --git a/barray-meat-operators_8hpp.html b/barray-meat-operators_8hpp.html index 230d316ed..8fb27a4d2 100644 --- a/barray-meat-operators_8hpp.html +++ b/barray-meat-operators_8hpp.html @@ -576,7 +576,7 @@

diff --git a/barray-meat-operators_8hpp_source.html b/barray-meat-operators_8hpp_source.html index d490aa955..ed4e76971 100644 --- a/barray-meat-operators_8hpp_source.html +++ b/barray-meat-operators_8hpp_source.html @@ -240,7 +240,7 @@ diff --git a/barray-meat_8hpp.html b/barray-meat_8hpp.html index f39fab211..99540a864 100644 --- a/barray-meat_8hpp.html +++ b/barray-meat_8hpp.html @@ -164,7 +164,7 @@

  • include
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    • -
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    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barray-meat_8hpp_source.html b/barray-meat_8hpp_source.html index 3e01ae6bf..f115f7f09 100644 --- a/barray-meat_8hpp_source.html +++ b/barray-meat_8hpp_source.html @@ -1441,7 +1441,7 @@ diff --git a/barraycell-bones_8hpp.html b/barraycell-bones_8hpp.html index bf618bbbd..779e30e1d 100644 --- a/barraycell-bones_8hpp.html +++ b/barraycell-bones_8hpp.html @@ -123,7 +123,7 @@ diff --git a/barraycell-bones_8hpp_source.html b/barraycell-bones_8hpp_source.html index 89407af25..e8a12b9be 100644 --- a/barraycell-bones_8hpp_source.html +++ b/barraycell-bones_8hpp_source.html @@ -204,7 +204,7 @@ diff --git a/barraycell-meat_8hpp.html b/barraycell-meat_8hpp.html index 626b424f3..3e0437857 100644 --- a/barraycell-meat_8hpp.html +++ b/barraycell-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/barraycell-meat_8hpp_source.html b/barraycell-meat_8hpp_source.html index 00a29b84d..00f5a7f88 100644 --- a/barraycell-meat_8hpp_source.html +++ b/barraycell-meat_8hpp_source.html @@ -220,7 +220,7 @@ diff --git a/barraydense-bones_8hpp.html b/barraydense-bones_8hpp.html index 86777bb63..8c911c839 100644 --- a/barraydense-bones_8hpp.html +++ b/barraydense-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/barraydense-bones_8hpp_source.html b/barraydense-bones_8hpp_source.html index f37f9e7e1..d5c993328 100644 --- a/barraydense-bones_8hpp_source.html +++ b/barraydense-bones_8hpp_source.html @@ -340,7 +340,7 @@ diff --git a/barraydense-meat-operators_8hpp.html b/barraydense-meat-operators_8hpp.html index 12d576886..24607ff33 100644 --- a/barraydense-meat-operators_8hpp.html +++ b/barraydense-meat-operators_8hpp.html @@ -481,7 +481,7 @@

  • include
  • barry
  • barraydense-meat-operators.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydense-meat-operators_8hpp_source.html b/barraydense-meat-operators_8hpp_source.html index c5e62e147..33cda638f 100644 --- a/barraydense-meat-operators_8hpp_source.html +++ b/barraydense-meat-operators_8hpp_source.html @@ -231,7 +231,7 @@ diff --git a/barraydense-meat_8hpp.html b/barraydense-meat_8hpp.html index 9cf36dd03..c5254d6cc 100644 --- a/barraydense-meat_8hpp.html +++ b/barraydense-meat_8hpp.html @@ -252,7 +252,7 @@

  • include
  • barry
  • barraydense-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydense-meat_8hpp_source.html b/barraydense-meat_8hpp_source.html index 640720a5c..a098646dd 100644 --- a/barraydense-meat_8hpp_source.html +++ b/barraydense-meat_8hpp_source.html @@ -1192,7 +1192,7 @@ diff --git a/barraydensecell-bones_8hpp.html b/barraydensecell-bones_8hpp.html index e6126fdcf..bb2bb0ec9 100644 --- a/barraydensecell-bones_8hpp.html +++ b/barraydensecell-bones_8hpp.html @@ -158,7 +158,7 @@

  • include
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  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecell-bones_8hpp_source.html b/barraydensecell-bones_8hpp_source.html index 739e7a824..8a9df64bd 100644 --- a/barraydensecell-bones_8hpp_source.html +++ b/barraydensecell-bones_8hpp_source.html @@ -189,7 +189,7 @@ diff --git a/barraydensecell-meat_8hpp.html b/barraydensecell-meat_8hpp.html index 6dda7ef66..6eec6e04e 100644 --- a/barraydensecell-meat_8hpp.html +++ b/barraydensecell-meat_8hpp.html @@ -152,7 +152,7 @@

  • include
  • barry
  • barraydensecell-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecell-meat_8hpp_source.html b/barraydensecell-meat_8hpp_source.html index 09bb780f0..74bbeb95b 100644 --- a/barraydensecell-meat_8hpp_source.html +++ b/barraydensecell-meat_8hpp_source.html @@ -235,7 +235,7 @@ diff --git a/barraydensecol-bones_8hpp.html b/barraydensecol-bones_8hpp.html index 538025da5..949c69c4d 100644 --- a/barraydensecol-bones_8hpp.html +++ b/barraydensecol-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecol-bones_8hpp_source.html b/barraydensecol-bones_8hpp_source.html index ecad5550e..c6907f3c3 100644 --- a/barraydensecol-bones_8hpp_source.html +++ b/barraydensecol-bones_8hpp_source.html @@ -246,7 +246,7 @@ diff --git a/barraydenserow-bones_8hpp.html b/barraydenserow-bones_8hpp.html index 18868fe72..aabb95665 100644 --- a/barraydenserow-bones_8hpp.html +++ b/barraydenserow-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydenserow-bones_8hpp_source.html b/barraydenserow-bones_8hpp_source.html index 819f21195..9c4edb24f 100644 --- a/barraydenserow-bones_8hpp_source.html +++ b/barraydenserow-bones_8hpp_source.html @@ -257,7 +257,7 @@ diff --git a/barrayrow-bones_8hpp.html b/barrayrow-bones_8hpp.html index 129788bf7..7f3d03c36 100644 --- a/barrayrow-bones_8hpp.html +++ b/barrayrow-bones_8hpp.html @@ -114,7 +114,7 @@ diff --git a/barrayrow-bones_8hpp_source.html b/barrayrow-bones_8hpp_source.html index ee81aa938..fbfdfa37b 100644 --- a/barrayrow-bones_8hpp_source.html +++ b/barrayrow-bones_8hpp_source.html @@ -195,7 +195,7 @@ diff --git a/barrayrow-meat_8hpp.html b/barrayrow-meat_8hpp.html index fc6aaf70e..54298b400 100644 --- a/barrayrow-meat_8hpp.html +++ b/barrayrow-meat_8hpp.html @@ -350,7 +350,7 @@

  • include
  • barry
  • barrayrow-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barrayrow-meat_8hpp_source.html b/barrayrow-meat_8hpp_source.html index 29126db87..c761d05d6 100644 --- a/barrayrow-meat_8hpp_source.html +++ b/barrayrow-meat_8hpp_source.html @@ -229,7 +229,7 @@ diff --git a/barrayvector-bones_8hpp.html b/barrayvector-bones_8hpp.html index 9cf101e13..f032c8999 100644 --- a/barrayvector-bones_8hpp.html +++ b/barrayvector-bones_8hpp.html @@ -115,7 +115,7 @@ diff --git a/barrayvector-bones_8hpp_source.html b/barrayvector-bones_8hpp_source.html index 19c25bdc9..ec00c8725 100644 --- a/barrayvector-bones_8hpp_source.html +++ b/barrayvector-bones_8hpp_source.html @@ -232,7 +232,7 @@ diff --git a/barrayvector-meat_8hpp.html b/barrayvector-meat_8hpp.html index ed376ec8a..730ea59c6 100644 --- a/barrayvector-meat_8hpp.html +++ b/barrayvector-meat_8hpp.html @@ -104,7 +104,7 @@ diff --git a/barrayvector-meat_8hpp_source.html b/barrayvector-meat_8hpp_source.html index a2420c9b6..9e230f235 100644 --- a/barrayvector-meat_8hpp_source.html +++ b/barrayvector-meat_8hpp_source.html @@ -444,7 +444,7 @@ diff --git a/barry-configuration_8hpp.html b/barry-configuration_8hpp.html index 899ae471a..36e79c6e7 100644 --- a/barry-configuration_8hpp.html +++ b/barry-configuration_8hpp.html @@ -257,7 +257,7 @@

  • include
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    • -
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry-configuration_8hpp_source.html b/barry-configuration_8hpp_source.html index d7ce4c570..0f2af03d1 100644 --- a/barry-configuration_8hpp_source.html +++ b/barry-configuration_8hpp_source.html @@ -160,7 +160,7 @@ diff --git a/barry-debug_8hpp.html b/barry-debug_8hpp.html index a7367411a..804ea8257 100644 --- a/barry-debug_8hpp.html +++ b/barry-debug_8hpp.html @@ -139,7 +139,7 @@

  • include
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diff --git a/barry-debug_8hpp_source.html b/barry-debug_8hpp_source.html index 2598fef55..356f199d0 100644 --- a/barry-debug_8hpp_source.html +++ b/barry-debug_8hpp_source.html @@ -145,7 +145,7 @@ diff --git a/barry-macros_8hpp.html b/barry-macros_8hpp.html index 720e21e15..8d19d9be2 100644 --- a/barry-macros_8hpp.html +++ b/barry-macros_8hpp.html @@ -236,7 +236,7 @@

  • include
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry-macros_8hpp_source.html b/barry-macros_8hpp_source.html index c07bc0c94..6d7722ca2 100644 --- a/barry-macros_8hpp_source.html +++ b/barry-macros_8hpp_source.html @@ -121,7 +121,7 @@ diff --git a/barry_8hpp.html b/barry_8hpp.html index 97f597a3f..d5d5a774c 100644 --- a/barry_8hpp.html +++ b/barry_8hpp.html @@ -401,7 +401,7 @@

  • include
  • barry
  • barry.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry_8hpp_source.html b/barry_8hpp_source.html index f66c392c1..ed0dd73e3 100644 --- a/barry_8hpp_source.html +++ b/barry_8hpp_source.html @@ -237,7 +237,7 @@ diff --git a/cell-bones_8hpp.html b/cell-bones_8hpp.html index 4ef0b46ec..c2c61de50 100644 --- a/cell-bones_8hpp.html +++ b/cell-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/cell-bones_8hpp_source.html b/cell-bones_8hpp_source.html index 6b0e5094d..5aad6198d 100644 --- a/cell-bones_8hpp_source.html +++ b/cell-bones_8hpp_source.html @@ -159,7 +159,7 @@ diff --git a/cell-meat_8hpp.html b/cell-meat_8hpp.html index 99979e61f..09cc0feef 100644 --- a/cell-meat_8hpp.html +++ b/cell-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/cell-meat_8hpp_source.html b/cell-meat_8hpp_source.html index f5b459820..de89f1bb2 100644 --- a/cell-meat_8hpp_source.html +++ b/cell-meat_8hpp_source.html @@ -180,7 +180,7 @@ diff --git a/class_b_array-members.html b/class_b_array-members.html index ea36a0f46..ee0e3f407 100644 --- a/class_b_array-members.html +++ b/class_b_array-members.html @@ -165,7 +165,7 @@ diff --git a/class_b_array.html b/class_b_array.html index 042aa9758..d6c155b60 100644 --- a/class_b_array.html +++ b/class_b_array.html @@ -2141,7 +2141,7 @@

  • BArray
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  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_cell-members.html b/class_b_array_cell-members.html index 50e10c7d7..5143e7314 100644 --- a/class_b_array_cell-members.html +++ b/class_b_array_cell-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_cell.html b/class_b_array_cell.html index fdd2db34f..2e43d805a 100644 --- a/class_b_array_cell.html +++ b/class_b_array_cell.html @@ -430,7 +430,7 @@

  • BArrayCell
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diff --git a/class_b_array_cell__const-members.html b/class_b_array_cell__const-members.html index 2a5173a8e..7e27e0a38 100644 --- a/class_b_array_cell__const-members.html +++ b/class_b_array_cell__const-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_cell__const.html b/class_b_array_cell__const.html index 171dd36da..6909aa105 100644 --- a/class_b_array_cell__const.html +++ b/class_b_array_cell__const.html @@ -430,7 +430,7 @@

  • BArrayCell_const
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diff --git a/class_b_array_dense-members.html b/class_b_array_dense-members.html index 78627a6e4..6efa01876 100644 --- a/class_b_array_dense-members.html +++ b/class_b_array_dense-members.html @@ -170,7 +170,7 @@ diff --git a/class_b_array_dense.html b/class_b_array_dense.html index 282b85e73..65bd2641a 100644 --- a/class_b_array_dense.html +++ b/class_b_array_dense.html @@ -2668,7 +2668,7 @@

  • BArrayDense
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diff --git a/class_b_array_dense_cell-members.html b/class_b_array_dense_cell-members.html index 80e10d663..dd8bf1bb0 100644 --- a/class_b_array_dense_cell-members.html +++ b/class_b_array_dense_cell-members.html @@ -117,7 +117,7 @@ diff --git a/class_b_array_dense_cell.html b/class_b_array_dense_cell.html index 866d0fbc2..3be953a75 100644 --- a/class_b_array_dense_cell.html +++ b/class_b_array_dense_cell.html @@ -550,7 +550,7 @@

  • BArrayDenseCell
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diff --git a/class_b_array_dense_cell__const.html b/class_b_array_dense_cell__const.html index 596d4c1bb..57c0f237d 100644 --- a/class_b_array_dense_cell__const.html +++ b/class_b_array_dense_cell__const.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_col-members.html b/class_b_array_dense_col-members.html index 4f6557058..8e7aba9a6 100644 --- a/class_b_array_dense_col-members.html +++ b/class_b_array_dense_col-members.html @@ -112,7 +112,7 @@ diff --git a/class_b_array_dense_col.html b/class_b_array_dense_col.html index 044e4f815..70bdb5672 100644 --- a/class_b_array_dense_col.html +++ b/class_b_array_dense_col.html @@ -379,7 +379,7 @@

  • BArrayDenseCol
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  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_b_array_dense_col__const-members.html b/class_b_array_dense_col__const-members.html index 364e035d1..adc0fdd81 100644 --- a/class_b_array_dense_col__const-members.html +++ b/class_b_array_dense_col__const-members.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_col__const.html b/class_b_array_dense_col__const.html index 039e834e0..8f9dd34d4 100644 --- a/class_b_array_dense_col__const.html +++ b/class_b_array_dense_col__const.html @@ -351,7 +351,7 @@

  • BArrayDenseCol_const
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diff --git a/class_b_array_dense_row-members.html b/class_b_array_dense_row-members.html index a984a796b..bcfefbaad 100644 --- a/class_b_array_dense_row-members.html +++ b/class_b_array_dense_row-members.html @@ -112,7 +112,7 @@ diff --git a/class_b_array_dense_row.html b/class_b_array_dense_row.html index 065887554..91252b6ce 100644 --- a/class_b_array_dense_row.html +++ b/class_b_array_dense_row.html @@ -379,7 +379,7 @@

  • BArrayDenseRow
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diff --git a/class_b_array_dense_row__const-members.html b/class_b_array_dense_row__const-members.html index 85266f11f..d25ccceda 100644 --- a/class_b_array_dense_row__const-members.html +++ b/class_b_array_dense_row__const-members.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_row__const.html b/class_b_array_dense_row__const.html index 3ff1d3db2..9b67d9851 100644 --- a/class_b_array_dense_row__const.html +++ b/class_b_array_dense_row__const.html @@ -351,7 +351,7 @@

  • BArrayDenseRow_const
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  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_b_array_row-members.html b/class_b_array_row-members.html index 5edd3809c..2ed91256d 100644 --- a/class_b_array_row-members.html +++ b/class_b_array_row-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_row.html b/class_b_array_row.html index d4c98de41..53fcd7c91 100644 --- a/class_b_array_row.html +++ b/class_b_array_row.html @@ -354,7 +354,7 @@

  • BArrayRow
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diff --git a/class_b_array_row__const-members.html b/class_b_array_row__const-members.html index 20c75ee1e..6426d4682 100644 --- a/class_b_array_row__const-members.html +++ b/class_b_array_row__const-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_row__const.html b/class_b_array_row__const.html index 6d00c835a..285165550 100644 --- a/class_b_array_row__const.html +++ b/class_b_array_row__const.html @@ -354,7 +354,7 @@

  • BArrayRow_const
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_vector-members.html b/class_b_array_vector-members.html index 5fac0c97c..2d6bfb5b3 100644 --- a/class_b_array_vector-members.html +++ b/class_b_array_vector-members.html @@ -118,7 +118,7 @@ diff --git a/class_b_array_vector.html b/class_b_array_vector.html index 997c0be61..3d6337999 100644 --- a/class_b_array_vector.html +++ b/class_b_array_vector.html @@ -585,7 +585,7 @@

  • BArrayVector
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_vector__const-members.html b/class_b_array_vector__const-members.html index a3b1e884a..d3f0316de 100644 --- a/class_b_array_vector__const-members.html +++ b/class_b_array_vector__const-members.html @@ -118,7 +118,7 @@ diff --git a/class_b_array_vector__const.html b/class_b_array_vector__const.html index edb99a90f..1dbd6c839 100644 --- a/class_b_array_vector__const.html +++ b/class_b_array_vector__const.html @@ -567,7 +567,7 @@

  • BArrayVector_const
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_cell-members.html b/class_cell-members.html index 79bf5b57f..3cf2e9de7 100644 --- a/class_cell-members.html +++ b/class_cell-members.html @@ -124,7 +124,7 @@ diff --git a/class_cell.html b/class_cell.html index 7c127389f..7af8e4234 100644 --- a/class_cell.html +++ b/class_cell.html @@ -695,7 +695,7 @@

  • Cell
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_cell__const.html b/class_cell__const.html index 34fdb4503..f5b9b485f 100644 --- a/class_cell__const.html +++ b/class_cell__const.html @@ -111,7 +111,7 @@ diff --git a/class_const_b_array_row_iter-members.html b/class_const_b_array_row_iter-members.html index 0213d0c53..8f3d34967 100644 --- a/class_const_b_array_row_iter-members.html +++ b/class_const_b_array_row_iter-members.html @@ -110,7 +110,7 @@ diff --git a/class_const_b_array_row_iter.html b/class_const_b_array_row_iter.html index 0e2cbf4ea..229131594 100644 --- a/class_const_b_array_row_iter.html +++ b/class_const_b_array_row_iter.html @@ -278,7 +278,7 @@

  • ConstBArrayRowIter
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_counter-members.html b/class_counter-members.html index f8c9feb97..927aa1031 100644 --- a/class_counter-members.html +++ b/class_counter-members.html @@ -123,7 +123,7 @@ diff --git a/class_counter.html b/class_counter.html index 8a8211af5..653874651 100644 --- a/class_counter.html +++ b/class_counter.html @@ -679,7 +679,7 @@

  • Counter
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_counters-members.html b/class_counters-members.html index 5a7e63c4b..302406210 100644 --- a/class_counters-members.html +++ b/class_counters-members.html @@ -118,7 +118,7 @@ diff --git a/class_counters.html b/class_counters.html index 5da538fd9..747046419 100644 --- a/class_counters.html +++ b/class_counters.html @@ -573,7 +573,7 @@

  • Counters
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_d_e_f_m-members.html b/class_d_e_f_m-members.html index b6031871d..3b8edf253 100644 --- a/class_d_e_f_m-members.html +++ b/class_d_e_f_m-members.html @@ -124,7 +124,7 @@ diff --git a/class_d_e_f_m.html b/class_d_e_f_m.html index 378cbfab8..0f8f203ee 100644 --- a/class_d_e_f_m.html +++ b/class_d_e_f_m.html @@ -811,7 +811,7 @@

  • DEFM
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_d_e_f_m_counter_data-members.html b/class_d_e_f_m_counter_data-members.html index ef3e923aa..0c6c7ee43 100644 --- a/class_d_e_f_m_counter_data-members.html +++ b/class_d_e_f_m_counter_data-members.html @@ -114,7 +114,7 @@ diff --git a/class_d_e_f_m_counter_data.html b/class_d_e_f_m_counter_data.html index 1f8b30640..27f6a9959 100644 --- a/class_d_e_f_m_counter_data.html +++ b/class_d_e_f_m_counter_data.html @@ -146,7 +146,7 @@ diff --git a/class_d_e_f_m_data-members.html b/class_d_e_f_m_data-members.html index 102846092..ec26843de 100644 --- a/class_d_e_f_m_data-members.html +++ b/class_d_e_f_m_data-members.html @@ -119,7 +119,7 @@ diff --git a/class_d_e_f_m_data.html b/class_d_e_f_m_data.html index 60f714697..519034cbe 100644 --- a/class_d_e_f_m_data.html +++ b/class_d_e_f_m_data.html @@ -164,7 +164,7 @@ diff --git a/class_d_e_f_m_rule_data-members.html b/class_d_e_f_m_rule_data-members.html index 1aab17ba3..94e44b329 100644 --- a/class_d_e_f_m_rule_data-members.html +++ b/class_d_e_f_m_rule_data-members.html @@ -114,7 +114,7 @@ diff --git a/class_d_e_f_m_rule_data.html b/class_d_e_f_m_rule_data.html index ce04ad054..cd47ff2ca 100644 --- a/class_d_e_f_m_rule_data.html +++ b/class_d_e_f_m_rule_data.html @@ -150,7 +150,7 @@ diff --git a/class_d_e_f_m_rule_dyn_data-members.html b/class_d_e_f_m_rule_dyn_data-members.html index ed3d7e254..06f0871e1 100644 --- a/class_d_e_f_m_rule_dyn_data-members.html +++ b/class_d_e_f_m_rule_dyn_data-members.html @@ -117,7 +117,7 @@ diff --git a/class_d_e_f_m_rule_dyn_data.html b/class_d_e_f_m_rule_dyn_data.html index c22adb983..d18be6f85 100644 --- a/class_d_e_f_m_rule_dyn_data.html +++ b/class_d_e_f_m_rule_dyn_data.html @@ -167,7 +167,7 @@ diff --git a/class_entries-members.html b/class_entries-members.html index 879f1e7fe..63bb4880c 100644 --- a/class_entries-members.html +++ b/class_entries-members.html @@ -111,7 +111,7 @@ diff --git a/class_entries.html b/class_entries.html index e4f2b381e..81ae49d3f 100644 --- a/class_entries.html +++ b/class_entries.html @@ -323,7 +323,7 @@

  • Entries
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_flock-members.html b/class_flock-members.html index 5f356d601..771a143f1 100644 --- a/class_flock-members.html +++ b/class_flock-members.html @@ -130,7 +130,7 @@ diff --git a/class_flock.html b/class_flock.html index 57d225cb7..747a2c9b1 100644 --- a/class_flock.html +++ b/class_flock.html @@ -948,7 +948,7 @@

  • Flock
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_freq_table-members.html b/class_freq_table-members.html index 2ebbe5880..8052abcce 100644 --- a/class_freq_table-members.html +++ b/class_freq_table-members.html @@ -115,7 +115,7 @@ diff --git a/class_freq_table.html b/class_freq_table.html index b381df5cb..12ee374aa 100644 --- a/class_freq_table.html +++ b/class_freq_table.html @@ -491,7 +491,7 @@

  • FreqTable
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_geese-members.html b/class_geese-members.html index fd4b498e7..5c6445833 100644 --- a/class_geese-members.html +++ b/class_geese-members.html @@ -159,7 +159,7 @@ diff --git a/class_geese.html b/class_geese.html index 7e02c3eac..952213ae9 100644 --- a/class_geese.html +++ b/class_geese.html @@ -1895,7 +1895,7 @@

  • Geese
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_model-members.html b/class_model-members.html index 0e679d2b0..9f6754ad8 100644 --- a/class_model-members.html +++ b/class_model-members.html @@ -194,7 +194,7 @@ diff --git a/class_model.html b/class_model.html index 547e3ec6b..121951d42 100644 --- a/class_model.html +++ b/class_model.html @@ -3234,7 +3234,7 @@

  • Model
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_net_counter_data-members.html b/class_net_counter_data-members.html index bb42beae9..ba65a0d51 100644 --- a/class_net_counter_data-members.html +++ b/class_net_counter_data-members.html @@ -109,7 +109,7 @@ diff --git a/class_net_counter_data.html b/class_net_counter_data.html index 316d70a79..4ff7869ca 100644 --- a/class_net_counter_data.html +++ b/class_net_counter_data.html @@ -261,7 +261,7 @@

  • NetCounterData
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_network_data-members.html b/class_network_data-members.html index 9d0e48ac7..05c65f245 100644 --- a/class_network_data-members.html +++ b/class_network_data-members.html @@ -110,7 +110,7 @@ diff --git a/class_network_data.html b/class_network_data.html index 6f01bd534..e4469bfb1 100644 --- a/class_network_data.html +++ b/class_network_data.html @@ -323,7 +323,7 @@

  • NetworkData
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_node-members.html b/class_node-members.html index b0e031d85..bce43e40b 100644 --- a/class_node-members.html +++ b/class_node-members.html @@ -125,7 +125,7 @@ diff --git a/class_node.html b/class_node.html index da322bfc7..f4e6172ec 100644 --- a/class_node.html +++ b/class_node.html @@ -687,7 +687,7 @@

  • Node
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_node_data-members.html b/class_node_data-members.html index a3d57f852..8af7b7e75 100644 --- a/class_node_data-members.html +++ b/class_node_data-members.html @@ -109,7 +109,7 @@ diff --git a/class_node_data.html b/class_node_data.html index 7b6a6115e..fb43632b1 100644 --- a/class_node_data.html +++ b/class_node_data.html @@ -260,7 +260,7 @@

  • NodeData
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_phylo_counter_data-members.html b/class_phylo_counter_data-members.html index f0a2e567a..2e2fe6780 100644 --- a/class_phylo_counter_data-members.html +++ b/class_phylo_counter_data-members.html @@ -117,7 +117,7 @@ diff --git a/class_phylo_counter_data.html b/class_phylo_counter_data.html index 8945a31f8..d4762b774 100644 --- a/class_phylo_counter_data.html +++ b/class_phylo_counter_data.html @@ -512,7 +512,7 @@

  • PhyloCounterData
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_phylo_rule_dyn_data-members.html b/class_phylo_rule_dyn_data-members.html index ce9d6c99a..cae99244d 100644 --- a/class_phylo_rule_dyn_data-members.html +++ b/class_phylo_rule_dyn_data-members.html @@ -112,7 +112,7 @@ diff --git a/class_phylo_rule_dyn_data.html b/class_phylo_rule_dyn_data.html index 2e1965a0a..03ae24152 100644 --- a/class_phylo_rule_dyn_data.html +++ b/class_phylo_rule_dyn_data.html @@ -330,7 +330,7 @@

  • PhyloRuleDynData
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_power_set-members.html b/class_power_set-members.html index 19a1d389d..0068f4585 100644 --- a/class_power_set-members.html +++ b/class_power_set-members.html @@ -129,7 +129,7 @@ diff --git a/class_power_set.html b/class_power_set.html index d3038f9e5..7804ed16c 100644 --- a/class_power_set.html +++ b/class_power_set.html @@ -845,7 +845,7 @@

  • PowerSet
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_progress-members.html b/class_progress-members.html index a8de9cdc1..21a4f5f52 100644 --- a/class_progress-members.html +++ b/class_progress-members.html @@ -108,7 +108,7 @@ diff --git a/class_progress.html b/class_progress.html index 5855d666f..424c4fa85 100644 --- a/class_progress.html +++ b/class_progress.html @@ -250,7 +250,7 @@

  • Progress
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_rule-members.html b/class_rule-members.html index 2771a8f4f..fe764b1f1 100644 --- a/class_rule-members.html +++ b/class_rule-members.html @@ -113,7 +113,7 @@ diff --git a/class_rule.html b/class_rule.html index 80b3d0471..a4b0d5ff0 100644 --- a/class_rule.html +++ b/class_rule.html @@ -452,7 +452,7 @@

  • Rule
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_rules-members.html b/class_rules-members.html index 6e5fcef2f..f6b961fb3 100644 --- a/class_rules-members.html +++ b/class_rules-members.html @@ -117,7 +117,7 @@ diff --git a/class_rules.html b/class_rules.html index fa0c60a99..1e2bb4199 100644 --- a/class_rules.html +++ b/class_rules.html @@ -617,7 +617,7 @@

  • Rules
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_stats_counter-members.html b/class_stats_counter-members.html index bc2dd4175..6a71b7d9f 100644 --- a/class_stats_counter-members.html +++ b/class_stats_counter-members.html @@ -118,7 +118,7 @@ diff --git a/class_stats_counter.html b/class_stats_counter.html index c2bdd8dfa..1a3bf764a 100644 --- a/class_stats_counter.html +++ b/class_stats_counter.html @@ -519,7 +519,7 @@

  • StatsCounter
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_support-members.html b/class_support-members.html index cf649e210..6e185d097 100644 --- a/class_support-members.html +++ b/class_support-members.html @@ -143,7 +143,7 @@ diff --git a/class_support.html b/class_support.html index a9aefc729..c59e6a5f5 100644 --- a/class_support.html +++ b/class_support.html @@ -1277,7 +1277,7 @@

  • Support
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/classes.html b/classes.html index 893616612..8ee250f19 100644 --- a/classes.html +++ b/classes.html @@ -140,7 +140,7 @@ diff --git a/col-bones_8hpp.html b/col-bones_8hpp.html index 651fe3551..b4790f83e 100644 --- a/col-bones_8hpp.html +++ b/col-bones_8hpp.html @@ -104,7 +104,7 @@ diff --git a/col-bones_8hpp_source.html b/col-bones_8hpp_source.html index 880f29743..f07a363ee 100644 --- a/col-bones_8hpp_source.html +++ b/col-bones_8hpp_source.html @@ -159,7 +159,7 @@ diff --git a/counters-bones_8hpp.html b/counters-bones_8hpp.html index 731348f44..d08153812 100644 --- a/counters-bones_8hpp.html +++ b/counters-bones_8hpp.html @@ -125,7 +125,7 @@ diff --git a/counters-bones_8hpp_source.html b/counters-bones_8hpp_source.html index 47f519644..7f86d58e5 100644 --- a/counters-bones_8hpp_source.html +++ b/counters-bones_8hpp_source.html @@ -258,7 +258,7 @@ diff --git a/counters-meat_8hpp.html b/counters-meat_8hpp.html index b1df92750..811da304a 100644 --- a/counters-meat_8hpp.html +++ b/counters-meat_8hpp.html @@ -1560,7 +1560,7 @@

  • include
  • barry
  • counters-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/counters-meat_8hpp_source.html b/counters-meat_8hpp_source.html index 540d1bed1..6b6e86206 100644 --- a/counters-meat_8hpp_source.html +++ b/counters-meat_8hpp_source.html @@ -417,7 +417,7 @@ diff --git a/defm-bones_8hpp.html b/defm-bones_8hpp.html index eef1bf1bf..cbc02fa8b 100644 --- a/defm-bones_8hpp.html +++ b/defm-bones_8hpp.html @@ -121,7 +121,7 @@ diff --git a/defm-bones_8hpp_source.html b/defm-bones_8hpp_source.html index 56f264b5d..9db09dcb7 100644 --- a/defm-bones_8hpp_source.html +++ b/defm-bones_8hpp_source.html @@ -216,7 +216,7 @@ diff --git a/defm-meat_8hpp.html b/defm-meat_8hpp.html index 9f8598aee..efc6f5eb6 100644 --- a/defm-meat_8hpp.html +++ b/defm-meat_8hpp.html @@ -212,7 +212,7 @@

  • include
  • barry
  • models
  • defm
  • defm-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm-meat_8hpp_source.html b/defm-meat_8hpp_source.html index 9e02d0354..b3dcfaf5f 100644 --- a/defm-meat_8hpp_source.html +++ b/defm-meat_8hpp_source.html @@ -584,7 +584,7 @@
DEFM_LOOP_ARRAYS
#define DEFM_LOOP_ARRAYS(a)
Definition: defm-meat.hpp:36
DEFM_RANGES
#define DEFM_RANGES(a)
Definition: defm-meat.hpp:31
DEFMArray
barry::BArrayDense< int, DEFMData > DEFMArray
Definition: defm-types.hpp:3
-
rules_markov_fixed
void rules_markov_fixed(DEFMRules *rules, size_t markov_order)
Number of edges.
Definition: counters.hpp:674
+
rules_markov_fixed
void rules_markov_fixed(DEFMRules *rules, size_t markov_order)
Number of edges.
Definition: counters.hpp:723
@@ -592,7 +592,7 @@ diff --git a/defm-types_8hpp.html b/defm-types_8hpp.html index f404dd1b8..bef05d0db 100644 --- a/defm-types_8hpp.html +++ b/defm-types_8hpp.html @@ -171,7 +171,7 @@

  • include
  • barry
  • models
  • defm
  • defm-types.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm-types_8hpp_source.html b/defm-types_8hpp_source.html index 0ff3121a6..55164723f 100644 --- a/defm-types_8hpp_source.html +++ b/defm-types_8hpp_source.html @@ -305,7 +305,7 @@ diff --git a/defm_2counters_8hpp.html b/defm_2counters_8hpp.html index a3ff0a971..30d41f3a5 100644 --- a/defm_2counters_8hpp.html +++ b/defm_2counters_8hpp.html @@ -124,6 +124,7 @@

Macros

#define MAKE_DEFM_HASHER(hasher, a, cov) + Data for the counters. More...
  #define DEFM_RULEDYN_LAMBDA(a)   @@ -189,7 +190,7 @@

Function for definition of a network counter function

-

Definition at line 39 of file counters.hpp.

+

Definition at line 47 of file counters.hpp.

@@ -217,7 +218,7 @@

DEFMArray
barry::BArrayDense< int, DEFMData > DEFMArray
Definition: defm-types.hpp:3

Lambda function for definition of a network counter function

-

Definition at line 43 of file counters.hpp.

+

Definition at line 51 of file counters.hpp.

@@ -238,7 +239,7 @@

Function for definition of a network counter function

-

Definition at line 53 of file counters.hpp.

+

Definition at line 61 of file counters.hpp.

@@ -262,7 +263,7 @@

DEFMRuleData
Definition: defm-types.hpp:89

Lambda function for definition of a network counter function

-

Definition at line 57 of file counters.hpp.

+

Definition at line 65 of file counters.hpp.

@@ -286,7 +287,7 @@

DEFMRuleDynData
Definition: defm-types.hpp:152

Lambda function for definition of a network counter function

-

Definition at line 63 of file counters.hpp.

+

Definition at line 71 of file counters.hpp.

@@ -326,7 +327,7 @@

  • include
  • barry
  • models
  • defm
  • counters.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm_2counters_8hpp_source.html b/defm_2counters_8hpp_source.html index 3faa6145e..2a2a2198c 100644 --- a/defm_2counters_8hpp_source.html +++ b/defm_2counters_8hpp_source.html @@ -107,684 +107,715 @@
16 
17 
19 
-
20 
-
21 #define MAKE_DEFM_HASHER(hasher,a,cov) barry::Hasher_fun_type<DEFMArray,DEFMCounterData> \
-
22  hasher = [cov](const DEFMArray & array, DEFMCounterData * d) { \
-
23  std::vector< double > res; \
-
24  /* Adding the column feature */ \
-
25  for (size_t i = 0u; i < array.nrow(); ++i) \
-
26  res.push_back(array.D()(i, cov)); \
-
27  /* Adding the fixed dims */ \
-
28  for (size_t i = 0u; i < (array.nrow() - 1); ++i) \
-
29  for (size_t j = 0u; j < array.ncol(); ++j) \
-
30  res.push_back(array(i, j)); \
-
31  return res;\
-
32  };
-
33 
-
34 
-
38 
-
39 #define DEFM_COUNTER(a) \
-
40 inline double (a) (const DEFMArray & Array, size_t i, size_t j, DEFMCounterData & data)
+
27 #define MAKE_DEFM_HASHER(hasher,a,cov) \
+
28  barry::Hasher_fun_type<DEFMArray, DEFMCounterData> \
+
29  hasher = [cov](const DEFMArray & array, DEFMCounterData * d) -> \
+
30  std::vector< double > { \
+
31  std::vector< double > res; \
+
32  /* Adding the column feature */ \
+
33  for (size_t i = 0u; i < array.nrow(); ++i) \
+
34  res.push_back(array.D()(i, cov)); \
+
35  /* Adding the fixed dims */ \
+
36  for (size_t i = 0u; i < (array.nrow() - 1); ++i) \
+
37  for (size_t j = 0u; j < array.ncol(); ++j) \
+
38  res.push_back(array(i, j)); \
+
39  return res;\
+
40  };
41 
-
43 #define DEFM_COUNTER_LAMBDA(a) \
-
44 barry::Counter_fun_type<DEFMArray, DEFMCounterData> a = \
-
45  [](const DEFMArray & Array, size_t i, size_t j, DEFMCounterData & data) -> double
+
42 
46 
-
48 
-
52 
-
53 #define DEFM_RULE(a) \
-
54 inline bool (a) (const DEFMArray & Array, size_t i, size_t j, bool & data)
-
55 
-
57 #define DEFM_RULE_LAMBDA(a) \
-
58 barry::Rule_fun_type<DEFMArray, DEFMRuleData> a = \
-
59 [](const DEFMArray & Array, size_t i, size_t j, DEFMRuleData & data) -> bool
-
61 
-
63 #define DEFM_RULEDYN_LAMBDA(a) \
-
64 barry::Rule_fun_type<DEFMArray, DEFMRuleDynData> a = \
-
65 [](const DEFMArray & Array, size_t i, size_t j, DEFMRuleDynData & data) -> bool
-
67 
-
74 // -----------------------------------------------------------------------------
-
81 inline void counter_ones(
-
82  DEFMCounters * counters,
-
83  int covar_index = -1,
-
84  std::string vname = "",
-
85  const std::vector< std::string > * x_names = nullptr
-
86 )
-
87 {
-
88 
-
89  // Weighted by a feature of the array
-
90  if (covar_index >= 0)
-
91  {
-
92 
-
93  MAKE_DEFM_HASHER(hasher, array, covar_index)
-
94 
-
95  DEFM_COUNTER_LAMBDA(counter_tmp)
-
96  {
-
97 
-
98  // Only count the current
-
99  if (i != (Array.nrow() - 1))
-
100  return 0.0;
-
101 
-
102  return Array.D()(i, data.idx(0u));
-
103 
-
104  };
+
47 #define DEFM_COUNTER(a) \
+
48 inline double (a) (const DEFMArray & Array, size_t i, size_t j, DEFMCounterData & data)
+
49 
+
51 #define DEFM_COUNTER_LAMBDA(a) \
+
52 barry::Counter_fun_type<DEFMArray, DEFMCounterData> a = \
+
53  [](const DEFMArray & Array, size_t i, size_t j, DEFMCounterData & data) -> double
+
54 
+
56 
+
60 
+
61 #define DEFM_RULE(a) \
+
62 inline bool (a) (const DEFMArray & Array, size_t i, size_t j, bool & data)
+
63 
+
65 #define DEFM_RULE_LAMBDA(a) \
+
66 barry::Rule_fun_type<DEFMArray, DEFMRuleData> a = \
+
67 [](const DEFMArray & Array, size_t i, size_t j, DEFMRuleData & data) -> bool
+
69 
+
71 #define DEFM_RULEDYN_LAMBDA(a) \
+
72 barry::Rule_fun_type<DEFMArray, DEFMRuleDynData> a = \
+
73 [](const DEFMArray & Array, size_t i, size_t j, DEFMRuleDynData & data) -> bool
+
75 
+
82 // -----------------------------------------------------------------------------
+
89 inline void counter_ones(
+
90  DEFMCounters * counters,
+
91  int covar_index = -1,
+
92  std::string vname = "",
+
93  const std::vector< std::string > * x_names = nullptr
+
94 )
+
95 {
+
96 
+
97  // Weighted by a feature of the array
+
98  if (covar_index >= 0)
+
99  {
+
100 
+
101  MAKE_DEFM_HASHER(hasher, array, covar_index)
+
102 
+
103  DEFM_COUNTER_LAMBDA(counter_tmp)
+
104  {
105 
-
106  if (vname == "")
-
107  {
-
108  if (x_names != nullptr)
-
109  vname = x_names->operator[](covar_index);
-
110  else
-
111  vname = std::string("attr")+ std::to_string(covar_index);
-
112  }
+
106  // Only count the current
+
107  if (i != (Array.nrow() - 1))
+
108  return 0.0;
+
109 
+
110  return Array.D()(i, data.idx(0u));
+
111 
+
112  };
113 
-
114  counters->add_counter(
-
115  counter_tmp, nullptr, hasher,
-
116  DEFMCounterData({static_cast<size_t>(covar_index)}, {}, {}, true),
-
117  "Num. of ones x " + vname,
-
118  "Overall number of ones"
-
119  );
-
120 
-
121  }
-
122  else
-
123  {
-
124 
-
125  DEFM_COUNTER_LAMBDA(count_ones)
-
126  {
-
127 
-
128  // Only count the current
-
129  if (i != (Array.nrow() - 1))
-
130  return 0.0;
-
131 
-
132  return 1.0;
-
133  };
-
134 
-
135  DEFMCounterData dat;
-
136  dat.is_motif = true;
-
137 
-
138  counters->add_counter(
-
139  count_ones, nullptr, nullptr,
-
140  dat, // DEFMCounterData(),
-
141  "Num. of ones",
-
142  "Overall number of ones"
-
143  );
-
144  }
+
114  if (vname == "")
+
115  {
+
116  if (x_names != nullptr)
+
117  vname = x_names->operator[](covar_index);
+
118  else
+
119  vname = std::string("attr")+ std::to_string(covar_index);
+
120  }
+
121 
+
122  counters->add_counter(
+
123  counter_tmp, nullptr, hasher,
+
124  DEFMCounterData({static_cast<size_t>(covar_index)}, {}, {}, true),
+
125  "Num. of ones x " + vname,
+
126  "Overall number of ones"
+
127  );
+
128 
+
129  }
+
130  else
+
131  {
+
132 
+
133  DEFM_COUNTER_LAMBDA(count_ones)
+
134  {
+
135 
+
136  // Only count the current
+
137  if (i != (Array.nrow() - 1))
+
138  return 0.0;
+
139 
+
140  return 1.0;
+
141  };
+
142 
+
143  DEFMCounterData dat;
+
144  dat.is_motif = true;
145 
-
146  return;
-
147 
-
148 }
-
149 
-
150 inline void counter_logit_intercept(
-
151  DEFMCounters * counters,
-
152  size_t n_y,
-
153  std::vector< size_t > which = {},
-
154  int covar_index = -1,
-
155  std::string vname = "",
-
156  const std::vector< std::string > * x_names = nullptr,
-
157  const std::vector< std::string > * y_names = nullptr
-
158 ) {
-
159 
-
160 
-
161  if (which.size() == 0u)
-
162  {
-
163  which.resize(n_y, 0u);
-
164  std::iota(which.begin(), which.end(), 0u);
-
165  } else {
-
166  for (auto w : which)
-
167  if (w >= n_y)
-
168  throw std::logic_error("Values in `which` are out of range.");
-
169  }
-
170 
-
171  // Case when no interaction happens, whatsoever.
-
172  if (covar_index < 0)
-
173  {
-
174 
-
175  DEFM_COUNTER_LAMBDA(tmp_counter)
-
176  {
-
177  if (i != (Array.nrow() - 1))
-
178  return 0.0;
+
146  counters->add_counter(
+
147  count_ones, nullptr, nullptr,
+
148  dat, // DEFMCounterData(),
+
149  "Num. of ones",
+
150  "Overall number of ones"
+
151  );
+
152  }
+
153 
+
154  return;
+
155 
+
156 }
+
157 
+
158 
+
170 inline void counter_logit_intercept(
+
171  DEFMCounters * counters,
+
172  size_t n_y,
+
173  std::vector< size_t > which = {},
+
174  int covar_index = -1,
+
175  std::string vname = "",
+
176  const std::vector< std::string > * x_names = nullptr,
+
177  const std::vector< std::string > * y_names = nullptr
+
178 ) {
179 
-
180  if (j != data.idx(0u))
-
181  return 0.0;
-
182 
-
183  return 1.0;
-
184  };
-
185 
-
186  for (auto i : which)
-
187  {
-
188 
-
189  if (y_names != nullptr)
-
190  vname = y_names->operator[](i);
-
191  else
-
192  vname = std::to_string(i);
-
193 
-
194  counters->add_counter(
-
195  tmp_counter, nullptr, nullptr,
-
196  DEFMCounterData({i}, {}, {}, false),
-
197  "Logit intercept " + vname,
-
198  "Equal to one if the outcome " + vname + " is one. Equivalent to the logistic regression intercept."
-
199  );
-
200 
-
201  }
+
180 
+
181  if (which.size() == 0u)
+
182  {
+
183  which.resize(n_y, 0u);
+
184  std::iota(which.begin(), which.end(), 0u);
+
185  } else {
+
186  for (auto w : which)
+
187  if (w >= n_y)
+
188  throw std::logic_error("Values in `which` are out of range.");
+
189  }
+
190 
+
191  // Case when no interaction happens, whatsoever.
+
192  if (covar_index < 0)
+
193  {
+
194 
+
195  DEFM_COUNTER_LAMBDA(tmp_counter)
+
196  {
+
197  if (i != (Array.nrow() - 1))
+
198  return 0.0;
+
199 
+
200  if (j != data.idx(0u))
+
201  return 0.0;
202 
-
203  } else {
-
204 
-
205  DEFM_COUNTER_LAMBDA(tmp_counter)
-
206  {
-
207  if (i != Array.nrow() - 1)
-
208  return 0.0;
-
209 
-
210  if (j != data.idx(0u))
-
211  return 0.0;
-
212 
-
213  return Array.D()(i, data.idx(1u));
-
214  };
-
215 
-
216  MAKE_DEFM_HASHER(hasher, array, covar_index)
-
217  bool hasher_added = false;
-
218 
-
219  std::string yname;
-
220  for (auto i : which)
-
221  {
+
203  return 1.0;
+
204  };
+
205 
+
206  for (auto i : which)
+
207  {
+
208 
+
209  if (y_names != nullptr)
+
210  vname = y_names->operator[](i);
+
211  else
+
212  vname = std::to_string(i);
+
213 
+
214  counters->add_counter(
+
215  tmp_counter, nullptr, nullptr,
+
216  DEFMCounterData({i}, {}, {}, false),
+
217  "Logit intercept " + vname,
+
218  "Equal to one if the outcome " + vname + " is one. Equivalent to the logistic regression intercept."
+
219  );
+
220 
+
221  }
222 
-
223  if (y_names != nullptr)
-
224  yname = y_names->operator[](i);
-
225  else
-
226  yname = std::to_string(i);
-
227 
-
228  if (vname == "")
-
229  {
-
230  if (x_names != nullptr)
-
231  vname = x_names->operator[](covar_index);
-
232  else
-
233  vname = std::string("attr")+ std::to_string(covar_index);
-
234  }
+
223  } else {
+
224 
+
225  DEFM_COUNTER_LAMBDA(tmp_counter)
+
226  {
+
227  if (i != Array.nrow() - 1)
+
228  return 0.0;
+
229 
+
230  if (j != data.idx(0u))
+
231  return 0.0;
+
232 
+
233  return Array.D()(i, data.idx(1u));
+
234  };
235 
-
236  if (hasher_added)
-
237  counters->add_counter(
-
238  tmp_counter, nullptr, nullptr,
-
239  DEFMCounterData({i, static_cast<size_t>(covar_index)}, {}, {}, false),
-
240  "Logit intercept " + yname + " x " + vname,
-
241  "Equal to one if the outcome " + yname + " is one. Equivalent to the logistic regression intercept."
-
242  );
-
243  else {
-
244 
-
245  hasher_added = true;
-
246 
-
247  counters->add_counter(
-
248  tmp_counter, nullptr, hasher,
-
249  DEFMCounterData({i, static_cast<size_t>(covar_index)}, {}, {}, false),
-
250  "Logit intercept " + yname + " x " + vname,
-
251  "Equal to one if the outcome " + yname + " is one. Equivalent to the logistic regression intercept."
-
252  );
-
253 
+
236  MAKE_DEFM_HASHER(hasher, array, covar_index)
+
237  bool hasher_added = false;
+
238 
+
239  std::string yname;
+
240  for (auto i : which)
+
241  {
+
242 
+
243  if (y_names != nullptr)
+
244  yname = y_names->operator[](i);
+
245  else
+
246  yname = std::to_string(i);
+
247 
+
248  if (vname == "")
+
249  {
+
250  if (x_names != nullptr)
+
251  vname = x_names->operator[](covar_index);
+
252  else
+
253  vname = std::string("attr")+ std::to_string(covar_index);
254  }
255 
-
256  }
-
257 
-
258  }
-
259 
-
260 
-
261 }
-
262 
-
269 inline void counter_transition(
-
270  DEFMCounters * counters,
-
271  std::vector< size_t > coords,
-
272  std::vector< bool > signs,
-
273  size_t m_order,
-
274  size_t n_y,
-
275  int covar_index = -1,
-
276  std::string vname = "",
-
277  const std::vector< std::string > * x_names = nullptr,
-
278  const std::vector< std::string > * y_names = nullptr
-
279 )
-
280 {
-
281 
-
282  // A vector to store the type of dat
-
283  if (signs.size() == 0u)
-
284  signs.resize(coords.size(), true);
-
285  else if (signs.size() != coords.size())
-
286  throw std::length_error("Size of -coords- and -signs- must match.");
-
287 
-
288  if (covar_index >= 0)
-
289  coords.push_back(static_cast<size_t>(covar_index));
-
290  else
-
291  coords.push_back(1000u);
-
292 
-
293  DEFM_COUNTER_LAMBDA(count_init)
-
294  {
-
295 
-
296  auto indices = data.indices;
-
297 
-
298  for (size_t i = 0u; i < (indices.size() - 1u); ++i)
-
299  {
-
300  if (
-
301  std::floor(indices[i] / Array.nrow()) >=
-
302  static_cast<int>(Array.ncol())
-
303  )
-
304  throw std::range_error("The motif includes entries out of range.");
-
305  }
-
306 
-
307  return 0.0;
-
308 
-
309  };
-
310 
-
311  DEFM_COUNTER_LAMBDA(count_ones)
-
312  {
-
313 
-
314  auto dat = data.indices;
-
315  auto sgn = data.logical;
-
316  int covaridx = dat[dat.size() - 1u];
+
256  if (hasher_added)
+
257  counters->add_counter(
+
258  tmp_counter, nullptr, nullptr,
+
259  DEFMCounterData({i, static_cast<size_t>(covar_index)}, {}, {}, false),
+
260  "Logit intercept " + yname + " x " + vname,
+
261  "Equal to one if the outcome " + yname + " is one. Equivalent to the logistic regression intercept."
+
262  );
+
263  else {
+
264 
+
265  hasher_added = true;
+
266 
+
267  counters->add_counter(
+
268  tmp_counter, nullptr, hasher,
+
269  DEFMCounterData({i, static_cast<size_t>(covar_index)}, {}, {}, false),
+
270  "Logit intercept " + yname + " x " + vname,
+
271  "Equal to one if the outcome " + yname + " is one. Equivalent to the logistic regression intercept."
+
272  );
+
273 
+
274  }
+
275 
+
276  }
+
277 
+
278  }
+
279 
+
280 
+
281 }
+
282 
+
289 inline void counter_transition(
+
290  DEFMCounters * counters,
+
291  std::vector< size_t > coords,
+
292  std::vector< bool > signs,
+
293  size_t m_order,
+
294  size_t n_y,
+
295  int covar_index = -1,
+
296  std::string vname = "",
+
297  const std::vector< std::string > * x_names = nullptr,
+
298  const std::vector< std::string > * y_names = nullptr
+
299 )
+
300 {
+
301 
+
302  // A vector to store the type of dat
+
303  if (signs.size() == 0u)
+
304  signs.resize(coords.size(), true);
+
305  else if (signs.size() != coords.size())
+
306  throw std::length_error("Size of -coords- and -signs- must match.");
+
307 
+
308  if (covar_index >= 0)
+
309  coords.push_back(static_cast<size_t>(covar_index));
+
310  else
+
311  coords.push_back(1000u);
+
312 
+
313  DEFM_COUNTER_LAMBDA(count_init)
+
314  {
+
315 
+
316  auto indices = data.indices;
317 
-
318  // Checking if the observation is in the stat. We
-
319  const auto & array = Array.get_data();
-
320  size_t loc = i + j * Array.nrow();
-
321  size_t n_cells = dat.size() - 1u;
-
322 
-
323  // Only one currently needs to be a zero for it
-
324  // to change
-
325  size_t n_now = 0;
-
326  bool baseline_value = false;
-
327  bool i_in_array = false;
-
328  for (size_t e = 0u; e < n_cells; ++e)
-
329  {
+
318  for (size_t i = 0u; i < (indices.size() - 1u); ++i)
+
319  {
+
320  if (
+
321  std::floor(indices[i] / Array.nrow()) >=
+
322  static_cast<int>(Array.ncol())
+
323  )
+
324  throw std::range_error("The motif includes entries out of range.");
+
325  }
+
326 
+
327  return 0.0;
+
328 
+
329  };
330 
-
331  // Is the current cell in the list?
-
332  if (dat[e] == loc)
-
333  {
-
334  i_in_array = true;
-
335  baseline_value = sgn[e];
-
336  }
+
331  DEFM_COUNTER_LAMBDA(count_ones)
+
332  {
+
333 
+
334  auto dat = data.indices;
+
335  auto sgn = data.logical;
+
336  int covaridx = dat[dat.size() - 1u];
337 
-
338  if ((sgn[e] && (array[dat[e]] == 1)) || (!sgn[e] && (array[dat[e]] == 0)))
-
339  n_now++;
-
340 
-
341  }
+
338  // Checking if the observation is in the stat. We
+
339  const auto & array = Array.get_data();
+
340  size_t loc = i + j * Array.nrow();
+
341  size_t n_cells = dat.size() - 1u;
342 
-
343  // If i in array still false, then no change
-
344  if (!i_in_array)
-
345  return 0.0;
-
346 
-
347  size_t n_prev = n_now;
-
348  if (baseline_value)
-
349  n_prev--;
-
350  else
-
351  n_prev++;
-
352 
-
353  // Computing stats
-
354  if (covaridx < 1000)
-
355  {
-
356 
-
357  double val = Array.D()(Array.nrow() - 1u, covaridx);
-
358  double value_now = n_now == n_cells ? val : 0.0;
-
359  double value_prev = n_prev == n_cells ? val : 0.0;
-
360 
-
361  return value_now - value_prev;
+
343  // Only one currently needs to be a zero for it
+
344  // to change
+
345  size_t n_now = 0;
+
346  bool baseline_value = false;
+
347  bool i_in_array = false;
+
348  for (size_t e = 0u; e < n_cells; ++e)
+
349  {
+
350 
+
351  // Is the current cell in the list?
+
352  if (dat[e] == loc)
+
353  {
+
354  i_in_array = true;
+
355  baseline_value = sgn[e];
+
356  }
+
357 
+
358  if ((sgn[e] && (array[dat[e]] == 1)) || (!sgn[e] && (array[dat[e]] == 0)))
+
359  n_now++;
+
360 
+
361  }
362 
-
363  }
-
364  else
-
365  {
-
366 
-
367  double value_now = n_now == n_cells ? 1.0 : 0.0;
-
368  double value_prev = n_prev == n_cells ? 1.0 : 0.0;
-
369 
-
370  return value_now - value_prev;
-
371 
-
372  }
-
373 
-
374  };
-
375 
-
376  // Creating name of the structure
-
377  std::string name;
-
378  if (coords.size() == 1u)
-
379  name = "";
-
380  else
-
381  name = "Motif ";
+
363  // If i in array still false, then no change
+
364  if (!i_in_array)
+
365  return 0.0;
+
366 
+
367  size_t n_prev = n_now;
+
368  if (baseline_value)
+
369  n_prev--;
+
370  else
+
371  n_prev++;
+
372 
+
373  // Computing stats
+
374  if (covaridx < 1000)
+
375  {
+
376 
+
377  double val = Array.D()(Array.nrow() - 1u, covaridx);
+
378  double value_now = n_now == n_cells ? val : 0.0;
+
379  double value_prev = n_prev == n_cells ? val : 0.0;
+
380 
+
381  return value_now - value_prev;
382 
-
383  // Creating an empty motif filled with zeros
-
384  barry::BArrayDense<int> motif(m_order + 1u, n_y, 0);
-
385 
-
386  // Filling the matrix in, negative values are 0s and 1s are... 1s.
-
387  // Zero are values not used.
-
388  size_t n_cells = coords.size() - 1u;
-
389  for (size_t d = 0u; d < n_cells; ++d)
-
390  {
-
391  size_t c = std::floor(coords[d] / (m_order + 1u));
-
392  size_t r = coords[d] - c * (m_order + 1u);
-
393  motif(r, c) = signs[d] ? 1 : -1;
-
394 
-
395  }
-
396 
-
397  // Checking if any prior to the event
-
398  bool any_before_event = false;
-
399 
-
400  for (size_t i = 0u; i < m_order; ++i)
-
401  {
-
402  for (size_t j = 0u; j < n_y; ++j)
-
403  {
-
404  if (motif(i,j) != 0)
-
405  {
-
406  any_before_event = true;
-
407  break;
-
408  }
-
409 
-
410  }
-
411  }
-
412 
-
413  #ifdef BARRY_WITH_LATEX
-
414  name += "$";
-
415  #endif
+
383  }
+
384  else
+
385  {
+
386 
+
387  double value_now = n_now == n_cells ? 1.0 : 0.0;
+
388  double value_prev = n_prev == n_cells ? 1.0 : 0.0;
+
389 
+
390  return value_now - value_prev;
+
391 
+
392  }
+
393 
+
394  };
+
395 
+
396  // Creating name of the structure
+
397  std::string name;
+
398  if (coords.size() == 1u)
+
399  name = "";
+
400  else
+
401  name = "Motif ";
+
402 
+
403  // Creating an empty motif filled with zeros
+
404  barry::BArrayDense<int> motif(m_order + 1u, n_y, 0);
+
405 
+
406  // Filling the matrix in, negative values are 0s and 1s are... 1s.
+
407  // Zero are values not used.
+
408  size_t n_cells = coords.size() - 1u;
+
409  for (size_t d = 0u; d < n_cells; ++d)
+
410  {
+
411  size_t c = std::floor(coords[d] / (m_order + 1u));
+
412  size_t r = coords[d] - c * (m_order + 1u);
+
413  motif(r, c) = signs[d] ? 1 : -1;
+
414 
+
415  }
416 
-
417  if (any_before_event)
-
418  #ifdef BARRY_WITH_LATEX
-
419  name += "(";
-
420  #else
-
421  name += "{";
-
422  #endif
-
423 
-
424  #ifdef BARRY_WITH_LATEX
-
425  #define UNI_SUB(a) \
-
426  (\
-
427  ((a) == 0) ? "_0" : (\
-
428  ((a) == 1) ? "_1" : (\
-
429  ((a) == 2) ? "_2" : (\
-
430  ((a) == 3) ? "_3" : (\
-
431  ((a) == 4) ? "_4" : (\
-
432  ((a) == 5) ? "_5" : (\
-
433  ((a) == 6) ? "_6" : (\
-
434  ((a) == 7) ? "_7" : (\
-
435  ((a) == 8) ? "_8" : \
-
436  "_9"))))))))\
-
437  )
-
438  #else
-
439  #define UNI_SUB(a) \
-
440  (\
-
441  ((a) == 0) ? u8"\u2080" : (\
-
442  ((a) == 1) ? u8"\u2081" : (\
-
443  ((a) == 2) ? u8"\u2082" : (\
-
444  ((a) == 3) ? u8"\u2083" : (\
-
445  ((a) == 4) ? u8"\u2084" : (\
-
446  ((a) == 5) ? u8"\u2085" : (\
-
447  ((a) == 6) ? u8"\u2086" : (\
-
448  ((a) == 7) ? u8"\u2087" : (\
-
449  ((a) == 8) ? u8"\u2088" : \
-
450  u8"\u2089"))))))))\
-
451  )
-
452  #endif
-
453 
-
454  // If order is greater than zero, the starting point of the transtion
-
455  for (size_t i = 0u; i < m_order; ++i)
-
456  {
-
457 
-
458  bool row_start = true;
-
459  for (size_t j = 0u; j < n_y; ++j)
-
460  {
-
461 
-
462  // Is it included?
-
463  if (motif(i,j) == 0)
-
464  continue;
-
465 
-
466  // Is not the first?
-
467  if (row_start)
-
468  row_start = false;
-
469  else
-
470  name += ", ";
-
471 
-
472  if (y_names != nullptr)
-
473  name += y_names->operator[](j);
-
474  else
-
475  name += (std::string("y") + std::to_string(j));
-
476 
-
477  #ifdef BARRY_WITH_LATEX
-
478  name += (motif(i,j) < 0 ? "^-" : "^+");
-
479  #else
-
480  name += (motif(i,j) < 0 ? u8"\u207B" : u8"\u207A");
-
481  #endif
-
482 
-
483  }
-
484 
-
485  }
-
486 
-
487  // If it has starting point, then need to close.
-
488  if (any_before_event & (m_order > 0u))
-
489  #ifdef BARRY_WITH_LATEX
-
490  name += ") -> (";
-
491  #else
-
492  name += std::string("}") + u8"\u21E8" + std::string("{");
-
493  #endif
-
494  else
-
495  #ifdef BARRY_WITH_LATEX
-
496  name += "(";
-
497  #else
-
498  name += "{";
-
499  #endif
-
500 
-
501  // Looking onto the transtions
-
502  bool row_start = true;
-
503  for (size_t j = 0u; j < n_y; ++j)
-
504  {
-
505 
-
506  if (motif(m_order, j) == 0)
-
507  continue;
-
508 
-
509  if (row_start)
-
510  row_start = false;
-
511  else
-
512  name += ", ";
-
513 
-
514  if (y_names != nullptr)
-
515  name += y_names->operator[](j);
-
516  else
-
517  name += (std::string("y") + std::to_string(j));
-
518 
-
519  #ifdef BARRY_WITH_LATEX
-
520  name += (motif(m_order, j) < 0 ? "^-" : "^+" );
-
521  #else
-
522  name += (motif(m_order, j) < 0 ? u8"\u207B" : u8"\u207A" );
-
523  #endif
-
524 
+
417  // Checking if any prior to the event
+
418  bool any_before_event = false;
+
419 
+
420  for (size_t i = 0u; i < m_order; ++i)
+
421  {
+
422  for (size_t j = 0u; j < n_y; ++j)
+
423  {
+
424  if (motif(i,j) != 0)
+
425  {
+
426  any_before_event = true;
+
427  break;
+
428  }
+
429 
+
430  }
+
431  }
+
432 
+
433  #ifdef BARRY_WITH_LATEX
+
434  name += "$";
+
435  #endif
+
436 
+
437  if (any_before_event)
+
438  #ifdef BARRY_WITH_LATEX
+
439  name += "(";
+
440  #else
+
441  name += "{";
+
442  #endif
+
443 
+
444  #ifdef BARRY_WITH_LATEX
+
445  #define UNI_SUB(a) \
+
446  (\
+
447  ((a) == 0) ? "_0" : (\
+
448  ((a) == 1) ? "_1" : (\
+
449  ((a) == 2) ? "_2" : (\
+
450  ((a) == 3) ? "_3" : (\
+
451  ((a) == 4) ? "_4" : (\
+
452  ((a) == 5) ? "_5" : (\
+
453  ((a) == 6) ? "_6" : (\
+
454  ((a) == 7) ? "_7" : (\
+
455  ((a) == 8) ? "_8" : \
+
456  "_9"))))))))\
+
457  )
+
458  #else
+
459  #define UNI_SUB(a) \
+
460  (\
+
461  ((a) == 0) ? u8"\u2080" : (\
+
462  ((a) == 1) ? u8"\u2081" : (\
+
463  ((a) == 2) ? u8"\u2082" : (\
+
464  ((a) == 3) ? u8"\u2083" : (\
+
465  ((a) == 4) ? u8"\u2084" : (\
+
466  ((a) == 5) ? u8"\u2085" : (\
+
467  ((a) == 6) ? u8"\u2086" : (\
+
468  ((a) == 7) ? u8"\u2087" : (\
+
469  ((a) == 8) ? u8"\u2088" : \
+
470  u8"\u2089"))))))))\
+
471  )
+
472  #endif
+
473 
+
474  // If order is greater than zero, the starting point of the transtion
+
475  for (size_t i = 0u; i < m_order; ++i)
+
476  {
+
477 
+
478  bool row_start = true;
+
479  for (size_t j = 0u; j < n_y; ++j)
+
480  {
+
481 
+
482  // Is it included?
+
483  if (motif(i,j) == 0)
+
484  continue;
+
485 
+
486  // Is not the first?
+
487  if (row_start)
+
488  row_start = false;
+
489  else
+
490  name += ", ";
+
491 
+
492  if (y_names != nullptr)
+
493  name += y_names->operator[](j);
+
494  else
+
495  name += (std::string("y") + std::to_string(j));
+
496 
+
497  #ifdef BARRY_WITH_LATEX
+
498  name += (motif(i,j) < 0 ? "^-" : "^+");
+
499  #else
+
500  name += (motif(i,j) < 0 ? u8"\u207B" : u8"\u207A");
+
501  #endif
+
502 
+
503  }
+
504 
+
505  }
+
506 
+
507  // If it has starting point, then need to close.
+
508  if (any_before_event & (m_order > 0u))
+
509  #ifdef BARRY_WITH_LATEX
+
510  name += ") -> (";
+
511  #else
+
512  name += std::string("}") + u8"\u21E8" + std::string("{");
+
513  #endif
+
514  else
+
515  #ifdef BARRY_WITH_LATEX
+
516  name += "(";
+
517  #else
+
518  name += "{";
+
519  #endif
+
520 
+
521  // Looking onto the transtions
+
522  bool row_start = true;
+
523  for (size_t j = 0u; j < n_y; ++j)
+
524  {
525 
-
526  }
-
527 
-
528  #undef UNI_SUB
-
529 
-
530  #ifdef BARRY_WITH_LATEX
-
531  name += ")$";
-
532  #else
-
533  name += "}";
-
534  #endif
-
535 
-
536  if (covar_index >= 0)
-
537  {
+
526  if (motif(m_order, j) == 0)
+
527  continue;
+
528 
+
529  if (row_start)
+
530  row_start = false;
+
531  else
+
532  name += ", ";
+
533 
+
534  if (y_names != nullptr)
+
535  name += y_names->operator[](j);
+
536  else
+
537  name += (std::string("y") + std::to_string(j));
538 
-
539  MAKE_DEFM_HASHER(hasher, array, covar_index)
-
540 
-
541  if (vname == "")
-
542  {
-
543  if (x_names != nullptr)
-
544  vname = x_names->operator[](covar_index);
-
545  else
-
546  vname = std::string("attr")+ std::to_string(covar_index);
-
547  }
-
548 
-
549  counters->add_counter(
-
550  count_ones, count_init, hasher,
-
551  DEFMCounterData(coords, {}, signs, coords.size() > 1u ? true : false),
-
552  name + " x " + vname,
-
553  "Motif weighted by single attribute"
-
554  );
+
539  #ifdef BARRY_WITH_LATEX
+
540  name += (motif(m_order, j) < 0 ? "^-" : "^+" );
+
541  #else
+
542  name += (motif(m_order, j) < 0 ? u8"\u207B" : u8"\u207A" );
+
543  #endif
+
544 
+
545 
+
546  }
+
547 
+
548  #undef UNI_SUB
+
549 
+
550  #ifdef BARRY_WITH_LATEX
+
551  name += ")$";
+
552  #else
+
553  name += "}";
+
554  #endif
555 
-
556  } else {
-
557 
-
558  counters->add_counter(
-
559  count_ones, count_init, nullptr,
-
560  DEFMCounterData(coords, {}, signs, coords.size() > 1u ? true : false),
-
561  name,
-
562  "Motif"
-
563  );
-
564 
-
565  }
-
566 
-
567 
-
568  return;
-
569 
-
570 }
-
571 
-
578 inline void counter_transition_formula(
-
579  DEFMCounters * counters,
-
580  std::string formula,
-
581  size_t m_order,
-
582  size_t n_y,
-
583  int covar_index = -1,
-
584  std::string vname = "",
-
585  const std::vector< std::string > * x_names = nullptr,
-
586  const std::vector< std::string > * y_names = nullptr
-
587 ) {
-
588 
-
589  std::vector< size_t > coords;
-
590  std::vector< bool > signs;
-
591  std::string covar_name = "";
-
592 
-
593  defm_motif_parser(
-
594  formula, coords, signs, m_order, n_y, covar_name, vname
-
595  );
-
596 
-
597  if ((covar_name != "") && (covar_index >= 0))
-
598  throw std::logic_error("Can't have both a formula and a covariate index.");
-
599 
-
600  if (covar_name != "")
-
601  {
-
602 
-
603  if (x_names != nullptr)
-
604  {
-
605  for (size_t i = 0u; i < x_names->size(); ++i)
-
606  if (x_names->operator[](i) == covar_name)
-
607  {
-
608  covar_index = static_cast<int>(i);
-
609  break;
-
610  }
-
611  }
+
556  if (covar_index >= 0)
+
557  {
+
558 
+
559  MAKE_DEFM_HASHER(hasher, array, covar_index)
+
560 
+
561  if (vname == "")
+
562  {
+
563  if (x_names != nullptr)
+
564  vname = x_names->operator[](covar_index);
+
565  else
+
566  vname = std::string("attr")+ std::to_string(covar_index);
+
567  }
+
568 
+
569  counters->add_counter(
+
570  count_ones, count_init, hasher,
+
571  DEFMCounterData(coords, {}, signs, coords.size() > 1u ? true : false),
+
572  name + " x " + vname,
+
573  "Motif weighted by single attribute"
+
574  );
+
575 
+
576  } else {
+
577 
+
578  counters->add_counter(
+
579  count_ones, count_init, nullptr,
+
580  DEFMCounterData(coords, {}, signs, coords.size() > 1u ? true : false),
+
581  name,
+
582  "Motif"
+
583  );
+
584 
+
585  }
+
586 
+
587 
+
588  return;
+
589 
+
590 }
+
591 
+
598 inline void counter_transition_formula(
+
599  DEFMCounters * counters,
+
600  std::string formula,
+
601  size_t m_order,
+
602  size_t n_y,
+
603  int covar_index = -1,
+
604  std::string vname = "",
+
605  const std::vector< std::string > * x_names = nullptr,
+
606  const std::vector< std::string > * y_names = nullptr
+
607 ) {
+
608 
+
609  std::vector< size_t > coords;
+
610  std::vector< bool > signs;
+
611  std::string covar_name = "";
612 
-
613  if (covar_index < 0)
-
614  throw std::logic_error("The covariate name was not found in the list of covariates.");
-
615 
-
616  }
-
617 
-
618  counter_transition(
-
619  counters, coords, signs, m_order, n_y, covar_index, vname,
-
620  x_names, y_names
-
621  );
+
613  defm_motif_parser(
+
614  formula, coords, signs, m_order, n_y, covar_name, vname
+
615  );
+
616 
+
617  if ((covar_name != "") && (covar_index >= 0))
+
618  throw std::logic_error("Can't have both a formula and a covariate index.");
+
619 
+
620  if (covar_name != "")
+
621  {
622 
-
623 }
-
624 
-
631 inline void counter_fixed_effect(
-
632  DEFMCounters * counters,
-
633  int covar_index,
-
634  double k,
-
635  std::string vname = "",
-
636  const std::vector< std::string > * x_names = nullptr
-
637 )
-
638 {
+
623  if (x_names != nullptr)
+
624  {
+
625  for (size_t i = 0u; i < x_names->size(); ++i)
+
626  if (x_names->operator[](i) == covar_name)
+
627  {
+
628  covar_index = static_cast<int>(i);
+
629  break;
+
630  }
+
631  }
+
632 
+
633  if (covar_index < 0)
+
634  throw std::logic_error(
+
635  std::string("The covariate name '") +
+
636  covar_name +
+
637  std::string("' was not found in the list of covariates.")
+
638  );
639 
-
640  DEFM_COUNTER_LAMBDA(count_init)
-
641  {
-
642  return std::pow(Array.D()((size_t) i, data.idx(0u)), data.num(0u));
-
643  };
-
644 
-
645  DEFM_COUNTER_LAMBDA(count_tmp)
-
646  {
-
647  return 0.0;
-
648  };
-
649 
-
650  MAKE_DEFM_HASHER(hasher, array, covar_index)
+
640  }
+
641 
+
642  // Checking the number of coords, could be single intercept
+
643  if (coords.size() == 1u)
+
644  {
+
645 
+
646  // Getting the column
+
647  size_t coord = static_cast< size_t >(
+
648  std::floor(
+
649  static_cast<double>(coords[0u]) / static_cast<double>(m_order + 1)
+
650  ));
651 
-
652  if (x_names != nullptr)
-
653  vname = x_names->operator[](covar_index);
-
654  else
-
655  vname = std::string("attr")+ std::to_string(covar_index);
-
656 
-
657  counters->add_counter(
-
658  count_tmp, count_init, hasher,
-
659  DEFMCounterData({static_cast<size_t>(covar_index)}, {k}, {}),
-
660  "Fixed effect feature (" + vname + ")^" + std::to_string(k)
-
661  );
-
662 
-
663  return;
-
664 
-
665 }
-
666 
-
672 // -----------------------------------------------------------------------------
-
674 inline void rules_markov_fixed(
-
675  DEFMRules * rules,
-
676  size_t markov_order
-
677  ) {
-
678 
-
679  DEFM_RULE_LAMBDA(no_self_tie) {
-
680  return i >= data.idx(0u);
-
681  };
-
682 
-
683  rules->add_rule(
-
684  no_self_tie,
-
685  DEFMRuleData({},{markov_order}),
-
686  std::string("Markov model of order ") + std::to_string(markov_order),
-
687  std::string("Blocks the first morder cells of the array.")
-
688  );
-
689 
-
690  return;
-
691 }
-
692 
-
699 inline void rules_dont_become_zero(
-
700  DEFMSupport * support,
-
701  std::vector<size_t> ids
-
702  ) {
-
703 
-
704  DEFM_RULE_LAMBDA(rule) {
+
652  counter_logit_intercept(
+
653  counters, n_y, {coord},
+
654  covar_index,
+
655  vname,
+
656  x_names,
+
657  y_names
+
658  );
+
659 
+
660  }
+
661  else
+
662  {
+
663 
+
664  counter_transition(
+
665  counters, coords, signs, m_order, n_y, covar_index, vname,
+
666  x_names, y_names
+
667  );
+
668 
+
669  }
+
670 
+
671 
+
672 }
+
673 
+
680 inline void counter_fixed_effect(
+
681  DEFMCounters * counters,
+
682  int covar_index,
+
683  double k,
+
684  std::string vname = "",
+
685  const std::vector< std::string > * x_names = nullptr
+
686 )
+
687 {
+
688 
+
689  DEFM_COUNTER_LAMBDA(count_init)
+
690  {
+
691  return std::pow(Array.D()((size_t) i, data.idx(0u)), data.num(0u));
+
692  };
+
693 
+
694  DEFM_COUNTER_LAMBDA(count_tmp)
+
695  {
+
696  return 0.0;
+
697  };
+
698 
+
699  MAKE_DEFM_HASHER(hasher, array, covar_index)
+
700 
+
701  if (x_names != nullptr)
+
702  vname = x_names->operator[](covar_index);
+
703  else
+
704  vname = std::string("attr")+ std::to_string(covar_index);
705 
-
706  if (!data.init)
-
707  {
-
708  std::vector< size_t > tmp(Array.ncol(), 0u);
-
709 
-
710  for (auto v : data.indices)
-
711  {
-
712  if (v >= Array.ncol())
-
713  throw std::range_error("The specified id for `dont_become_zero` is out of range.");
-
714 
-
715  tmp[v] = 1u;
-
716  }
-
717 
-
718  data.indices.resize(Array.ncol());
-
719  for (size_t v = 0u; v < tmp.size(); ++v)
-
720  data.indices[v] = tmp[v];
-
721 
-
722  data.init = true;
-
723  }
-
724 
-
725  // If not considered, then continue
-
726  if (data.indices[j] == 0u)
-
727  return true;
-
728 
-
729  // The data outside of the markov chain is checked by other rule
-
730  if (i != (Array.nrow() - 1))
-
731  return true;
-
732 
-
733  // This is now one, is the next different zero? If so,
-
734  // we can include it (1->1)
-
735  return (Array(i - 1, j) != 1) || (Array(i, j) != 1);
-
736 
-
737  };
+
706  counters->add_counter(
+
707  count_tmp, count_init, hasher,
+
708  DEFMCounterData({static_cast<size_t>(covar_index)}, {k}, {}),
+
709  "Fixed effect feature (" + vname + ")^" + std::to_string(k)
+
710  );
+
711 
+
712  return;
+
713 
+
714 }
+
715 
+
721 // -----------------------------------------------------------------------------
+
723 inline void rules_markov_fixed(
+
724  DEFMRules * rules,
+
725  size_t markov_order
+
726  ) {
+
727 
+
728  DEFM_RULE_LAMBDA(no_self_tie) {
+
729  return i >= data.idx(0u);
+
730  };
+
731 
+
732  rules->add_rule(
+
733  no_self_tie,
+
734  DEFMRuleData({},{markov_order}),
+
735  std::string("Markov model of order ") + std::to_string(markov_order),
+
736  std::string("Blocks the first morder cells of the array.")
+
737  );
738 
-
739  support->get_rules()->add_rule(
-
740  rule,
-
741  DEFMRuleData({}, {ids}),
-
742  std::string("Ones can't become zero"),
-
743  std::string("Blocks cells that have became equal to one.")
-
744  );
-
745 
-
746  return;
-
747 }
-
748 
-
750 
-
752 
-
753 #endif
+
739  return;
+
740 }
+
741 
+
748 inline void rules_dont_become_zero(
+
749  DEFMSupport * support,
+
750  std::vector<size_t> ids
+
751  ) {
+
752 
+
753  DEFM_RULE_LAMBDA(rule) {
+
754 
+
755  if (!data.init)
+
756  {
+
757  std::vector< size_t > tmp(Array.ncol(), 0u);
+
758 
+
759  for (auto v : data.indices)
+
760  {
+
761  if (v >= Array.ncol())
+
762  throw std::range_error("The specified id for `dont_become_zero` is out of range.");
+
763 
+
764  tmp[v] = 1u;
+
765  }
+
766 
+
767  data.indices.resize(Array.ncol());
+
768  for (size_t v = 0u; v < tmp.size(); ++v)
+
769  data.indices[v] = tmp[v];
+
770 
+
771  data.init = true;
+
772  }
+
773 
+
774  // If not considered, then continue
+
775  if (data.indices[j] == 0u)
+
776  return true;
+
777 
+
778  // The data outside of the markov chain is checked by other rule
+
779  if (i != (Array.nrow() - 1))
+
780  return true;
+
781 
+
782  // This is now one, is the next different zero? If so,
+
783  // we can include it (1->1)
+
784  return (Array(i - 1, j) != 1) || (Array(i, j) != 1);
+
785 
+
786  };
+
787 
+
788  support->get_rules()->add_rule(
+
789  rule,
+
790  DEFMRuleData({}, {ids}),
+
791  std::string("Ones can't become zero"),
+
792  std::string("Blocks cells that have became equal to one.")
+
793  );
+
794 
+
795  return;
+
796 }
+
797 
+
799 
+
801 
+
802 #endif
DEFMCounterData
Data class used to store arbitrary size_t or double vectors.
Definition: defm-types.hpp:64
name
Data_Type &&counter_ name(std::move(counter_.name))
@@ -792,18 +823,18 @@
hasher
Data_Type hasher(counter_.hasher)
Definition: counters-meat.hpp:141
j
size_t size_t j
Definition: counters-meat.hpp:84
i
size_t i
Definition: counters-meat.hpp:83
-
DEFM_COUNTER_LAMBDA
#define DEFM_COUNTER_LAMBDA(a)
Definition: counters.hpp:43
-
DEFM_RULE_LAMBDA
#define DEFM_RULE_LAMBDA(a)
Definition: counters.hpp:57
+
DEFM_COUNTER_LAMBDA
#define DEFM_COUNTER_LAMBDA(a)
Definition: counters.hpp:51
+
DEFM_RULE_LAMBDA
#define DEFM_RULE_LAMBDA(a)
Definition: counters.hpp:65
defm_motif_parser
void defm_motif_parser(std::string formula, std::vector< size_t > &locations, std::vector< bool > &signs, size_t m_order, size_t y_ncol, std::string &covar_name, std::string &vname)
Parses a motif formula.
Definition: formula.hpp:46
-
counter_transition
void counter_transition(DEFMCounters *counters, std::vector< size_t > coords, std::vector< bool > signs, size_t m_order, size_t n_y, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:269
-
rules_markov_fixed
void rules_markov_fixed(DEFMRules *rules, size_t markov_order)
Number of edges.
Definition: counters.hpp:674
-
counter_ones
void counter_ones(DEFMCounters *counters, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:81
-
counter_fixed_effect
void counter_fixed_effect(DEFMCounters *counters, int covar_index, double k, std::string vname="", const std::vector< std::string > *x_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:631
-
counter_logit_intercept
void counter_logit_intercept(DEFMCounters *counters, size_t n_y, std::vector< size_t > which={}, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Definition: counters.hpp:150
-
rules_dont_become_zero
void rules_dont_become_zero(DEFMSupport *support, std::vector< size_t > ids)
Blocks switching a one to zero.
Definition: counters.hpp:699
-
counter_transition_formula
void counter_transition_formula(DEFMCounters *counters, std::string formula, size_t m_order, size_t n_y, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:578
-
MAKE_DEFM_HASHER
#define MAKE_DEFM_HASHER(hasher, a, cov)
Definition: counters.hpp:21
+
counter_transition
void counter_transition(DEFMCounters *counters, std::vector< size_t > coords, std::vector< bool > signs, size_t m_order, size_t n_y, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:289
+
rules_markov_fixed
void rules_markov_fixed(DEFMRules *rules, size_t markov_order)
Number of edges.
Definition: counters.hpp:723
+
counter_ones
void counter_ones(DEFMCounters *counters, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:89
+
counter_fixed_effect
void counter_fixed_effect(DEFMCounters *counters, int covar_index, double k, std::string vname="", const std::vector< std::string > *x_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:680
+
counter_logit_intercept
void counter_logit_intercept(DEFMCounters *counters, size_t n_y, std::vector< size_t > which={}, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Definition: counters.hpp:170
+
rules_dont_become_zero
void rules_dont_become_zero(DEFMSupport *support, std::vector< size_t > ids)
Blocks switching a one to zero.
Definition: counters.hpp:748
+
counter_transition_formula
void counter_transition_formula(DEFMCounters *counters, std::string formula, size_t m_order, size_t n_y, int covar_index=-1, std::string vname="", const std::vector< std::string > *x_names=nullptr, const std::vector< std::string > *y_names=nullptr)
Prevalence of ones.
Definition: counters.hpp:598
+
MAKE_DEFM_HASHER
#define MAKE_DEFM_HASHER(hasher, a, cov)
Data for the counters.
Definition: counters.hpp:27
DEFMCounterData::is_motif
bool is_motif
If false, then is a logit intercept.
Definition: defm-types.hpp:70
DEFMCounters
barry::Counters< DEFMArray, DEFMCounterData > DEFMCounters
Definition: defm-types.hpp:172
DEFMRules
barry::Rules< DEFMArray, DEFMRuleData > DEFMRules
Definition: defm-types.hpp:179
@@ -815,7 +846,7 @@ diff --git a/defm_8hpp.html b/defm_8hpp.html index 040a78ead..7e57d4ae3 100644 --- a/defm_8hpp.html +++ b/defm_8hpp.html @@ -133,7 +133,7 @@ diff --git a/defm_8hpp_source.html b/defm_8hpp_source.html index 2a35e1a33..63cb6271a 100644 --- a/defm_8hpp_source.html +++ b/defm_8hpp_source.html @@ -126,7 +126,7 @@ diff --git a/dir_000001_000002.html b/dir_000001_000002.html index 6d31819e9..b66ad2d32 100644 --- a/dir_000001_000002.html +++ b/dir_000001_000002.html @@ -98,7 +98,7 @@

barry → counters Relation

diff --git a/dir_000003_000004.html b/dir_000003_000004.html index 1f93b2895..15de41f62 100644 --- a/dir_000003_000004.html +++ b/dir_000003_000004.html @@ -98,7 +98,7 @@

models → defm Relation

+ @@ -352,26 +353,30 @@

-Value:
barry::Hasher_fun_type<DEFMArray,DEFMCounterData> \
-
hasher = [cov](const DEFMArray & array, DEFMCounterData * d) { \
-
std::vector< double > res; \
-
/* Adding the column feature */ \
-
for (size_t i = 0u; i < array.nrow(); ++i) \
-
res.push_back(array.D()(i, cov)); \
-
/* Adding the fixed dims */ \
-
for (size_t i = 0u; i < (array.nrow() - 1); ++i) \
-
for (size_t j = 0u; j < array.ncol(); ++j) \
-
res.push_back(array(i, j)); \
-
return res;\
-
};
+Value:
barry::Hasher_fun_type<DEFMArray, DEFMCounterData> \
+
hasher = [cov](const DEFMArray & array, DEFMCounterData * d) -> \
+
std::vector< double > { \
+
std::vector< double > res; \
+
/* Adding the column feature */ \
+
for (size_t i = 0u; i < array.nrow(); ++i) \
+
res.push_back(array.D()(i, cov)); \
+
/* Adding the fixed dims */ \
+
for (size_t i = 0u; i < (array.nrow() - 1); ++i) \
+
for (size_t j = 0u; j < array.ncol(); ++j) \
+
res.push_back(array(i, j)); \
+
return res;\
+
};
DEFMCounterData
Data class used to store arbitrary size_t or double vectors.
Definition: defm-types.hpp:64
res
return res
Definition: counters-meat.hpp:265
j
size_t size_t j
Definition: counters-meat.hpp:84
i
size_t i
Definition: counters-meat.hpp:83
DEFMArray
barry::BArrayDense< int, DEFMData > DEFMArray
Definition: defm-types.hpp:3
-

Details on the available counters for DEFMworkData can be found in the Network counters section.

+
+

Data for the counters.

+

Details on the available counters for DEFMworkData can be found in the Network counters section.

+

This class is used to store the data for the counters. It is used by the Counters class.

-

Definition at line 21 of file counters.hpp.

+

Definition at line 27 of file counters.hpp.

@@ -1657,7 +1662,7 @@

diff --git a/group__rules-phylo.html b/group__rules-phylo.html index 6a4d93f30..07f382ec8 100644 --- a/group__rules-phylo.html +++ b/group__rules-phylo.html @@ -1495,7 +1495,7 @@

diff --git a/group__stat-models.html b/group__stat-models.html index c19abd29f..818db5c2d 100644 --- a/group__stat-models.html +++ b/group__stat-models.html @@ -121,7 +121,7 @@ diff --git a/hierarchy.html b/hierarchy.html index 60731e31d..4d68f17e7 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -161,7 +161,7 @@ diff --git a/index.html b/index.html index f20980e9c..74001fb24 100644 --- a/index.html +++ b/index.html @@ -206,7 +206,7 @@

Code of Conduct

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\mbox{\Hypertarget{defm_2counters_8hpp_a0de627ee2d314d645cf885c7cc0ee36b}\label{defm_2counters_8hpp_a0de627ee2d314d645cf885c7cc0ee36b}} \index{counters.hpp@{counters.hpp}!DEFM\_COUNTER\_LAMBDA@{DEFM\_COUNTER\_LAMBDA}} @@ -95,7 +95,7 @@ \end{DoxyCode} Lambda function for definition of a network counter function -Definition at line 43 of file counters.\+hpp. +Definition at line 51 of file counters.\+hpp. \mbox{\Hypertarget{defm_2counters_8hpp_af210bb3f47af7995ff200264370d9db6}\label{defm_2counters_8hpp_af210bb3f47af7995ff200264370d9db6}} \index{counters.hpp@{counters.hpp}!DEFM\_RULE@{DEFM\_RULE}} @@ -105,7 +105,7 @@ Function for definition of a network counter function -Definition at line 53 of file counters.\+hpp. +Definition at line 61 of file counters.\+hpp. \mbox{\Hypertarget{defm_2counters_8hpp_a94148d8866c1e18cbb02be5ba7d233ba}\label{defm_2counters_8hpp_a94148d8866c1e18cbb02be5ba7d233ba}} \index{counters.hpp@{counters.hpp}!DEFM\_RULE\_LAMBDA@{DEFM\_RULE\_LAMBDA}} @@ -121,7 +121,7 @@ \end{DoxyCode} Lambda function for definition of a network counter function -Definition at line 57 of file counters.\+hpp. +Definition at line 65 of file counters.\+hpp. \mbox{\Hypertarget{defm_2counters_8hpp_ac6f3765d01ec78962d3bacb6d9934331}\label{defm_2counters_8hpp_ac6f3765d01ec78962d3bacb6d9934331}} \index{counters.hpp@{counters.hpp}!DEFM\_RULEDYN\_LAMBDA@{DEFM\_RULEDYN\_LAMBDA}} @@ -137,7 +137,7 @@ \end{DoxyCode} Lambda function for definition of a network counter function -Definition at line 63 of file counters.\+hpp. +Definition at line 71 of file counters.\+hpp. \mbox{\Hypertarget{defm_2counters_8hpp_a7a02efb9a9ac7cb0f4b8659e2b2529e0}\label{defm_2counters_8hpp_a7a02efb9a9ac7cb0f4b8659e2b2529e0}} \index{counters.hpp@{counters.hpp}!UNI\_SUB@{UNI\_SUB}} diff --git a/latex/defm_2counters_8hpp__dep__incl.pdf b/latex/defm_2counters_8hpp__dep__incl.pdf index 373a03bbd..444a50dfe 100644 Binary files a/latex/defm_2counters_8hpp__dep__incl.pdf and 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-216,7 +216,7 @@ \end{DoxyParams} -Definition at line 631 of file counters.\+hpp. +Definition at line 680 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_ga99a2fb5a5521bb37e251ee1d638f9ba7}\label{group__counters-network_ga99a2fb5a5521bb37e251ee1d638f9ba7}} \index{Network counters@{Network counters}!counter\_idegree@{counter\_idegree}} @@ -320,9 +320,28 @@ \doxysubsubsection{\texorpdfstring{counter\_logit\_intercept()}{counter\_logit\_intercept()}} {\footnotesize\ttfamily void counter\+\_\+logit\+\_\+intercept (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{group__rules-phylo_ga5c89d811265cdc84066476226ea138a8}{DEFMCounters}} $\ast$}]{counters, }\item[{size\+\_\+t}]{n\+\_\+y, }\item[{std\+::vector$<$ size\+\_\+t $>$}]{which = {\ttfamily \{\}}, }\item[{int}]{covar\+\_\+index = {\ttfamily -\/1}, }\item[{std\+::string}]{vname = {\ttfamily \char`\"{}\char`\"{}}, }\item[{const std\+::vector$<$ std\+::string $>$ $\ast$}]{x\+\_\+names = {\ttfamily nullptr}, }\item[{const std\+::vector$<$ std\+::string $>$ $\ast$}]{y\+\_\+names = {\ttfamily nullptr} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} +Calculates the logit intercept for the \mbox{\hyperlink{class_d_e_f_m}{DEFM}} model. -Definition at line 150 of file counters.\+hpp. +\begin{DoxyParams}{Parameters} +{\em counters} & A pointer to the DEFMCounters object. \\ +\hline +{\em n\+\_\+y} & The number of response variables. \\ +\hline +{\em which} & A vector of indices indicating which response variables to use. If empty, all response variables are used. \\ +\hline +{\em covar\+\_\+index} & The index of the covariate to use as the intercept. \\ +\hline +{\em vname} & The name of the variable to use as the intercept. If empty, the intercept is set to zero. \\ +\hline +{\em x\+\_\+names} & A pointer to a vector of strings containing the names of the covariates. \\ +\hline +{\em y\+\_\+names} & A pointer to a vector of strings containing the names of the response variables. \\ +\hline +\end{DoxyParams} + + +Definition at line 170 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_ga1605cc66474b3b960bddd7c0adebcfc7}\label{group__counters-network_ga1605cc66474b3b960bddd7c0adebcfc7}} \index{Network counters@{Network counters}!counter\_mutual@{counter\_mutual}} @@ -450,7 +469,7 @@ \end{DoxyParams} -Definition at line 81 of file counters.\+hpp. +Definition at line 89 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_gad2e83eeaed6f17346ac8ac1ca64b327a}\label{group__counters-network_gad2e83eeaed6f17346ac8ac1ca64b327a}} \index{Network counters@{Network counters}!counter\_ostar2@{counter\_ostar2}} @@ -493,7 +512,7 @@ \end{DoxyParams} -Definition at line 269 of file counters.\+hpp. +Definition at line 289 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_gad8c9e9b4e4a57e96cd604e8e4832a272}\label{group__counters-network_gad8c9e9b4e4a57e96cd604e8e4832a272}} \index{Network counters@{Network counters}!counter\_transition\_formula@{counter\_transition\_formula}} @@ -514,7 +533,7 @@ \end{DoxyParams} -Definition at line 578 of file counters.\+hpp. +Definition at line 598 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_gadadede01536081fb8b79e4d14368f946}\label{group__counters-network_gadadede01536081fb8b79e4d14368f946}} \index{Network counters@{Network counters}!counter\_ttriads@{counter\_ttriads}} @@ -567,7 +586,7 @@ \end{DoxyParams} -Definition at line 699 of file counters.\+hpp. +Definition at line 748 of file counters.\+hpp. \mbox{\Hypertarget{group__counters-network_ga31452452bf9dad7f6c5767dcabfb4dbe}\label{group__counters-network_ga31452452bf9dad7f6c5767dcabfb4dbe}} \index{Network counters@{Network counters}!rules\_markov\_fixed@{rules\_markov\_fixed}} @@ -581,5 +600,5 @@ -Definition at line 674 of file counters.\+hpp. +Definition at line 723 of file counters.\+hpp. diff --git a/latex/group__counters-phylo.pdf b/latex/group__counters-phylo.pdf index 9b0d44598..f207a0dee 100644 Binary files a/latex/group__counters-phylo.pdf and b/latex/group__counters-phylo.pdf differ diff --git a/latex/group__counting.tex b/latex/group__counting.tex index 8731c001c..fd9906468 100644 --- a/latex/group__counting.tex +++ b/latex/group__counting.tex @@ -11,7 +11,7 @@ \begin{DoxyCompactItemize} \item \#define \mbox{\hyperlink{group__counting_ga172b737bbafc10829969ae80428ae682}{MAKE\+\_\+\+DEFM\+\_\+\+HASHER}}(\mbox{\hyperlink{counters-meat_8hpp_a51327367202f40175dea83db9095a0da}{hasher}}, a, cov) -\end{DoxyCompactItemize} +\begin{DoxyCompactList}\small\item\em Data for the counters. \end{DoxyCompactList}\end{DoxyCompactItemize} \begin{DoxyCompactItemize} \item \#define \mbox{\hyperlink{group__counting_gaa723b014f0985d974ac55ce671689f65}{MAKE\+\_\+\+DUPL\+\_\+\+VARS}}() @@ -168,23 +168,30 @@ {\bfseries Value\+:} \begin{DoxyCode}{0} -\DoxyCodeLine{ barry::Hasher\_fun\_type \(\backslash\)} -\DoxyCodeLine{ hasher = [cov](\textcolor{keyword}{const} \mbox{\hyperlink{defm-types_8hpp_a3ed5e2f1747dd4f4893565699469438f}{DEFMArray}} \& array, \mbox{\hyperlink{class_d_e_f_m_counter_data}{DEFMCounterData}} * d) \{ \(\backslash\)} -\DoxyCodeLine{ std::vector< double > \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}; \(\backslash\)} -\DoxyCodeLine{ \textcolor{comment}{/* Adding the column feature */} \(\backslash\)} -\DoxyCodeLine{ for (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} < array.nrow(); ++\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}) \(\backslash\)} -\DoxyCodeLine{ \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}.push\_back(array.D()(\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}, cov)); \(\backslash\)} -\DoxyCodeLine{ \textcolor{comment}{/* Adding the fixed dims */} \(\backslash\)} -\DoxyCodeLine{ for (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} < (array.nrow() -\/ 1); ++\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}) \(\backslash\)} -\DoxyCodeLine{ \textcolor{keywordflow}{for} (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}} < array.ncol(); ++\mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}}) \(\backslash\)} -\DoxyCodeLine{ \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}.push\_back(array(\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}, \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}})); \(\backslash\)} -\DoxyCodeLine{ return \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}};\(\backslash\)} -\DoxyCodeLine{ \};} +\DoxyCodeLine{ barry::Hasher\_fun\_type \(\backslash\)} +\DoxyCodeLine{ hasher = [cov](\textcolor{keyword}{const} \mbox{\hyperlink{defm-types_8hpp_a3ed5e2f1747dd4f4893565699469438f}{DEFMArray}} \& array, \mbox{\hyperlink{class_d_e_f_m_counter_data}{DEFMCounterData}} * d) -\/> \(\backslash\)} +\DoxyCodeLine{ std::vector< double > \{ \(\backslash\)} +\DoxyCodeLine{ std::vector< double > \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}; \(\backslash\)} +\DoxyCodeLine{ \textcolor{comment}{/* Adding the column feature */} \(\backslash\)} +\DoxyCodeLine{ for (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} < array.nrow(); ++\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}) \(\backslash\)} +\DoxyCodeLine{ \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}.push\_back(array.D()(\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}, cov)); \(\backslash\)} +\DoxyCodeLine{ \textcolor{comment}{/* Adding the fixed dims */} \(\backslash\)} +\DoxyCodeLine{ for (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}} < (array.nrow() -\/ 1); ++\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}) \(\backslash\)} +\DoxyCodeLine{ \textcolor{keywordflow}{for} (\textcolor{keywordtype}{size\_t} \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}} = 0u; \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}} < array.ncol(); ++\mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}}) \(\backslash\)} +\DoxyCodeLine{ \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}}.push\_back(array(\mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}, \mbox{\hyperlink{counters-meat_8hpp_abf2d9f657468255c5b9964ea2b6e9e15}{j}})); \(\backslash\)} +\DoxyCodeLine{ return \mbox{\hyperlink{counters-meat_8hpp_a5e111f6687f261e4e28bd6528e7f5b48}{res}};\(\backslash\)} +\DoxyCodeLine{ \};} \end{DoxyCode} -Details on the available counters for {\ttfamily DEFMwork\+Data} can be found in the \mbox{\hyperlink{group__counters-network}{Network counters}} section. -Definition at line 21 of file counters.\+hpp. + +Data for the counters. + +Details on the available counters for {\ttfamily DEFMwork\+Data} can be found in the \mbox{\hyperlink{group__counters-network}{Network counters}} section. + +This class is used to store the data for the counters. It is used by the {\ttfamily \mbox{\hyperlink{class_counters}{Counters}}} class. + +Definition at line 27 of file counters.\+hpp. \mbox{\Hypertarget{group__counting_gaa723b014f0985d974ac55ce671689f65}\label{group__counting_gaa723b014f0985d974ac55ce671689f65}} \index{Counting@{Counting}!MAKE\_DUPL\_VARS@{MAKE\_DUPL\_VARS}} diff --git a/latex/group__rules-phylo.pdf b/latex/group__rules-phylo.pdf index e90b974d6..cfdd26238 100644 Binary files a/latex/group__rules-phylo.pdf and b/latex/group__rules-phylo.pdf differ diff --git a/latex/model-bones_8hpp__dep__incl.pdf b/latex/model-bones_8hpp__dep__incl.pdf index 258000696..09dec951e 100644 Binary files a/latex/model-bones_8hpp__dep__incl.pdf and b/latex/model-bones_8hpp__dep__incl.pdf differ diff --git a/latex/model-meat_8hpp__dep__incl.pdf b/latex/model-meat_8hpp__dep__incl.pdf index 325515600..11d9093ca 100644 Binary files a/latex/model-meat_8hpp__dep__incl.pdf and b/latex/model-meat_8hpp__dep__incl.pdf differ diff --git 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files a/latex/powerset-meat_8hpp__dep__incl.pdf and b/latex/powerset-meat_8hpp__dep__incl.pdf differ diff --git a/latex/progress_8hpp__dep__incl.pdf b/latex/progress_8hpp__dep__incl.pdf index 50d94614d..135f578f1 100644 Binary files a/latex/progress_8hpp__dep__incl.pdf and b/latex/progress_8hpp__dep__incl.pdf differ diff --git a/latex/refman.aux b/latex/refman.aux index 0fa9a410e..dd755d595 100644 --- a/latex/refman.aux +++ b/latex/refman.aux @@ -170,80 +170,83 @@ \@writefile{toc}{\contentsline {subsubsection}{\numberline {6.3.2.16}counter\_istar2()\hspace {0.1cm}{\footnotesize \ttfamily [2/2]}}{30}{subsubsection.6.3.2.16}\protected@file@percent } \newlabel{group__counters-network_ga8e24b6a576b9091b2c366ed4e424ec73}{{6.3.2.16}{30}{\texorpdfstring {counter\_istar2()}{counter\_istar2()}\hspace {0.1cm}{\footnotesize \ttfamily [2/2]}}{subsubsection.6.3.2.16}{}} \@writefile{toc}{\contentsline {subsubsection}{\numberline 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counters@{Network counters}|hyperpage}{30} \indexentry{Network counters@{Network counters}!counter\_logit\_intercept@{counter\_logit\_intercept}|hyperpage}{30} \indexentry{counter\_logit\_intercept@{counter\_logit\_intercept}!Network counters@{Network counters}|hyperpage}{30} -\indexentry{Network counters@{Network counters}!counter\_mutual@{counter\_mutual}|hyperpage}{30} -\indexentry{counter\_mutual@{counter\_mutual}!Network counters@{Network counters}|hyperpage}{30} +\indexentry{Network counters@{Network counters}!counter\_mutual@{counter\_mutual}|hyperpage}{31} +\indexentry{counter\_mutual@{counter\_mutual}!Network counters@{Network counters}|hyperpage}{31} \indexentry{Network counters@{Network counters}!counter\_nodecov@{counter\_nodecov}|hyperpage}{31} \indexentry{counter\_nodecov@{counter\_nodecov}!Network counters@{Network counters}|hyperpage}{31} \indexentry{Network counters@{Network counters}!counter\_nodeicov@{counter\_nodeicov}|hyperpage}{31} \indexentry{counter\_nodeicov@{counter\_nodeicov}!Network counters@{Network counters}|hyperpage}{31} \indexentry{Network counters@{Network counters}!counter\_nodematch@{counter\_nodematch}|hyperpage}{31} \indexentry{counter\_nodematch@{counter\_nodematch}!Network counters@{Network counters}|hyperpage}{31} -\indexentry{Network counters@{Network counters}!counter\_nodeocov@{counter\_nodeocov}|hyperpage}{31} -\indexentry{counter\_nodeocov@{counter\_nodeocov}!Network counters@{Network counters}|hyperpage}{31} -\indexentry{Network counters@{Network counters}!counter\_odegree@{counter\_odegree}|hyperpage}{31} -\indexentry{counter\_odegree@{counter\_odegree}!Network counters@{Network counters}|hyperpage}{31} +\indexentry{Network counters@{Network counters}!counter\_nodeocov@{counter\_nodeocov}|hyperpage}{32} +\indexentry{counter\_nodeocov@{counter\_nodeocov}!Network counters@{Network counters}|hyperpage}{32} +\indexentry{Network counters@{Network counters}!counter\_odegree@{counter\_odegree}|hyperpage}{32} +\indexentry{counter\_odegree@{counter\_odegree}!Network counters@{Network counters}|hyperpage}{32} \indexentry{Network counters@{Network counters}!counter\_odegree@{counter\_odegree}|hyperpage}{32} \indexentry{counter\_odegree@{counter\_odegree}!Network counters@{Network counters}|hyperpage}{32} \indexentry{Network counters@{Network counters}!counter\_odegree15@{counter\_odegree15}|hyperpage}{32} \indexentry{counter\_odegree15@{counter\_odegree15}!Network counters@{Network counters}|hyperpage}{32} \indexentry{Network counters@{Network counters}!counter\_odegree15@{counter\_odegree15}|hyperpage}{32} \indexentry{counter\_odegree15@{counter\_odegree15}!Network counters@{Network counters}|hyperpage}{32} -\indexentry{Network counters@{Network counters}!counter\_ones@{counter\_ones}|hyperpage}{32} -\indexentry{counter\_ones@{counter\_ones}!Network counters@{Network counters}|hyperpage}{32} +\indexentry{Network counters@{Network counters}!counter\_ones@{counter\_ones}|hyperpage}{33} +\indexentry{counter\_ones@{counter\_ones}!Network counters@{Network counters}|hyperpage}{33} \indexentry{Network counters@{Network counters}!counter\_ostar2@{counter\_ostar2}|hyperpage}{33} \indexentry{counter\_ostar2@{counter\_ostar2}!Network counters@{Network counters}|hyperpage}{33} \indexentry{Network counters@{Network counters}!counter\_ostar2@{counter\_ostar2}|hyperpage}{33} @@ -137,91 +137,91 @@ \indexentry{counter\_transition\_formula@{counter\_transition\_formula}!Network counters@{Network counters}|hyperpage}{34} \indexentry{Network counters@{Network counters}!counter\_ttriads@{counter\_ttriads}|hyperpage}{34} \indexentry{counter\_ttriads@{counter\_ttriads}!Network counters@{Network counters}|hyperpage}{34} -\indexentry{Network counters@{Network counters}!counter\_ttriads@{counter\_ttriads}|hyperpage}{34} -\indexentry{counter\_ttriads@{counter\_ttriads}!Network counters@{Network counters}|hyperpage}{34} -\indexentry{Network counters@{Network counters}!NETWORK\_COUNTER@{NETWORK\_COUNTER}|hyperpage}{34} -\indexentry{NETWORK\_COUNTER@{NETWORK\_COUNTER}!Network counters@{Network counters}|hyperpage}{34} -\indexentry{Network counters@{Network counters}!rules\_dont\_become\_zero@{rules\_dont\_become\_zero}|hyperpage}{34} -\indexentry{rules\_dont\_become\_zero@{rules\_dont\_become\_zero}!Network counters@{Network counters}|hyperpage}{34} +\indexentry{Network counters@{Network counters}!counter\_ttriads@{counter\_ttriads}|hyperpage}{35} +\indexentry{counter\_ttriads@{counter\_ttriads}!Network counters@{Network counters}|hyperpage}{35} +\indexentry{Network counters@{Network counters}!NETWORK\_COUNTER@{NETWORK\_COUNTER}|hyperpage}{35} +\indexentry{NETWORK\_COUNTER@{NETWORK\_COUNTER}!Network counters@{Network counters}|hyperpage}{35} +\indexentry{Network counters@{Network counters}!rules\_dont\_become\_zero@{rules\_dont\_become\_zero}|hyperpage}{35} +\indexentry{rules\_dont\_become\_zero@{rules\_dont\_become\_zero}!Network counters@{Network counters}|hyperpage}{35} \indexentry{Network counters@{Network counters}!rules\_markov\_fixed@{rules\_markov\_fixed}|hyperpage}{35} \indexentry{rules\_markov\_fixed@{rules\_markov\_fixed}!Network counters@{Network counters}|hyperpage}{35} -\indexentry{Phylo rules@{Phylo rules}|hyperpage}{35} -\indexentry{Phylo rules@{Phylo rules}!DEFMCounter@{DEFMCounter}|hyperpage}{37} -\indexentry{DEFMCounter@{DEFMCounter}!Phylo rules@{Phylo rules}|hyperpage}{37} -\indexentry{Phylo rules@{Phylo rules}!DEFMCounters@{DEFMCounters}|hyperpage}{37} -\indexentry{DEFMCounters@{DEFMCounters}!Phylo rules@{Phylo rules}|hyperpage}{37} -\indexentry{Phylo rules@{Phylo rules}!DEFMModel@{DEFMModel}|hyperpage}{37} -\indexentry{DEFMModel@{DEFMModel}!Phylo rules@{Phylo rules}|hyperpage}{37} +\indexentry{Phylo rules@{Phylo rules}|hyperpage}{36} +\indexentry{Phylo rules@{Phylo rules}!DEFMCounter@{DEFMCounter}|hyperpage}{38} +\indexentry{DEFMCounter@{DEFMCounter}!Phylo rules@{Phylo rules}|hyperpage}{38} +\indexentry{Phylo rules@{Phylo rules}!DEFMCounters@{DEFMCounters}|hyperpage}{38} +\indexentry{DEFMCounters@{DEFMCounters}!Phylo rules@{Phylo rules}|hyperpage}{38} +\indexentry{Phylo rules@{Phylo rules}!DEFMModel@{DEFMModel}|hyperpage}{38} +\indexentry{DEFMModel@{DEFMModel}!Phylo rules@{Phylo rules}|hyperpage}{38} \indexentry{Phylo rules@{Phylo rules}!DEFMRule@{DEFMRule}|hyperpage}{38} \indexentry{DEFMRule@{DEFMRule}!Phylo rules@{Phylo rules}|hyperpage}{38} \indexentry{Phylo rules@{Phylo rules}!DEFMRuleDyn@{DEFMRuleDyn}|hyperpage}{38} \indexentry{DEFMRuleDyn@{DEFMRuleDyn}!Phylo rules@{Phylo rules}|hyperpage}{38} \indexentry{Phylo rules@{Phylo rules}!DEFMRules@{DEFMRules}|hyperpage}{38} \indexentry{DEFMRules@{DEFMRules}!Phylo rules@{Phylo rules}|hyperpage}{38} -\indexentry{Phylo rules@{Phylo rules}!DEFMRulesDyn@{DEFMRulesDyn}|hyperpage}{38} -\indexentry{DEFMRulesDyn@{DEFMRulesDyn}!Phylo rules@{Phylo rules}|hyperpage}{38} -\indexentry{Phylo rules@{Phylo rules}!DEFMStatsCounter@{DEFMStatsCounter}|hyperpage}{38} -\indexentry{DEFMStatsCounter@{DEFMStatsCounter}!Phylo rules@{Phylo rules}|hyperpage}{38} -\indexentry{Phylo rules@{Phylo rules}!DEFMSupport@{DEFMSupport}|hyperpage}{38} -\indexentry{DEFMSupport@{DEFMSupport}!Phylo rules@{Phylo rules}|hyperpage}{38} +\indexentry{Phylo rules@{Phylo rules}!DEFMRulesDyn@{DEFMRulesDyn}|hyperpage}{39} +\indexentry{DEFMRulesDyn@{DEFMRulesDyn}!Phylo rules@{Phylo rules}|hyperpage}{39} +\indexentry{Phylo rules@{Phylo rules}!DEFMStatsCounter@{DEFMStatsCounter}|hyperpage}{39} +\indexentry{DEFMStatsCounter@{DEFMStatsCounter}!Phylo rules@{Phylo rules}|hyperpage}{39} +\indexentry{Phylo rules@{Phylo rules}!DEFMSupport@{DEFMSupport}|hyperpage}{39} +\indexentry{DEFMSupport@{DEFMSupport}!Phylo rules@{Phylo rules}|hyperpage}{39} \indexentry{Phylo rules@{Phylo rules}!at@{at}|hyperpage}{39} \indexentry{at@{at}!Phylo rules@{Phylo rules}|hyperpage}{39} \indexentry{Phylo rules@{Phylo rules}!DEFMCounterData@{DEFMCounterData}|hyperpage}{39} \indexentry{DEFMCounterData@{DEFMCounterData}!Phylo rules@{Phylo rules}|hyperpage}{39} \indexentry{Phylo rules@{Phylo rules}!DEFMCounterData@{DEFMCounterData}|hyperpage}{39} \indexentry{DEFMCounterData@{DEFMCounterData}!Phylo rules@{Phylo rules}|hyperpage}{39} -\indexentry{Phylo rules@{Phylo rules}!DEFMData@{DEFMData}|hyperpage}{39} -\indexentry{DEFMData@{DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{39} -\indexentry{Phylo rules@{Phylo rules}!DEFMData@{DEFMData}|hyperpage}{39} -\indexentry{DEFMData@{DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{39} -\indexentry{Phylo rules@{Phylo rules}!DEFMRuleData@{DEFMRuleData}|hyperpage}{40} -\indexentry{DEFMRuleData@{DEFMRuleData}!Phylo rules@{Phylo rules}|hyperpage}{40} +\indexentry{Phylo rules@{Phylo rules}!DEFMData@{DEFMData}|hyperpage}{40} +\indexentry{DEFMData@{DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{40} +\indexentry{Phylo rules@{Phylo rules}!DEFMData@{DEFMData}|hyperpage}{40} +\indexentry{DEFMData@{DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{40} \indexentry{Phylo rules@{Phylo rules}!DEFMRuleData@{DEFMRuleData}|hyperpage}{40} \indexentry{DEFMRuleData@{DEFMRuleData}!Phylo rules@{Phylo rules}|hyperpage}{40} \indexentry{Phylo rules@{Phylo rules}!DEFMRuleData@{DEFMRuleData}|hyperpage}{40} \indexentry{DEFMRuleData@{DEFMRuleData}!Phylo rules@{Phylo rules}|hyperpage}{40} -\indexentry{Phylo rules@{Phylo rules}!DEFMRuleDynData@{DEFMRuleDynData}|hyperpage}{40} -\indexentry{DEFMRuleDynData@{DEFMRuleDynData}!Phylo rules@{Phylo rules}|hyperpage}{40} -\indexentry{Phylo rules@{Phylo rules}!idx@{idx}|hyperpage}{40} -\indexentry{idx@{idx}!Phylo rules@{Phylo rules}|hyperpage}{40} +\indexentry{Phylo rules@{Phylo rules}!DEFMRuleData@{DEFMRuleData}|hyperpage}{41} +\indexentry{DEFMRuleData@{DEFMRuleData}!Phylo rules@{Phylo rules}|hyperpage}{41} +\indexentry{Phylo rules@{Phylo rules}!DEFMRuleDynData@{DEFMRuleDynData}|hyperpage}{41} +\indexentry{DEFMRuleDynData@{DEFMRuleDynData}!Phylo rules@{Phylo rules}|hyperpage}{41} +\indexentry{Phylo rules@{Phylo rules}!idx@{idx}|hyperpage}{41} +\indexentry{idx@{idx}!Phylo rules@{Phylo rules}|hyperpage}{41} \indexentry{Phylo rules@{Phylo rules}!idx@{idx}|hyperpage}{41} \indexentry{idx@{idx}!Phylo rules@{Phylo rules}|hyperpage}{41} \indexentry{Phylo rules@{Phylo rules}!is\_true@{is\_true}|hyperpage}{41} \indexentry{is\_true@{is\_true}!Phylo rules@{Phylo rules}|hyperpage}{41} -\indexentry{Phylo rules@{Phylo rules}!is\_true@{is\_true}|hyperpage}{41} -\indexentry{is\_true@{is\_true}!Phylo rules@{Phylo rules}|hyperpage}{41} -\indexentry{Phylo rules@{Phylo rules}!ncol@{ncol}|hyperpage}{41} -\indexentry{ncol@{ncol}!Phylo rules@{Phylo rules}|hyperpage}{41} -\indexentry{Phylo rules@{Phylo rules}!nrow@{nrow}|hyperpage}{41} -\indexentry{nrow@{nrow}!Phylo rules@{Phylo rules}|hyperpage}{41} -\indexentry{Phylo rules@{Phylo rules}!num@{num}|hyperpage}{41} -\indexentry{num@{num}!Phylo rules@{Phylo rules}|hyperpage}{41} +\indexentry{Phylo rules@{Phylo rules}!is\_true@{is\_true}|hyperpage}{42} +\indexentry{is\_true@{is\_true}!Phylo rules@{Phylo rules}|hyperpage}{42} +\indexentry{Phylo rules@{Phylo rules}!ncol@{ncol}|hyperpage}{42} +\indexentry{ncol@{ncol}!Phylo rules@{Phylo rules}|hyperpage}{42} +\indexentry{Phylo rules@{Phylo rules}!nrow@{nrow}|hyperpage}{42} +\indexentry{nrow@{nrow}!Phylo rules@{Phylo rules}|hyperpage}{42} +\indexentry{Phylo rules@{Phylo rules}!num@{num}|hyperpage}{42} +\indexentry{num@{num}!Phylo rules@{Phylo rules}|hyperpage}{42} \indexentry{Phylo rules@{Phylo rules}!num@{num}|hyperpage}{42} \indexentry{num@{num}!Phylo rules@{Phylo rules}|hyperpage}{42} \indexentry{Phylo rules@{Phylo rules}!operator()@{operator()}|hyperpage}{42} \indexentry{operator()@{operator()}!Phylo rules@{Phylo rules}|hyperpage}{42} -\indexentry{Phylo rules@{Phylo rules}!print@{print}|hyperpage}{42} -\indexentry{print@{print}!Phylo rules@{Phylo rules}|hyperpage}{42} -\indexentry{Phylo rules@{Phylo rules}!rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}|hyperpage}{42} -\indexentry{rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}!Phylo rules@{Phylo rules}|hyperpage}{42} +\indexentry{Phylo rules@{Phylo rules}!print@{print}|hyperpage}{43} +\indexentry{print@{print}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}|hyperpage}{43} +\indexentry{rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}!Phylo rules@{Phylo rules}|hyperpage}{43} \indexentry{Phylo rules@{Phylo rules}!rule\_leafs@{rule\_leafs}|hyperpage}{43} \indexentry{rule\_leafs@{rule\_leafs}!Phylo rules@{Phylo rules}|hyperpage}{43} -\indexentry{Phylo rules@{Phylo rules}!````~DEFMCounterData@{$\sim$DEFMCounterData}|hyperpage}{43} -\indexentry{````~DEFMCounterData@{$\sim$DEFMCounterData}!Phylo rules@{Phylo rules}|hyperpage}{43} -\indexentry{Phylo rules@{Phylo rules}!````~DEFMData@{$\sim$DEFMData}|hyperpage}{43} -\indexentry{````~DEFMData@{$\sim$DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{43} -\indexentry{Phylo rules@{Phylo rules}!````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}|hyperpage}{43} -\indexentry{````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMCounterData@{$\sim$DEFMCounterData}|hyperpage}{44} +\indexentry{````~DEFMCounterData@{$\sim$DEFMCounterData}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMData@{$\sim$DEFMData}|hyperpage}{44} +\indexentry{````~DEFMData@{$\sim$DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}|hyperpage}{44} +\indexentry{````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}!Phylo rules@{Phylo rules}|hyperpage}{44} \indexentry{Phylo rules@{Phylo rules}!array@{array}|hyperpage}{44} \indexentry{array@{array}!Phylo rules@{Phylo rules}|hyperpage}{44} \indexentry{Phylo rules@{Phylo rules}!counts@{counts}|hyperpage}{44} \indexentry{counts@{counts}!Phylo rules@{Phylo rules}|hyperpage}{44} \indexentry{Phylo rules@{Phylo rules}!covar\_sort@{covar\_sort}|hyperpage}{44} \indexentry{covar\_sort@{covar\_sort}!Phylo rules@{Phylo rules}|hyperpage}{44} -\indexentry{Phylo rules@{Phylo rules}!covar\_used@{covar\_used}|hyperpage}{44} -\indexentry{covar\_used@{covar\_used}!Phylo rules@{Phylo rules}|hyperpage}{44} -\indexentry{Phylo rules@{Phylo rules}!covariates@{covariates}|hyperpage}{44} -\indexentry{covariates@{covariates}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!covar\_used@{covar\_used}|hyperpage}{45} +\indexentry{covar\_used@{covar\_used}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!covariates@{covariates}|hyperpage}{45} +\indexentry{covariates@{covariates}!Phylo rules@{Phylo rules}|hyperpage}{45} \indexentry{Phylo rules@{Phylo rules}!indices@{indices}|hyperpage}{45} \indexentry{indices@{indices}!Phylo rules@{Phylo rules}|hyperpage}{45} \indexentry{Phylo rules@{Phylo rules}!indices@{indices}|hyperpage}{45} @@ -230,10 +230,10 @@ \indexentry{init@{init}!Phylo rules@{Phylo rules}|hyperpage}{45} \indexentry{Phylo rules@{Phylo rules}!is\_motif@{is\_motif}|hyperpage}{45} \indexentry{is\_motif@{is\_motif}!Phylo rules@{Phylo rules}|hyperpage}{45} -\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{45} -\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{45} -\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{45} -\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{46} +\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{46} +\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{46} \indexentry{Phylo rules@{Phylo rules}!numbers@{numbers}|hyperpage}{46} \indexentry{numbers@{numbers}!Phylo rules@{Phylo rules}|hyperpage}{46} \indexentry{Phylo rules@{Phylo rules}!numbers@{numbers}|hyperpage}{46} @@ -242,2010 +242,2010 @@ \indexentry{obs\_start@{obs\_start}!Phylo rules@{Phylo rules}|hyperpage}{46} \indexentry{Phylo rules@{Phylo rules}!X\_ncol@{X\_ncol}|hyperpage}{46} \indexentry{X\_ncol@{X\_ncol}!Phylo rules@{Phylo rules}|hyperpage}{46} -\indexentry{Phylo rules@{Phylo rules}!X\_nrow@{X\_nrow}|hyperpage}{46} -\indexentry{X\_nrow@{X\_nrow}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!X\_nrow@{X\_nrow}|hyperpage}{47} +\indexentry{X\_nrow@{X\_nrow}!Phylo rules@{Phylo rules}|hyperpage}{47} \indexentry{Phylo counters@{Phylo counters}|hyperpage}{47} -\indexentry{Phylo counters@{Phylo counters}!counter\_co\_opt@{counter\_co\_opt}|hyperpage}{48} -\indexentry{counter\_co\_opt@{counter\_co\_opt}!Phylo counters@{Phylo counters}|hyperpage}{48} +\indexentry{Phylo counters@{Phylo counters}!counter\_co\_opt@{counter\_co\_opt}|hyperpage}{49} +\indexentry{counter\_co\_opt@{counter\_co\_opt}!Phylo counters@{Phylo counters}|hyperpage}{49} \indexentry{Phylo counters@{Phylo counters}!counter\_cogain@{counter\_cogain}|hyperpage}{49} \indexentry{counter\_cogain@{counter\_cogain}!Phylo counters@{Phylo counters}|hyperpage}{49} \indexentry{Phylo counters@{Phylo counters}!counter\_gains@{counter\_gains}|hyperpage}{49} \indexentry{counter\_gains@{counter\_gains}!Phylo counters@{Phylo counters}|hyperpage}{49} \indexentry{Phylo counters@{Phylo counters}!counter\_gains\_from\_0@{counter\_gains\_from\_0}|hyperpage}{49} \indexentry{counter\_gains\_from\_0@{counter\_gains\_from\_0}!Phylo counters@{Phylo counters}|hyperpage}{49} -\indexentry{Phylo counters@{Phylo counters}!counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}|hyperpage}{49} -\indexentry{counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}!Phylo counters@{Phylo counters}|hyperpage}{49} +\indexentry{Phylo counters@{Phylo counters}!counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}|hyperpage}{50} +\indexentry{counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}!Phylo counters@{Phylo counters}|hyperpage}{50} \indexentry{Phylo counters@{Phylo counters}!counter\_genes\_changing@{counter\_genes\_changing}|hyperpage}{50} \indexentry{counter\_genes\_changing@{counter\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{50} \indexentry{Phylo counters@{Phylo counters}!counter\_k\_genes\_changing@{counter\_k\_genes\_changing}|hyperpage}{50} \indexentry{counter\_k\_genes\_changing@{counter\_k\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{50} \indexentry{Phylo counters@{Phylo counters}!counter\_less\_than\_p\_prop\_genes\_changing@{counter\_less\_than\_p\_prop\_genes\_changing}|hyperpage}{50} \indexentry{counter\_less\_than\_p\_prop\_genes\_changing@{counter\_less\_than\_p\_prop\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{50} -\indexentry{Phylo counters@{Phylo counters}!counter\_longest@{counter\_longest}|hyperpage}{50} -\indexentry{counter\_longest@{counter\_longest}!Phylo counters@{Phylo counters}|hyperpage}{50} +\indexentry{Phylo counters@{Phylo counters}!counter\_longest@{counter\_longest}|hyperpage}{51} +\indexentry{counter\_longest@{counter\_longest}!Phylo counters@{Phylo counters}|hyperpage}{51} \indexentry{Phylo counters@{Phylo counters}!counter\_loss@{counter\_loss}|hyperpage}{51} \indexentry{counter\_loss@{counter\_loss}!Phylo counters@{Phylo counters}|hyperpage}{51} \indexentry{Phylo counters@{Phylo counters}!counter\_maxfuns@{counter\_maxfuns}|hyperpage}{51} \indexentry{counter\_maxfuns@{counter\_maxfuns}!Phylo counters@{Phylo counters}|hyperpage}{51} \indexentry{Phylo counters@{Phylo counters}!counter\_neofun@{counter\_neofun}|hyperpage}{51} \indexentry{counter\_neofun@{counter\_neofun}!Phylo counters@{Phylo counters}|hyperpage}{51} -\indexentry{Phylo counters@{Phylo counters}!counter\_neofun\_a2b@{counter\_neofun\_a2b}|hyperpage}{51} -\indexentry{counter\_neofun\_a2b@{counter\_neofun\_a2b}!Phylo counters@{Phylo counters}|hyperpage}{51} +\indexentry{Phylo counters@{Phylo counters}!counter\_neofun\_a2b@{counter\_neofun\_a2b}|hyperpage}{52} +\indexentry{counter\_neofun\_a2b@{counter\_neofun\_a2b}!Phylo counters@{Phylo counters}|hyperpage}{52} \indexentry{Phylo counters@{Phylo counters}!counter\_overall\_changes@{counter\_overall\_changes}|hyperpage}{52} \indexentry{counter\_overall\_changes@{counter\_overall\_changes}!Phylo counters@{Phylo counters}|hyperpage}{52} \indexentry{Phylo counters@{Phylo counters}!counter\_overall\_gains@{counter\_overall\_gains}|hyperpage}{52} \indexentry{counter\_overall\_gains@{counter\_overall\_gains}!Phylo counters@{Phylo counters}|hyperpage}{52} \indexentry{Phylo counters@{Phylo counters}!counter\_overall\_gains\_from\_0@{counter\_overall\_gains\_from\_0}|hyperpage}{52} \indexentry{counter\_overall\_gains\_from\_0@{counter\_overall\_gains\_from\_0}!Phylo counters@{Phylo counters}|hyperpage}{52} -\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_loss@{counter\_overall\_loss}|hyperpage}{52} -\indexentry{counter\_overall\_loss@{counter\_overall\_loss}!Phylo counters@{Phylo counters}|hyperpage}{52} +\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_loss@{counter\_overall\_loss}|hyperpage}{53} +\indexentry{counter\_overall\_loss@{counter\_overall\_loss}!Phylo counters@{Phylo counters}|hyperpage}{53} \indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_first\_gain@{counter\_pairwise\_first\_gain}|hyperpage}{53} \indexentry{counter\_pairwise\_first\_gain@{counter\_pairwise\_first\_gain}!Phylo counters@{Phylo counters}|hyperpage}{53} \indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_neofun\_singlefun@{counter\_pairwise\_neofun\_singlefun}|hyperpage}{53} \indexentry{counter\_pairwise\_neofun\_singlefun@{counter\_pairwise\_neofun\_singlefun}!Phylo counters@{Phylo counters}|hyperpage}{53} \indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_overall\_change@{counter\_pairwise\_overall\_change}|hyperpage}{53} \indexentry{counter\_pairwise\_overall\_change@{counter\_pairwise\_overall\_change}!Phylo counters@{Phylo counters}|hyperpage}{53} -\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_preserving@{counter\_pairwise\_preserving}|hyperpage}{53} -\indexentry{counter\_pairwise\_preserving@{counter\_pairwise\_preserving}!Phylo counters@{Phylo counters}|hyperpage}{53} +\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_preserving@{counter\_pairwise\_preserving}|hyperpage}{54} +\indexentry{counter\_pairwise\_preserving@{counter\_pairwise\_preserving}!Phylo counters@{Phylo counters}|hyperpage}{54} \indexentry{Phylo counters@{Phylo counters}!counter\_preserve\_pseudogene@{counter\_preserve\_pseudogene}|hyperpage}{54} \indexentry{counter\_preserve\_pseudogene@{counter\_preserve\_pseudogene}!Phylo counters@{Phylo counters}|hyperpage}{54} \indexentry{Phylo counters@{Phylo counters}!counter\_prop\_genes\_changing@{counter\_prop\_genes\_changing}|hyperpage}{54} \indexentry{counter\_prop\_genes\_changing@{counter\_prop\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{54} \indexentry{Phylo counters@{Phylo counters}!counter\_subfun@{counter\_subfun}|hyperpage}{54} \indexentry{counter\_subfun@{counter\_subfun}!Phylo counters@{Phylo counters}|hyperpage}{54} -\indexentry{barry@{barry}|hyperpage}{55} -\indexentry{barry::counters@{barry::counters}|hyperpage}{55} -\indexentry{barry::counters::network@{barry::counters::network}|hyperpage}{56} -\indexentry{CHECK@{CHECK}|hyperpage}{56} -\indexentry{CHECK@{CHECK}!BOTH@{BOTH}|hyperpage}{56} -\indexentry{BOTH@{BOTH}!CHECK@{CHECK}|hyperpage}{56} -\indexentry{CHECK@{CHECK}!NONE@{NONE}|hyperpage}{56} -\indexentry{NONE@{NONE}!CHECK@{CHECK}|hyperpage}{56} -\indexentry{CHECK@{CHECK}!ONE@{ONE}|hyperpage}{56} -\indexentry{ONE@{ONE}!CHECK@{CHECK}|hyperpage}{56} -\indexentry{CHECK@{CHECK}!TWO@{TWO}|hyperpage}{56} -\indexentry{TWO@{TWO}!CHECK@{CHECK}|hyperpage}{56} -\indexentry{defm@{defm}|hyperpage}{57} -\indexentry{EXISTS@{EXISTS}|hyperpage}{57} -\indexentry{EXISTS@{EXISTS}!AS\_ONE@{AS\_ONE}|hyperpage}{57} -\indexentry{AS\_ONE@{AS\_ONE}!EXISTS@{EXISTS}|hyperpage}{57} -\indexentry{EXISTS@{EXISTS}!AS\_ZERO@{AS\_ZERO}|hyperpage}{57} -\indexentry{AS\_ZERO@{AS\_ZERO}!EXISTS@{EXISTS}|hyperpage}{57} -\indexentry{EXISTS@{EXISTS}!BOTH@{BOTH}|hyperpage}{57} -\indexentry{BOTH@{BOTH}!EXISTS@{EXISTS}|hyperpage}{57} -\indexentry{EXISTS@{EXISTS}!NONE@{NONE}|hyperpage}{58} -\indexentry{NONE@{NONE}!EXISTS@{EXISTS}|hyperpage}{58} -\indexentry{EXISTS@{EXISTS}!ONE@{ONE}|hyperpage}{58} -\indexentry{ONE@{ONE}!EXISTS@{EXISTS}|hyperpage}{58} -\indexentry{EXISTS@{EXISTS}!TWO@{TWO}|hyperpage}{58} -\indexentry{TWO@{TWO}!EXISTS@{EXISTS}|hyperpage}{58} -\indexentry{EXISTS@{EXISTS}!UKNOWN@{UKNOWN}|hyperpage}{58} -\indexentry{UKNOWN@{UKNOWN}!EXISTS@{EXISTS}|hyperpage}{58} -\indexentry{geese@{geese}|hyperpage}{58} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{59} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{62} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{62} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{62} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{62} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{62} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{62} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{62} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{62} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{63} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{63} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArray@{BArray}|hyperpage}{63} -\indexentry{BArray@{BArray}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{63} -\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!````~BArray@{$\sim$BArray}|hyperpage}{63} 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Data\_Type $>$}|hyperpage}{84} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D@{D}|hyperpage}{84} -\indexentry{D@{D}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D@{D}|hyperpage}{84} -\indexentry{D@{D}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D\_ptr@{D\_ptr}|hyperpage}{85} -\indexentry{D\_ptr@{D\_ptr}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D\_ptr@{D\_ptr}|hyperpage}{85} -\indexentry{D\_ptr@{D\_ptr}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!default\_val@{default\_val}|hyperpage}{85} -\indexentry{default\_val@{default\_val}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_cell@{get\_cell}|hyperpage}{85} -\indexentry{get\_cell@{get\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_col\_vec@{get\_col\_vec}|hyperpage}{85} -\indexentry{get\_col\_vec@{get\_col\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_col\_vec@{get\_col\_vec}|hyperpage}{86} -\indexentry{get\_col\_vec@{get\_col\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_data@{get\_data}|hyperpage}{86} -\indexentry{get\_data@{get\_data}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_entries@{get\_entries}|hyperpage}{86} -\indexentry{get\_entries@{get\_entries}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_row\_vec@{get\_row\_vec}|hyperpage}{86} -\indexentry{get\_row\_vec@{get\_row\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_row\_vec@{get\_row\_vec}|hyperpage}{87} -\indexentry{get\_row\_vec@{get\_row\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!insert\_cell@{insert\_cell}|hyperpage}{87} -\indexentry{insert\_cell@{insert\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!insert\_cell@{insert\_cell}|hyperpage}{87} -\indexentry{insert\_cell@{insert\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!is\_dense@{is\_dense}|hyperpage}{87} -\indexentry{is\_dense@{is\_dense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!is\_empty@{is\_empty}|hyperpage}{88} -\indexentry{is\_empty@{is\_empty}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!ncol@{ncol}|hyperpage}{88} -\indexentry{ncol@{ncol}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!nnozero@{nnozero}|hyperpage}{88} -\indexentry{nnozero@{nnozero}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!nrow@{nrow}|hyperpage}{88} -\indexentry{nrow@{nrow}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{88} -\indexentry{operator()@{operator()}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{89} -\indexentry{operator()@{operator()}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{89} -\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{89} -\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{89} -\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{89} -\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{90} -\indexentry{operator-\/=@{operator-\/=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{90} -\indexentry{operator-\/=@{operator-\/=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{90} -\indexentry{operator-\/=@{operator-\/=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{90} -\indexentry{operator/=@{operator/=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{90} -\indexentry{operator=@{operator=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{91} -\indexentry{operator=@{operator=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{91} -\indexentry{operator==@{operator==}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!out\_of\_range@{out\_of\_range}|hyperpage}{91} -\indexentry{out\_of\_range@{out\_of\_range}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!print@{print}|hyperpage}{91} -\indexentry{print@{print}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!reserve@{reserve}|hyperpage}{91} -\indexentry{reserve@{reserve}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!resize@{resize}|hyperpage}{92} -\indexentry{resize@{resize}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{92} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!rm\_cell@{rm\_cell}|hyperpage}{92} -\indexentry{rm\_cell@{rm\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{92} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!row@{row}|hyperpage}{92} -\indexentry{row@{row}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{92} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!row@{row}|hyperpage}{92} -\indexentry{row@{row}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{92} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!rowsum@{rowsum}|hyperpage}{92} -\indexentry{rowsum@{rowsum}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{92} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!set\_data@{set\_data}|hyperpage}{93} -\indexentry{set\_data@{set\_data}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{93} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!swap\_cells@{swap\_cells}|hyperpage}{93} -\indexentry{swap\_cells@{swap\_cells}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{93} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!swap\_cols@{swap\_cols}|hyperpage}{93} -\indexentry{swap\_cols@{swap\_cols}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{93} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!swap\_rows@{swap\_rows}|hyperpage}{93} -\indexentry{swap\_rows@{swap\_rows}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{93} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!toggle\_cell@{toggle\_cell}|hyperpage}{94} -\indexentry{toggle\_cell@{toggle\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{94} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!toggle\_lock@{toggle\_lock}|hyperpage}{94} -\indexentry{toggle\_lock@{toggle\_lock}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{94} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!transpose@{transpose}|hyperpage}{94} -\indexentry{transpose@{transpose}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{94} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!zero\_col@{zero\_col}|hyperpage}{94} -\indexentry{zero\_col@{zero\_col}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{94} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!zero\_row@{zero\_row}|hyperpage}{94} -\indexentry{zero\_row@{zero\_row}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{94} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{95} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!visited@{visited}|hyperpage}{96} -\indexentry{visited@{visited}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{96} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{96} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell@{BArrayDenseCell}|hyperpage}{97} -\indexentry{BArrayDenseCell@{BArrayDenseCell}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{97} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!````~BArrayDenseCell@{$\sim$BArrayDenseCell}|hyperpage}{97} -\indexentry{````~BArrayDenseCell@{$\sim$BArrayDenseCell}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{97} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator Cell\_Type@{operator Cell\_Type}|hyperpage}{97} -\indexentry{operator Cell\_Type@{operator Cell\_Type}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{97} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{97} -\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{97} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{98} -\indexentry{operator+=@{operator+=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{98} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{98} -\indexentry{operator-\/=@{operator-\/=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{98} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{98} -\indexentry{operator/=@{operator/=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{98} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{98} -\indexentry{operator=@{operator=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{98} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{98} -\indexentry{operator=@{operator=}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{98} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{99} -\indexentry{operator==@{operator==}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{99} -\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{100} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{100} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol@{BArrayDenseCol}|hyperpage}{100} -\indexentry{BArrayDenseCol@{BArrayDenseCol}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{100} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{101} -\indexentry{begin@{begin}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{101} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{101} -\indexentry{end@{end}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{101} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{101} -\indexentry{operator()@{operator()}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{101} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{101} -\indexentry{size@{size}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{101} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const@{BArrayDenseCol\_const}|hyperpage}{103} -\indexentry{BArrayDenseCol\_const@{BArrayDenseCol\_const}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{103} -\indexentry{begin@{begin}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{103} -\indexentry{end@{end}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{103} -\indexentry{operator()@{operator()}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{104} -\indexentry{size@{size}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow@{BArrayDenseRow}|hyperpage}{105} -\indexentry{BArrayDenseRow@{BArrayDenseRow}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{105} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{105} -\indexentry{begin@{begin}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{105} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{105} -\indexentry{end@{end}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{105} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{106} -\indexentry{operator()@{operator()}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{106} -\indexentry{size@{size}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{107} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const@{BArrayDenseRow\_const}|hyperpage}{107} -\indexentry{BArrayDenseRow\_const@{BArrayDenseRow\_const}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{107} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{108} -\indexentry{begin@{begin}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{108} -\indexentry{end@{end}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{108} -\indexentry{operator()@{operator()}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{108} -\indexentry{size@{size}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} -\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} -\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} -\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!BArrayRow@{BArrayRow}|hyperpage}{110} -\indexentry{BArrayRow@{BArrayRow}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!````~BArrayRow@{$\sim$BArrayRow}|hyperpage}{110} -\indexentry{````~BArrayRow@{$\sim$BArrayRow}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator BArrayRow$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{110} -\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{110} -\indexentry{operator+=@{operator+=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{110} -\indexentry{operator-\/=@{operator-\/=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{111} -\indexentry{operator/=@{operator/=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{111} -\indexentry{operator=@{operator=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} -\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{111} -\indexentry{operator==@{operator==}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayRow\_const@{BArrayRow\_const}|hyperpage}{112} -\indexentry{BArrayRow\_const@{BArrayRow\_const}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!````~BArrayRow\_const@{$\sim$BArrayRow\_const}|hyperpage}{112} -\indexentry{````~BArrayRow\_const@{$\sim$BArrayRow\_const}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator"!=@{operator"!=}|hyperpage}{112} -\indexentry{operator"!=@{operator"!=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$@{operator$<$}|hyperpage}{112} -\indexentry{operator$<$@{operator$<$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$=@{operator$<$=}|hyperpage}{113} -\indexentry{operator$<$=@{operator$<$=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{113} -\indexentry{operator==@{operator==}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$@{operator$>$}|hyperpage}{113} -\indexentry{operator$>$@{operator$>$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} -\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$=@{operator$>$=}|hyperpage}{113} -\indexentry{operator$>$=@{operator$>$=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!BArrayVector@{BArrayVector}|hyperpage}{114} -\indexentry{BArrayVector@{BArrayVector}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!````~BArrayVector@{$\sim$BArrayVector}|hyperpage}{115} -\indexentry{````~BArrayVector@{$\sim$BArrayVector}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{115} -\indexentry{begin@{begin}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{115} -\indexentry{end@{end}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} -\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!is\_col@{is\_col}|hyperpage}{115} -\indexentry{is\_col@{is\_col}!BArrayVector$<$ Cell\_Type, Data\_Type 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$>$}|hyperpage}{158} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!add@{add}|hyperpage}{158} -\indexentry{add@{add}!FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{158} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!as\_vector@{as\_vector}|hyperpage}{158} -\indexentry{as\_vector@{as\_vector}!FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{158} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!clear@{clear}|hyperpage}{158} -\indexentry{clear@{clear}!FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{158} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!get\_data@{get\_data}|hyperpage}{159} -\indexentry{get\_data@{get\_data}!FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{159} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!get\_index@{get\_index}|hyperpage}{159} -\indexentry{get\_index@{get\_index}!FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{159} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!make\_hash@{make\_hash}|hyperpage}{159} 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-\indexentry{Geese@{Geese}!Geese@{Geese}|hyperpage}{164} -\indexentry{Geese@{Geese}!Geese@{Geese}|hyperpage}{164} -\indexentry{Geese@{Geese}!````~Geese@{$\sim$Geese}|hyperpage}{164} -\indexentry{````~Geese@{$\sim$Geese}!Geese@{Geese}|hyperpage}{164} -\indexentry{Geese@{Geese}!calc\_reduced\_sequence@{calc\_reduced\_sequence}|hyperpage}{164} -\indexentry{calc\_reduced\_sequence@{calc\_reduced\_sequence}!Geese@{Geese}|hyperpage}{164} -\indexentry{Geese@{Geese}!calc\_sequence@{calc\_sequence}|hyperpage}{165} -\indexentry{calc\_sequence@{calc\_sequence}!Geese@{Geese}|hyperpage}{165} -\indexentry{Geese@{Geese}!colnames@{colnames}|hyperpage}{165} -\indexentry{colnames@{colnames}!Geese@{Geese}|hyperpage}{165} -\indexentry{Geese@{Geese}!get\_annotated\_nodes@{get\_annotated\_nodes}|hyperpage}{165} -\indexentry{get\_annotated\_nodes@{get\_annotated\_nodes}!Geese@{Geese}|hyperpage}{165} -\indexentry{Geese@{Geese}!get\_annotations@{get\_annotations}|hyperpage}{165} 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-\indexentry{predict@{predict}!Geese@{Geese}|hyperpage}{169} -\indexentry{Geese@{Geese}!predict\_backend@{predict\_backend}|hyperpage}{170} -\indexentry{predict\_backend@{predict\_backend}!Geese@{Geese}|hyperpage}{170} -\indexentry{Geese@{Geese}!predict\_exhaust@{predict\_exhaust}|hyperpage}{170} -\indexentry{predict\_exhaust@{predict\_exhaust}!Geese@{Geese}|hyperpage}{170} -\indexentry{Geese@{Geese}!predict\_exhaust\_backend@{predict\_exhaust\_backend}|hyperpage}{170} -\indexentry{predict\_exhaust\_backend@{predict\_exhaust\_backend}!Geese@{Geese}|hyperpage}{170} -\indexentry{Geese@{Geese}!predict\_sim@{predict\_sim}|hyperpage}{170} -\indexentry{predict\_sim@{predict\_sim}!Geese@{Geese}|hyperpage}{170} -\indexentry{Geese@{Geese}!print@{print}|hyperpage}{170} -\indexentry{print@{print}!Geese@{Geese}|hyperpage}{170} -\indexentry{Geese@{Geese}!print\_nodes@{print\_nodes}|hyperpage}{171} -\indexentry{print\_nodes@{print\_nodes}!Geese@{Geese}|hyperpage}{171} 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-\indexentry{delete\_support@{delete\_support}!Geese@{Geese}|hyperpage}{172} -\indexentry{Geese@{Geese}!etype\_default@{etype\_default}|hyperpage}{172} -\indexentry{etype\_default@{etype\_default}!Geese@{Geese}|hyperpage}{172} -\indexentry{Geese@{Geese}!etype\_duplication@{etype\_duplication}|hyperpage}{172} -\indexentry{etype\_duplication@{etype\_duplication}!Geese@{Geese}|hyperpage}{172} -\indexentry{Geese@{Geese}!etype\_either@{etype\_either}|hyperpage}{172} -\indexentry{etype\_either@{etype\_either}!Geese@{Geese}|hyperpage}{172} -\indexentry{Geese@{Geese}!etype\_speciation@{etype\_speciation}|hyperpage}{173} -\indexentry{etype\_speciation@{etype\_speciation}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!initialized@{initialized}|hyperpage}{173} -\indexentry{initialized@{initialized}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!map\_to\_state\_id@{map\_to\_state\_id}|hyperpage}{173} -\indexentry{map\_to\_state\_id@{map\_to\_state\_id}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!nfunctions@{nfunctions}|hyperpage}{173} -\indexentry{nfunctions@{nfunctions}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!nodes@{nodes}|hyperpage}{173} -\indexentry{nodes@{nodes}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!pset\_loc@{pset\_loc}|hyperpage}{173} -\indexentry{pset\_loc@{pset\_loc}!Geese@{Geese}|hyperpage}{173} -\indexentry{Geese@{Geese}!reduced\_sequence@{reduced\_sequence}|hyperpage}{174} -\indexentry{reduced\_sequence@{reduced\_sequence}!Geese@{Geese}|hyperpage}{174} -\indexentry{Geese@{Geese}!sequence@{sequence}|hyperpage}{174} -\indexentry{sequence@{sequence}!Geese@{Geese}|hyperpage}{174} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{175} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!Model@{Model}|hyperpage}{179} -\indexentry{Model@{Model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{179} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!Model@{Model}|hyperpage}{180} -\indexentry{Model@{Model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{180} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!Model@{Model}|hyperpage}{180} -\indexentry{Model@{Model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{180} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!````~Model@{$\sim$Model}|hyperpage}{180} -\indexentry{````~Model@{$\sim$Model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{180} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_array@{add\_array}|hyperpage}{180} -\indexentry{add\_array@{add\_array}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{180} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_counter@{add\_counter}|hyperpage}{181} -\indexentry{add\_counter@{add\_counter}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{181} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_counter@{add\_counter}|hyperpage}{181} -\indexentry{add\_counter@{add\_counter}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{181} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_hasher@{add\_hasher}|hyperpage}{181} -\indexentry{add\_hasher@{add\_hasher}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{181} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_rule@{add\_rule}|hyperpage}{181} -\indexentry{add\_rule@{add\_rule}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{181} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_rule@{add\_rule}|hyperpage}{182} -\indexentry{add\_rule@{add\_rule}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_rule\_dyn@{add\_rule\_dyn}|hyperpage}{182} -\indexentry{add\_rule\_dyn@{add\_rule\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_rule\_dyn@{add\_rule\_dyn}|hyperpage}{182} -\indexentry{add\_rule\_dyn@{add\_rule\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!colnames@{colnames}|hyperpage}{182} -\indexentry{colnames@{colnames}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!conditional\_prob@{conditional\_prob}|hyperpage}{182} -\indexentry{conditional\_prob@{conditional\_prob}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!gen\_key@{gen\_key}|hyperpage}{183} -\indexentry{gen\_key@{gen\_key}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{183} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_arrays2support@{get\_arrays2support}|hyperpage}{183} -\indexentry{get\_arrays2support@{get\_arrays2support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{183} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_counters@{get\_counters}|hyperpage}{183} -\indexentry{get\_counters@{get\_counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{183} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_likelihoods@{get\_likelihoods}|hyperpage}{184} -\indexentry{get\_likelihoods@{get\_likelihoods}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{184} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_normalizing\_constants@{get\_normalizing\_constants}|hyperpage}{184} -\indexentry{get\_normalizing\_constants@{get\_normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{184} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset@{get\_pset}|hyperpage}{184} -\indexentry{get\_pset@{get\_pset}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{184} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_arrays@{get\_pset\_arrays}|hyperpage}{184} -\indexentry{get\_pset\_arrays@{get\_pset\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{184} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_locations@{get\_pset\_locations}|hyperpage}{184} -\indexentry{get\_pset\_locations@{get\_pset\_locations}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{184} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_probs@{get\_pset\_probs}|hyperpage}{185} -\indexentry{get\_pset\_probs@{get\_pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{185} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_sizes@{get\_pset\_sizes}|hyperpage}{185} -\indexentry{get\_pset\_sizes@{get\_pset\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{185} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_stats@{get\_pset\_stats}|hyperpage}{185} -\indexentry{get\_pset\_stats@{get\_pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{185} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_stats@{get\_pset\_stats}|hyperpage}{185} -\indexentry{get\_pset\_stats@{get\_pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{185} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rengine@{get\_rengine}|hyperpage}{186} -\indexentry{get\_rengine@{get\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rules@{get\_rules}|hyperpage}{186} -\indexentry{get\_rules@{get\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rules\_dyn@{get\_rules\_dyn}|hyperpage}{186} -\indexentry{get\_rules\_dyn@{get\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support@{get\_stats\_support}|hyperpage}{186} -\indexentry{get\_stats\_support@{get\_stats\_support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support\_sizes@{get\_stats\_support\_sizes}|hyperpage}{186} -\indexentry{get\_stats\_support\_sizes@{get\_stats\_support\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support\_sizes\_acc@{get\_stats\_support\_sizes\_acc}|hyperpage}{187} -\indexentry{get\_stats\_support\_sizes\_acc@{get\_stats\_support\_sizes\_acc}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_target@{get\_stats\_target}|hyperpage}{187} -\indexentry{get\_stats\_target@{get\_stats\_target}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_support\_fun@{get\_support\_fun}|hyperpage}{187} -\indexentry{get\_support\_fun@{get\_support\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{187} -\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{188} -\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{188} -\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{188} -\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood\_total@{likelihood\_total}|hyperpage}{189} -\indexentry{likelihood\_total@{likelihood\_total}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nrules@{nrules}|hyperpage}{189} -\indexentry{nrules@{nrules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nrules\_dyn@{nrules\_dyn}|hyperpage}{189} -\indexentry{nrules\_dyn@{nrules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nterms@{nterms}|hyperpage}{189} -\indexentry{nterms@{nterms}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!operator=@{operator=}|hyperpage}{190} -\indexentry{operator=@{operator=}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!print@{print}|hyperpage}{190} -\indexentry{print@{print}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!print\_stats@{print\_stats}|hyperpage}{190} -\indexentry{print\_stats@{print\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!sample@{sample}|hyperpage}{190} -\indexentry{sample@{sample}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!sample@{sample}|hyperpage}{191} -\indexentry{sample@{sample}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_counters@{set\_counters}|hyperpage}{191} -\indexentry{set\_counters@{set\_counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rengine@{set\_rengine}|hyperpage}{191} -\indexentry{set\_rengine@{set\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rules@{set\_rules}|hyperpage}{191} -\indexentry{set\_rules@{set\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rules\_dyn@{set\_rules\_dyn}|hyperpage}{192} -\indexentry{set\_rules\_dyn@{set\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_seed@{set\_seed}|hyperpage}{192} -\indexentry{set\_seed@{set\_seed}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_transform\_model@{set\_transform\_model}|hyperpage}{192} -\indexentry{set\_transform\_model@{set\_transform\_model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!size@{size}|hyperpage}{193} -\indexentry{size@{size}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!size\_unique@{size\_unique}|hyperpage}{193} -\indexentry{size\_unique@{size\_unique}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!store\_psets@{store\_psets}|hyperpage}{193} -\indexentry{store\_psets@{store\_psets}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!support\_size@{support\_size}|hyperpage}{193} -\indexentry{support\_size@{support\_size}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model@{transform\_model}|hyperpage}{193} -\indexentry{transform\_model@{transform\_model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_likelihoods@{update\_likelihoods}|hyperpage}{194} -\indexentry{update\_likelihoods@{update\_likelihoods}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_normalizing\_constants@{update\_normalizing\_constants}|hyperpage}{194} -\indexentry{update\_normalizing\_constants@{update\_normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_pset\_probs@{update\_pset\_probs}|hyperpage}{194} -\indexentry{update\_pset\_probs@{update\_pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!arrays2support@{arrays2support}|hyperpage}{195} -\indexentry{arrays2support@{arrays2support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!counter\_fun@{counter\_fun}|hyperpage}{195} -\indexentry{counter\_fun@{counter\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!counters@{counters}|hyperpage}{195} -\indexentry{counters@{counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_counters@{delete\_counters}|hyperpage}{195} -\indexentry{delete\_counters@{delete\_counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rengine@{delete\_rengine}|hyperpage}{195} -\indexentry{delete\_rengine@{delete\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rules@{delete\_rules}|hyperpage}{196} -\indexentry{delete\_rules@{delete\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rules\_dyn@{delete\_rules\_dyn}|hyperpage}{196} -\indexentry{delete\_rules\_dyn@{delete\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!first\_calc\_done@{first\_calc\_done}|hyperpage}{196} -\indexentry{first\_calc\_done@{first\_calc\_done}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!keys2support@{keys2support}|hyperpage}{196} -\indexentry{keys2support@{keys2support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!normalizing\_constants@{normalizing\_constants}|hyperpage}{196} -\indexentry{normalizing\_constants@{normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!params\_last@{params\_last}|hyperpage}{197} -\indexentry{params\_last@{params\_last}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_arrays@{pset\_arrays}|hyperpage}{197} -\indexentry{pset\_arrays@{pset\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_locations@{pset\_locations}|hyperpage}{197} -\indexentry{pset\_locations@{pset\_locations}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_probs@{pset\_probs}|hyperpage}{197} -\indexentry{pset\_probs@{pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_sizes@{pset\_sizes}|hyperpage}{198} -\indexentry{pset\_sizes@{pset\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_stats@{pset\_stats}|hyperpage}{198} -\indexentry{pset\_stats@{pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rengine@{rengine}|hyperpage}{198} -\indexentry{rengine@{rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rules@{rules}|hyperpage}{198} -\indexentry{rules@{rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rules\_dyn@{rules\_dyn}|hyperpage}{199} -\indexentry{rules\_dyn@{rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_likelihood@{stats\_likelihood}|hyperpage}{199} -\indexentry{stats\_likelihood@{stats\_likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support@{stats\_support}|hyperpage}{199} -\indexentry{stats\_support@{stats\_support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_n\_arrays@{stats\_support\_n\_arrays}|hyperpage}{199} -\indexentry{stats\_support\_n\_arrays@{stats\_support\_n\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_sizes@{stats\_support\_sizes}|hyperpage}{200} -\indexentry{stats\_support\_sizes@{stats\_support\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_sizes\_acc@{stats\_support\_sizes\_acc}|hyperpage}{200} -\indexentry{stats\_support\_sizes\_acc@{stats\_support\_sizes\_acc}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_target@{stats\_target}|hyperpage}{200} -\indexentry{stats\_target@{stats\_target}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!support\_fun@{support\_fun}|hyperpage}{200} -\indexentry{support\_fun@{support\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model\_fun@{transform\_model\_fun}|hyperpage}{201} -\indexentry{transform\_model\_fun@{transform\_model\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model\_term\_names@{transform\_model\_term\_names}|hyperpage}{201} -\indexentry{transform\_model\_term\_names@{transform\_model\_term\_names}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!with\_pset@{with\_pset}|hyperpage}{201} -\indexentry{with\_pset@{with\_pset}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} -\indexentry{NetCounterData@{NetCounterData}|hyperpage}{202} -\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{202} -\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{202} -\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{202} -\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{202} -\indexentry{NetCounterData@{NetCounterData}!````~NetCounterData@{$\sim$NetCounterData}|hyperpage}{203} -\indexentry{````~NetCounterData@{$\sim$NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{203} -\indexentry{NetCounterData@{NetCounterData}!indices@{indices}|hyperpage}{203} -\indexentry{indices@{indices}!NetCounterData@{NetCounterData}|hyperpage}{203} -\indexentry{NetCounterData@{NetCounterData}!numbers@{numbers}|hyperpage}{203} 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Cell\_Type, Data\_Type $>$}!toggle\_cell@{toggle\_cell}|hyperpage}{74} +\indexentry{toggle\_cell@{toggle\_cell}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{74} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!toggle\_lock@{toggle\_lock}|hyperpage}{74} +\indexentry{toggle\_lock@{toggle\_lock}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{74} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!transpose@{transpose}|hyperpage}{74} +\indexentry{transpose@{transpose}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{74} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!zero\_col@{zero\_col}|hyperpage}{74} +\indexentry{zero\_col@{zero\_col}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{74} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!zero\_row@{zero\_row}|hyperpage}{74} +\indexentry{zero\_row@{zero\_row}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{74} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{75} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{75} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{75} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{75} +\indexentry{BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}!visited@{visited}|hyperpage}{75} +\indexentry{visited@{visited}!BArray$<$ Cell\_Type, Data\_Type $>$@{BArray$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{75} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{76} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!BArrayCell@{BArrayCell}|hyperpage}{76} +\indexentry{BArrayCell@{BArrayCell}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{76} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!````~BArrayCell@{$\sim$BArrayCell}|hyperpage}{76} +\indexentry{````~BArrayCell@{$\sim$BArrayCell}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{76} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator Cell\_Type@{operator Cell\_Type}|hyperpage}{77} +\indexentry{operator Cell\_Type@{operator Cell\_Type}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{77} +\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{77} +\indexentry{operator+=@{operator+=}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{77} +\indexentry{operator-\/=@{operator-\/=}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{77} +\indexentry{operator/=@{operator/=}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{77} +\indexentry{operator=@{operator=}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{77} +\indexentry{BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{78} +\indexentry{operator==@{operator==}!BArrayCell$<$ Cell\_Type, Data\_Type $>$@{BArrayCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{78} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{78} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayCell\_const@{BArrayCell\_const}|hyperpage}{79} +\indexentry{BArrayCell\_const@{BArrayCell\_const}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{79} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!````~BArrayCell\_const@{$\sim$BArrayCell\_const}|hyperpage}{79} +\indexentry{````~BArrayCell\_const@{$\sim$BArrayCell\_const}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{79} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator Cell\_Type@{operator Cell\_Type}|hyperpage}{79} +\indexentry{operator Cell\_Type@{operator Cell\_Type}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{79} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator"!=@{operator"!=}|hyperpage}{79} +\indexentry{operator"!=@{operator"!=}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{79} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$@{operator$<$}|hyperpage}{79} +\indexentry{operator$<$@{operator$<$}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{79} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$=@{operator$<$=}|hyperpage}{80} +\indexentry{operator$<$=@{operator$<$=}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{80} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{80} +\indexentry{operator==@{operator==}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{80} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$@{operator$>$}|hyperpage}{80} +\indexentry{operator$>$@{operator$>$}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{80} +\indexentry{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$=@{operator$>$=}|hyperpage}{80} +\indexentry{operator$>$=@{operator$>$=}!BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{80} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{81} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{84} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{84} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{84} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{84} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{84} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{85} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDense@{BArrayDense}|hyperpage}{85} +\indexentry{BArrayDense@{BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!````~BArrayDense@{$\sim$BArrayDense}|hyperpage}{85} +\indexentry{````~BArrayDense@{$\sim$BArrayDense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!clear@{clear}|hyperpage}{85} +\indexentry{clear@{clear}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{85} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!col@{col}|hyperpage}{86} +\indexentry{col@{col}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!col@{col}|hyperpage}{86} +\indexentry{col@{col}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!colsum@{colsum}|hyperpage}{86} +\indexentry{colsum@{colsum}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D@{D}|hyperpage}{86} +\indexentry{D@{D}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D@{D}|hyperpage}{86} +\indexentry{D@{D}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{86} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D\_ptr@{D\_ptr}|hyperpage}{87} +\indexentry{D\_ptr@{D\_ptr}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!D\_ptr@{D\_ptr}|hyperpage}{87} +\indexentry{D\_ptr@{D\_ptr}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!default\_val@{default\_val}|hyperpage}{87} +\indexentry{default\_val@{default\_val}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_cell@{get\_cell}|hyperpage}{87} +\indexentry{get\_cell@{get\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_col\_vec@{get\_col\_vec}|hyperpage}{87} +\indexentry{get\_col\_vec@{get\_col\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{87} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_col\_vec@{get\_col\_vec}|hyperpage}{88} +\indexentry{get\_col\_vec@{get\_col\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_data@{get\_data}|hyperpage}{88} +\indexentry{get\_data@{get\_data}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_entries@{get\_entries}|hyperpage}{88} +\indexentry{get\_entries@{get\_entries}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_row\_vec@{get\_row\_vec}|hyperpage}{88} +\indexentry{get\_row\_vec@{get\_row\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{88} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!get\_row\_vec@{get\_row\_vec}|hyperpage}{89} +\indexentry{get\_row\_vec@{get\_row\_vec}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!insert\_cell@{insert\_cell}|hyperpage}{89} +\indexentry{insert\_cell@{insert\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!insert\_cell@{insert\_cell}|hyperpage}{89} +\indexentry{insert\_cell@{insert\_cell}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!is\_dense@{is\_dense}|hyperpage}{89} +\indexentry{is\_dense@{is\_dense}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{89} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!is\_empty@{is\_empty}|hyperpage}{90} +\indexentry{is\_empty@{is\_empty}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!ncol@{ncol}|hyperpage}{90} +\indexentry{ncol@{ncol}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!nnozero@{nnozero}|hyperpage}{90} +\indexentry{nnozero@{nnozero}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!nrow@{nrow}|hyperpage}{90} +\indexentry{nrow@{nrow}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{90} +\indexentry{operator()@{operator()}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{90} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{91} +\indexentry{operator()@{operator()}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{91} +\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{91} +\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{91} +\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{91} +\indexentry{operator+=@{operator+=}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{91} 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Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{102} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{103} +\indexentry{begin@{begin}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{103} +\indexentry{end@{end}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{103} +\indexentry{operator()@{operator()}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{103} +\indexentry{size@{size}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{103} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{104} +\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const@{BArrayDenseCol\_const}|hyperpage}{105} +\indexentry{BArrayDenseCol\_const@{BArrayDenseCol\_const}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{105} 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Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{106} +\indexentry{size@{size}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{106} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow@{BArrayDenseRow}|hyperpage}{107} +\indexentry{BArrayDenseRow@{BArrayDenseRow}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{107} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{107} +\indexentry{begin@{begin}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{107} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{107} +\indexentry{end@{end}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{107} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{108} +\indexentry{operator()@{operator()}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{108} +\indexentry{size@{size}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDense$<$ Cell\_Type, Data\_Type $>$@{BArrayDense$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{108} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const@{BArrayDenseRow\_const}|hyperpage}{109} +\indexentry{BArrayDenseRow\_const@{BArrayDenseRow\_const}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{109} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{110} +\indexentry{begin@{begin}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{110} +\indexentry{end@{end}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator()@{operator()}|hyperpage}{110} +\indexentry{operator()@{operator()}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{110} +\indexentry{size@{size}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{110} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} +\indexentry{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} +\indexentry{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} +\indexentry{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{111} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!BArrayRow@{BArrayRow}|hyperpage}{112} +\indexentry{BArrayRow@{BArrayRow}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!````~BArrayRow@{$\sim$BArrayRow}|hyperpage}{112} +\indexentry{````~BArrayRow@{$\sim$BArrayRow}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator BArrayRow$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow$<$ Cell\_Type, Data\_Type $>$}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{112} +\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{112} +\indexentry{operator+=@{operator+=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{112} +\indexentry{operator-\/=@{operator-\/=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{112} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{113} +\indexentry{operator/=@{operator/=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{113} +\indexentry{operator=@{operator=}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} +\indexentry{BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{113} +\indexentry{operator==@{operator==}!BArrayRow$<$ Cell\_Type, Data\_Type $>$@{BArrayRow$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{113} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayRow\_const@{BArrayRow\_const}|hyperpage}{114} +\indexentry{BArrayRow\_const@{BArrayRow\_const}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!````~BArrayRow\_const@{$\sim$BArrayRow\_const}|hyperpage}{114} +\indexentry{````~BArrayRow\_const@{$\sim$BArrayRow\_const}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator"!=@{operator"!=}|hyperpage}{114} +\indexentry{operator"!=@{operator"!=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$@{operator$<$}|hyperpage}{114} +\indexentry{operator$<$@{operator$<$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{114} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$=@{operator$<$=}|hyperpage}{115} +\indexentry{operator$<$=@{operator$<$=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{115} +\indexentry{operator==@{operator==}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$@{operator$>$}|hyperpage}{115} +\indexentry{operator$>$@{operator$>$}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} +\indexentry{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$=@{operator$>$=}|hyperpage}{115} +\indexentry{operator$>$=@{operator$>$=}!BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{115} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!BArrayVector@{BArrayVector}|hyperpage}{116} +\indexentry{BArrayVector@{BArrayVector}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{116} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!````~BArrayVector@{$\sim$BArrayVector}|hyperpage}{117} +\indexentry{````~BArrayVector@{$\sim$BArrayVector}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{117} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{117} +\indexentry{begin@{begin}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{117} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{117} +\indexentry{end@{end}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{117} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!is\_col@{is\_col}|hyperpage}{117} +\indexentry{is\_col@{is\_col}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{117} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!is\_row@{is\_row}|hyperpage}{117} +\indexentry{is\_row@{is\_row}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{117} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator std::vector$<$ Cell\_Type $>$@{operator std::vector$<$ Cell\_Type $>$}|hyperpage}{118} +\indexentry{operator std::vector$<$ Cell\_Type $>$@{operator std::vector$<$ Cell\_Type $>$}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{118} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator$\ast$=@{operator$\ast$=}|hyperpage}{118} +\indexentry{operator$\ast$=@{operator$\ast$=}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{118} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator+=@{operator+=}|hyperpage}{118} +\indexentry{operator+=@{operator+=}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{118} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator-\/=@{operator-\/=}|hyperpage}{118} +\indexentry{operator-\/=@{operator-\/=}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{118} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator/=@{operator/=}|hyperpage}{118} +\indexentry{operator/=@{operator/=}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{118} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator=@{operator=}|hyperpage}{119} +\indexentry{operator=@{operator=}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{119} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{119} +\indexentry{operator==@{operator==}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{119} +\indexentry{BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{119} +\indexentry{size@{size}!BArrayVector$<$ Cell\_Type, Data\_Type $>$@{BArrayVector$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{119} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{119} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!BArrayVector\_const@{BArrayVector\_const}|hyperpage}{120} +\indexentry{BArrayVector\_const@{BArrayVector\_const}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{120} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!````~BArrayVector\_const@{$\sim$BArrayVector\_const}|hyperpage}{120} +\indexentry{````~BArrayVector\_const@{$\sim$BArrayVector\_const}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{120} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!begin@{begin}|hyperpage}{121} +\indexentry{begin@{begin}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!end@{end}|hyperpage}{121} +\indexentry{end@{end}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!is\_col@{is\_col}|hyperpage}{121} +\indexentry{is\_col@{is\_col}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!is\_row@{is\_row}|hyperpage}{121} +\indexentry{is\_row@{is\_row}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator std::vector$<$ Cell\_Type $>$@{operator std::vector$<$ Cell\_Type $>$}|hyperpage}{121} +\indexentry{operator std::vector$<$ Cell\_Type $>$@{operator std::vector$<$ Cell\_Type $>$}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator"!=@{operator"!=}|hyperpage}{121} +\indexentry{operator"!=@{operator"!=}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{121} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$@{operator$<$}|hyperpage}{122} +\indexentry{operator$<$@{operator$<$}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{122} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator$<$=@{operator$<$=}|hyperpage}{122} +\indexentry{operator$<$=@{operator$<$=}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{122} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator==@{operator==}|hyperpage}{122} +\indexentry{operator==@{operator==}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{122} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$@{operator$>$}|hyperpage}{122} +\indexentry{operator$>$@{operator$>$}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{122} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!operator$>$=@{operator$>$=}|hyperpage}{122} +\indexentry{operator$>$=@{operator$>$=}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{122} +\indexentry{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}!size@{size}|hyperpage}{123} +\indexentry{size@{size}!BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$@{BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}|hyperpage}{123} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{123} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{124} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{124} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{124} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{124} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!````~Cell@{$\sim$Cell}|hyperpage}{124} +\indexentry{````~Cell@{$\sim$Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{124} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{124} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{124} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{125} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{125} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{125} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{125} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{125} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{125} +\indexentry{Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}!Cell@{Cell}|hyperpage}{125} +\indexentry{Cell@{Cell}!Cell$<$ Cell\_Type $>$@{Cell$<$ Cell\_Type $>$}|hyperpage}{125} 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Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{183} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_hasher@{add\_hasher}|hyperpage}{183} +\indexentry{add\_hasher@{add\_hasher}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{183} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!add\_rule@{add\_rule}|hyperpage}{183} +\indexentry{add\_rule@{add\_rule}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ 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Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_likelihoods@{get\_likelihoods}|hyperpage}{186} +\indexentry{get\_likelihoods@{get\_likelihoods}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_normalizing\_constants@{get\_normalizing\_constants}|hyperpage}{186} +\indexentry{get\_normalizing\_constants@{get\_normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset@{get\_pset}|hyperpage}{186} +\indexentry{get\_pset@{get\_pset}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_arrays@{get\_pset\_arrays}|hyperpage}{186} +\indexentry{get\_pset\_arrays@{get\_pset\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_locations@{get\_pset\_locations}|hyperpage}{186} +\indexentry{get\_pset\_locations@{get\_pset\_locations}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{186} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_probs@{get\_pset\_probs}|hyperpage}{187} +\indexentry{get\_pset\_probs@{get\_pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_sizes@{get\_pset\_sizes}|hyperpage}{187} +\indexentry{get\_pset\_sizes@{get\_pset\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_stats@{get\_pset\_stats}|hyperpage}{187} +\indexentry{get\_pset\_stats@{get\_pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_pset\_stats@{get\_pset\_stats}|hyperpage}{187} +\indexentry{get\_pset\_stats@{get\_pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{187} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rengine@{get\_rengine}|hyperpage}{188} +\indexentry{get\_rengine@{get\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rules@{get\_rules}|hyperpage}{188} +\indexentry{get\_rules@{get\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_rules\_dyn@{get\_rules\_dyn}|hyperpage}{188} +\indexentry{get\_rules\_dyn@{get\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support@{get\_stats\_support}|hyperpage}{188} +\indexentry{get\_stats\_support@{get\_stats\_support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support\_sizes@{get\_stats\_support\_sizes}|hyperpage}{188} +\indexentry{get\_stats\_support\_sizes@{get\_stats\_support\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{188} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_support\_sizes\_acc@{get\_stats\_support\_sizes\_acc}|hyperpage}{189} +\indexentry{get\_stats\_support\_sizes\_acc@{get\_stats\_support\_sizes\_acc}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_stats\_target@{get\_stats\_target}|hyperpage}{189} +\indexentry{get\_stats\_target@{get\_stats\_target}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!get\_support\_fun@{get\_support\_fun}|hyperpage}{189} +\indexentry{get\_support\_fun@{get\_support\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{189} +\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{189} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{190} +\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{190} +\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood@{likelihood}|hyperpage}{190} +\indexentry{likelihood@{likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{190} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!likelihood\_total@{likelihood\_total}|hyperpage}{191} +\indexentry{likelihood\_total@{likelihood\_total}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nrules@{nrules}|hyperpage}{191} +\indexentry{nrules@{nrules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nrules\_dyn@{nrules\_dyn}|hyperpage}{191} +\indexentry{nrules\_dyn@{nrules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!nterms@{nterms}|hyperpage}{191} +\indexentry{nterms@{nterms}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{191} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!operator=@{operator=}|hyperpage}{192} +\indexentry{operator=@{operator=}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!print@{print}|hyperpage}{192} +\indexentry{print@{print}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!print\_stats@{print\_stats}|hyperpage}{192} +\indexentry{print\_stats@{print\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!sample@{sample}|hyperpage}{192} +\indexentry{sample@{sample}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{192} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!sample@{sample}|hyperpage}{193} +\indexentry{sample@{sample}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_counters@{set\_counters}|hyperpage}{193} +\indexentry{set\_counters@{set\_counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rengine@{set\_rengine}|hyperpage}{193} +\indexentry{set\_rengine@{set\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rules@{set\_rules}|hyperpage}{193} +\indexentry{set\_rules@{set\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{193} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_rules\_dyn@{set\_rules\_dyn}|hyperpage}{194} +\indexentry{set\_rules\_dyn@{set\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_seed@{set\_seed}|hyperpage}{194} +\indexentry{set\_seed@{set\_seed}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!set\_transform\_model@{set\_transform\_model}|hyperpage}{194} +\indexentry{set\_transform\_model@{set\_transform\_model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{194} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!size@{size}|hyperpage}{195} +\indexentry{size@{size}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!size\_unique@{size\_unique}|hyperpage}{195} +\indexentry{size\_unique@{size\_unique}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!store\_psets@{store\_psets}|hyperpage}{195} +\indexentry{store\_psets@{store\_psets}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!support\_size@{support\_size}|hyperpage}{195} +\indexentry{support\_size@{support\_size}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model@{transform\_model}|hyperpage}{195} +\indexentry{transform\_model@{transform\_model}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{195} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_likelihoods@{update\_likelihoods}|hyperpage}{196} +\indexentry{update\_likelihoods@{update\_likelihoods}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_normalizing\_constants@{update\_normalizing\_constants}|hyperpage}{196} +\indexentry{update\_normalizing\_constants@{update\_normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!update\_pset\_probs@{update\_pset\_probs}|hyperpage}{196} +\indexentry{update\_pset\_probs@{update\_pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{196} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!arrays2support@{arrays2support}|hyperpage}{197} +\indexentry{arrays2support@{arrays2support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!counter\_fun@{counter\_fun}|hyperpage}{197} +\indexentry{counter\_fun@{counter\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!counters@{counters}|hyperpage}{197} +\indexentry{counters@{counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_counters@{delete\_counters}|hyperpage}{197} +\indexentry{delete\_counters@{delete\_counters}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rengine@{delete\_rengine}|hyperpage}{197} +\indexentry{delete\_rengine@{delete\_rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{197} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rules@{delete\_rules}|hyperpage}{198} +\indexentry{delete\_rules@{delete\_rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!delete\_rules\_dyn@{delete\_rules\_dyn}|hyperpage}{198} +\indexentry{delete\_rules\_dyn@{delete\_rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!first\_calc\_done@{first\_calc\_done}|hyperpage}{198} +\indexentry{first\_calc\_done@{first\_calc\_done}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!keys2support@{keys2support}|hyperpage}{198} +\indexentry{keys2support@{keys2support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!normalizing\_constants@{normalizing\_constants}|hyperpage}{198} +\indexentry{normalizing\_constants@{normalizing\_constants}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{198} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!params\_last@{params\_last}|hyperpage}{199} +\indexentry{params\_last@{params\_last}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_arrays@{pset\_arrays}|hyperpage}{199} +\indexentry{pset\_arrays@{pset\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_locations@{pset\_locations}|hyperpage}{199} +\indexentry{pset\_locations@{pset\_locations}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_probs@{pset\_probs}|hyperpage}{199} +\indexentry{pset\_probs@{pset\_probs}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{199} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_sizes@{pset\_sizes}|hyperpage}{200} +\indexentry{pset\_sizes@{pset\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!pset\_stats@{pset\_stats}|hyperpage}{200} +\indexentry{pset\_stats@{pset\_stats}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rengine@{rengine}|hyperpage}{200} +\indexentry{rengine@{rengine}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rules@{rules}|hyperpage}{200} +\indexentry{rules@{rules}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{200} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!rules\_dyn@{rules\_dyn}|hyperpage}{201} +\indexentry{rules\_dyn@{rules\_dyn}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_likelihood@{stats\_likelihood}|hyperpage}{201} +\indexentry{stats\_likelihood@{stats\_likelihood}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support@{stats\_support}|hyperpage}{201} +\indexentry{stats\_support@{stats\_support}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_n\_arrays@{stats\_support\_n\_arrays}|hyperpage}{201} +\indexentry{stats\_support\_n\_arrays@{stats\_support\_n\_arrays}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{201} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_sizes@{stats\_support\_sizes}|hyperpage}{202} +\indexentry{stats\_support\_sizes@{stats\_support\_sizes}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{202} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_support\_sizes\_acc@{stats\_support\_sizes\_acc}|hyperpage}{202} +\indexentry{stats\_support\_sizes\_acc@{stats\_support\_sizes\_acc}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{202} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!stats\_target@{stats\_target}|hyperpage}{202} +\indexentry{stats\_target@{stats\_target}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{202} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!support\_fun@{support\_fun}|hyperpage}{202} +\indexentry{support\_fun@{support\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{202} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model\_fun@{transform\_model\_fun}|hyperpage}{203} +\indexentry{transform\_model\_fun@{transform\_model\_fun}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{203} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!transform\_model\_term\_names@{transform\_model\_term\_names}|hyperpage}{203} +\indexentry{transform\_model\_term\_names@{transform\_model\_term\_names}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{203} +\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!with\_pset@{with\_pset}|hyperpage}{203} +\indexentry{with\_pset@{with\_pset}!Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!````~NetCounterData@{$\sim$NetCounterData}|hyperpage}{205} +\indexentry{````~NetCounterData@{$\sim$NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{205} +\indexentry{NetCounterData@{NetCounterData}!indices@{indices}|hyperpage}{205} +\indexentry{indices@{indices}!NetCounterData@{NetCounterData}|hyperpage}{205} +\indexentry{NetCounterData@{NetCounterData}!numbers@{numbers}|hyperpage}{205} +\indexentry{numbers@{numbers}!NetCounterData@{NetCounterData}|hyperpage}{205} +\indexentry{NetworkData@{NetworkData}|hyperpage}{205} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{206} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{206} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{206} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{206} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{207} +\indexentry{NetworkData@{NetworkData}!NetworkData@{NetworkData}|hyperpage}{207} +\indexentry{NetworkData@{NetworkData}!````~NetworkData@{$\sim$NetworkData}|hyperpage}{207} +\indexentry{````~NetworkData@{$\sim$NetworkData}!NetworkData@{NetworkData}|hyperpage}{207} +\indexentry{NetworkData@{NetworkData}!directed@{directed}|hyperpage}{207} +\indexentry{directed@{directed}!NetworkData@{NetworkData}|hyperpage}{207} +\indexentry{NetworkData@{NetworkData}!vertex\_attr@{vertex\_attr}|hyperpage}{207} +\indexentry{vertex\_attr@{vertex\_attr}!NetworkData@{NetworkData}|hyperpage}{207} +\indexentry{Node@{Node}|hyperpage}{208} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{209} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{209} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{209} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{209} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!````~Node@{$\sim$Node}|hyperpage}{210} +\indexentry{````~Node@{$\sim$Node}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!get\_parent@{get\_parent}|hyperpage}{210} +\indexentry{get\_parent@{get\_parent}!Node@{Node}|hyperpage}{210} +\indexentry{Node@{Node}!is\_leaf@{is\_leaf}|hyperpage}{211} +\indexentry{is\_leaf@{is\_leaf}!Node@{Node}|hyperpage}{211} +\indexentry{Node@{Node}!noffspring@{noffspring}|hyperpage}{211} +\indexentry{noffspring@{noffspring}!Node@{Node}|hyperpage}{211} +\indexentry{Node@{Node}!annotations@{annotations}|hyperpage}{211} +\indexentry{annotations@{annotations}!Node@{Node}|hyperpage}{211} +\indexentry{Node@{Node}!array@{array}|hyperpage}{211} +\indexentry{array@{array}!Node@{Node}|hyperpage}{211} +\indexentry{Node@{Node}!arrays@{arrays}|hyperpage}{211} +\indexentry{arrays@{arrays}!Node@{Node}|hyperpage}{211} +\indexentry{Node@{Node}!duplication@{duplication}|hyperpage}{212} +\indexentry{duplication@{duplication}!Node@{Node}|hyperpage}{212} +\indexentry{Node@{Node}!id@{id}|hyperpage}{212} +\indexentry{id@{id}!Node@{Node}|hyperpage}{212} +\indexentry{Node@{Node}!narray@{narray}|hyperpage}{212} +\indexentry{narray@{narray}!Node@{Node}|hyperpage}{212} +\indexentry{Node@{Node}!offspring@{offspring}|hyperpage}{212} +\indexentry{offspring@{offspring}!Node@{Node}|hyperpage}{212} +\indexentry{Node@{Node}!ord@{ord}|hyperpage}{212} +\indexentry{ord@{ord}!Node@{Node}|hyperpage}{212} +\indexentry{Node@{Node}!parent@{parent}|hyperpage}{213} +\indexentry{parent@{parent}!Node@{Node}|hyperpage}{213} +\indexentry{Node@{Node}!probability@{probability}|hyperpage}{213} +\indexentry{probability@{probability}!Node@{Node}|hyperpage}{213} +\indexentry{Node@{Node}!subtree\_prob@{subtree\_prob}|hyperpage}{213} +\indexentry{subtree\_prob@{subtree\_prob}!Node@{Node}|hyperpage}{213} +\indexentry{Node@{Node}!visited@{visited}|hyperpage}{213} +\indexentry{visited@{visited}!Node@{Node}|hyperpage}{213} +\indexentry{NodeData@{NodeData}|hyperpage}{214} +\indexentry{NodeData@{NodeData}!NodeData@{NodeData}|hyperpage}{214} +\indexentry{NodeData@{NodeData}!NodeData@{NodeData}|hyperpage}{214} +\indexentry{NodeData@{NodeData}!blengths@{blengths}|hyperpage}{214} +\indexentry{blengths@{blengths}!NodeData@{NodeData}|hyperpage}{214} +\indexentry{NodeData@{NodeData}!duplication@{duplication}|hyperpage}{215} +\indexentry{duplication@{duplication}!NodeData@{NodeData}|hyperpage}{215} +\indexentry{NodeData@{NodeData}!has\_leaf@{has\_leaf}|hyperpage}{215} +\indexentry{has\_leaf@{has\_leaf}!NodeData@{NodeData}|hyperpage}{215} +\indexentry{NodeData@{NodeData}!states@{states}|hyperpage}{215} +\indexentry{states@{states}!NodeData@{NodeData}|hyperpage}{215} +\indexentry{PhyloCounterData@{PhyloCounterData}|hyperpage}{215} +\indexentry{PhyloCounterData@{PhyloCounterData}!PhyloCounterData@{PhyloCounterData}|hyperpage}{216} +\indexentry{PhyloCounterData@{PhyloCounterData}!PhyloCounterData@{PhyloCounterData}|hyperpage}{216} +\indexentry{PhyloCounterData@{PhyloCounterData}!PhyloCounterData@{PhyloCounterData}|hyperpage}{216} +\indexentry{PhyloCounterData@{PhyloCounterData}!PhyloCounterData@{PhyloCounterData}|hyperpage}{216} +\indexentry{PhyloCounterData@{PhyloCounterData}!at@{at}|hyperpage}{216} +\indexentry{at@{at}!PhyloCounterData@{PhyloCounterData}|hyperpage}{216} +\indexentry{PhyloCounterData@{PhyloCounterData}!begin@{begin}|hyperpage}{217} +\indexentry{begin@{begin}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!empty@{empty}|hyperpage}{217} +\indexentry{empty@{empty}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!end@{end}|hyperpage}{217} +\indexentry{end@{end}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!get\_counters@{get\_counters}|hyperpage}{217} +\indexentry{get\_counters@{get\_counters}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!operator()@{operator()}|hyperpage}{217} +\indexentry{operator()@{operator()}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!operator\mbox{[}\mbox{]}@{operator[]}|hyperpage}{217} +\indexentry{operator\mbox{[}\mbox{]}@{operator[]}!PhyloCounterData@{PhyloCounterData}|hyperpage}{217} +\indexentry{PhyloCounterData@{PhyloCounterData}!push\_back@{push\_back}|hyperpage}{218} +\indexentry{push\_back@{push\_back}!PhyloCounterData@{PhyloCounterData}|hyperpage}{218} +\indexentry{PhyloCounterData@{PhyloCounterData}!reserve@{reserve}|hyperpage}{218} +\indexentry{reserve@{reserve}!PhyloCounterData@{PhyloCounterData}|hyperpage}{218} +\indexentry{PhyloCounterData@{PhyloCounterData}!shrink\_to\_fit@{shrink\_to\_fit}|hyperpage}{218} +\indexentry{shrink\_to\_fit@{shrink\_to\_fit}!PhyloCounterData@{PhyloCounterData}|hyperpage}{218} +\indexentry{PhyloCounterData@{PhyloCounterData}!size@{size}|hyperpage}{218} +\indexentry{size@{size}!PhyloCounterData@{PhyloCounterData}|hyperpage}{218} +\indexentry{PhyloRuleDynData@{PhyloRuleDynData}|hyperpage}{218} 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+\indexentry{Rule\_fun\_type@{Rule\_fun\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{347} +\indexentry{typedefs.hpp@{typedefs.hpp}!sort\_array@{sort\_array}|hyperpage}{347} +\indexentry{sort\_array@{sort\_array}!typedefs.hpp@{typedefs.hpp}|hyperpage}{347} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_equal@{vec\_equal}|hyperpage}{348} +\indexentry{vec\_equal@{vec\_equal}!typedefs.hpp@{typedefs.hpp}|hyperpage}{348} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_equal\_approx@{vec\_equal\_approx}|hyperpage}{348} +\indexentry{vec\_equal\_approx@{vec\_equal\_approx}!typedefs.hpp@{typedefs.hpp}|hyperpage}{348} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_inner\_prod@{vec\_inner\_prod}|hyperpage}{348} +\indexentry{vec\_inner\_prod@{vec\_inner\_prod}!typedefs.hpp@{typedefs.hpp}|hyperpage}{348} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_inner\_prod@{vec\_inner\_prod}|hyperpage}{349} +\indexentry{vec\_inner\_prod@{vec\_inner\_prod}!typedefs.hpp@{typedefs.hpp}|hyperpage}{349} +\indexentry{README.md@{README.md}|hyperpage}{349} diff --git a/latex/refman.ilg b/latex/refman.ilg index b0fcba0fd..5aed002d9 100644 --- a/latex/refman.ilg +++ b/latex/refman.ilg @@ -1,6 +1,6 @@ This is makeindex, version 2.15 [TeX Live 2020] (kpathsea + Thai support). Scanning input file refman.idx......done (2251 entries accepted, 0 rejected). -Sorting entries......................done (27766 comparisons). +Sorting entries......................done (27767 comparisons). Generating output file refman.ind......done (2926 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. diff --git a/latex/refman.ind b/latex/refman.ind index b4fcc9763..6427b25f9 100644 --- a/latex/refman.ind +++ b/latex/refman.ind @@ -1,764 +1,764 @@ \begin{theindex} \item {$\sim$BArray} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{63} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} \item {$\sim$BArrayCell} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} \item {$\sim$BArrayCell\_const} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{77} + \hyperpage{79} \item {$\sim$BArrayDense} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{83} + \hyperpage{85} \item {$\sim$BArrayDenseCell} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{97} + \hyperpage{99} \item {$\sim$BArrayRow} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} \item {$\sim$BArrayRow\_const} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} + \hyperpage{114} \item {$\sim$BArrayVector} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{115} + \hyperpage{117} \item {$\sim$BArrayVector\_const} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{118} + \hyperpage{120} \item {$\sim$Cell} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{122} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124} \item {$\sim$ConstBArrayRowIter} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{127} + \hyperpage{129} \item {$\sim$Counter} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{130} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} \item {$\sim$Counters} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{137} \item {$\sim$DEFMCounterData} - \subitem {Phylo rules}, \hyperpage{43} + \subitem {Phylo rules}, \hyperpage{44} \item {$\sim$DEFMData} - \subitem {Phylo rules}, \hyperpage{43} + \subitem {Phylo rules}, \hyperpage{44} \item {$\sim$DEFMRuleDynData} - \subitem {Phylo rules}, \hyperpage{43} + \subitem {Phylo rules}, \hyperpage{44} \item {$\sim$Entries} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} \item {$\sim$Flock} - \subitem {Flock}, \hyperpage{151} + \subitem {Flock}, \hyperpage{153} \item {$\sim$FreqTable} - \subitem {FreqTable$<$ T $>$}, \hyperpage{158} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \item {$\sim$Geese} - \subitem {Geese}, \hyperpage{164} + \subitem {Geese}, \hyperpage{166} \item {$\sim$Model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{180} + \hyperpage{182} \item {$\sim$NetCounterData} - \subitem {NetCounterData}, \hyperpage{203} + \subitem {NetCounterData}, \hyperpage{205} \item {$\sim$NetworkData} - \subitem {NetworkData}, \hyperpage{205} + \subitem {NetworkData}, \hyperpage{207} \item {$\sim$Node} - \subitem {Node}, \hyperpage{208} + \subitem {Node}, \hyperpage{210} \item {$\sim$PhyloRuleDynData} - \subitem {PhyloRuleDynData}, \hyperpage{217} + \subitem {PhyloRuleDynData}, \hyperpage{219} \item {$\sim$PowerSet} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{221} + \hyperpage{223} \item {$\sim$Progress} - \subitem {Progress}, \hyperpage{226} + \subitem {Progress}, \hyperpage{228} \item {$\sim$Rule} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{227} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} \item {$\sim$Rules} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \item {$\sim$StatsCounter} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{235} + \hyperpage{237} \item {$\sim$Support} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{240} + \hyperpage{242} \indexspace \item {active} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {add} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{123, 124} - \subitem {FreqTable$<$ T $>$}, \hyperpage{158} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125, 126} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \item {add\_array} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{180} + \hyperpage{182} \item {add\_counter} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{135, 136} + \hyperpage{137, 138} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{181} + \hyperpage{183} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{235} + \hyperpage{237} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{240} + \hyperpage{242} \item {add\_data} - \subitem {Flock}, \hyperpage{151} + \subitem {Flock}, \hyperpage{153} \item {add\_dims} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {add\_hash} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} \item {add\_hasher} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{181} + \hyperpage{183} \item {add\_rule} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{181, 182} + \hyperpage{183, 184} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{221} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \hyperpage{223} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{240, 241} + \hyperpage{242, 243} \item {add\_rule\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{182} + \hyperpage{184} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{241} + \hyperpage{243} \item {annotations} - \subitem {Node}, \hyperpage{209} + \subitem {Node}, \hyperpage{211} \item {Array} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{127} + \hyperpage{129} \item {array} - \subitem {Node}, \hyperpage{209} + \subitem {Node}, \hyperpage{211} \subitem {Phylo rules}, \hyperpage{44} \item {arrays} - \subitem {Node}, \hyperpage{209} + \subitem {Node}, \hyperpage{211} \item {arrays2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{197} \item {AS\_ONE} - \subitem {EXISTS}, \hyperpage{57} + \subitem {EXISTS}, \hyperpage{59} \item {as\_vector} - \subitem {FreqTable$<$ T $>$}, \hyperpage{158} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \item {AS\_ZERO} - \subitem {EXISTS}, \hyperpage{57} + \subitem {EXISTS}, \hyperpage{59} \item {at} \subitem {Phylo rules}, \hyperpage{39} - \subitem {PhyloCounterData}, \hyperpage{214} + \subitem {PhyloCounterData}, \hyperpage{216} \indexspace \item {BArray} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{62, 63} - \item {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{59} - \subitem {$\sim$BArray}, \hyperpage{63} - \subitem {BArray}, \hyperpage{62, 63} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64, 65} + \item {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{61} + \subitem {$\sim$BArray}, \hyperpage{65} + \subitem {BArray}, \hyperpage{64, 65} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{73} - \subitem {clear}, \hyperpage{63} - \subitem {col}, \hyperpage{63} - \subitem {D}, \hyperpage{64} - \subitem {D\_ptr}, \hyperpage{64} - \subitem {default\_val}, \hyperpage{64} - \subitem {flush\_data}, \hyperpage{64} - \subitem {get\_cell}, \hyperpage{64} - \subitem {get\_col\_vec}, \hyperpage{65} - \subitem {get\_entries}, \hyperpage{65} - \subitem {get\_row\_vec}, \hyperpage{65} - \subitem {insert\_cell}, \hyperpage{66} - \subitem {is\_dense}, \hyperpage{66} - \subitem {is\_empty}, \hyperpage{66} - \subitem {ncol}, \hyperpage{67} - \subitem {nnozero}, \hyperpage{67} - \subitem {nrow}, \hyperpage{67} - \subitem {operator$\ast$=}, \hyperpage{67} - \subitem {operator()}, \hyperpage{67} - \subitem {operator+=}, \hyperpage{68} - \subitem {operator-\/=}, \hyperpage{68} - \subitem {operator/=}, \hyperpage{69} - \subitem {operator=}, \hyperpage{69} - \subitem {operator==}, \hyperpage{69} - \subitem {out\_of\_range}, \hyperpage{69} - \subitem {print}, \hyperpage{69} - \subitem {print\_n}, \hyperpage{70} - \subitem {reserve}, \hyperpage{70} - \subitem {resize}, \hyperpage{70} - \subitem {rm\_cell}, \hyperpage{70} - \subitem {row}, \hyperpage{70} - \subitem {set\_data}, \hyperpage{71} - \subitem {swap\_cells}, \hyperpage{71} - \subitem {swap\_cols}, \hyperpage{71} - \subitem {swap\_rows}, \hyperpage{71} - \subitem {toggle\_cell}, \hyperpage{72} - \subitem {toggle\_lock}, \hyperpage{72} - \subitem {transpose}, \hyperpage{72} - \subitem {visited}, \hyperpage{73} - \subitem {zero\_col}, \hyperpage{72} - \subitem {zero\_row}, \hyperpage{72} + \hyperpage{75} + \subitem {clear}, \hyperpage{65} + \subitem {col}, \hyperpage{65} + \subitem {D}, \hyperpage{66} + \subitem {D\_ptr}, \hyperpage{66} + \subitem {default\_val}, \hyperpage{66} + \subitem {flush\_data}, \hyperpage{66} + \subitem {get\_cell}, \hyperpage{66} + \subitem {get\_col\_vec}, \hyperpage{67} + \subitem {get\_entries}, \hyperpage{67} + \subitem {get\_row\_vec}, \hyperpage{67} + \subitem {insert\_cell}, \hyperpage{68} + \subitem {is\_dense}, \hyperpage{68} + \subitem {is\_empty}, \hyperpage{68} + \subitem {ncol}, \hyperpage{69} + \subitem {nnozero}, \hyperpage{69} + \subitem {nrow}, \hyperpage{69} + \subitem {operator$\ast$=}, \hyperpage{69} + \subitem {operator()}, \hyperpage{69} + \subitem {operator+=}, \hyperpage{70} + \subitem {operator-\/=}, \hyperpage{70} + \subitem {operator/=}, \hyperpage{71} + \subitem {operator=}, \hyperpage{71} + \subitem {operator==}, \hyperpage{71} + \subitem {out\_of\_range}, \hyperpage{71} + \subitem {print}, \hyperpage{71} + \subitem {print\_n}, \hyperpage{72} + \subitem {reserve}, \hyperpage{72} + \subitem {resize}, \hyperpage{72} + \subitem {rm\_cell}, \hyperpage{72} + \subitem {row}, \hyperpage{72} + \subitem {set\_data}, \hyperpage{73} + \subitem {swap\_cells}, \hyperpage{73} + \subitem {swap\_cols}, \hyperpage{73} + \subitem {swap\_rows}, \hyperpage{73} + \subitem {toggle\_cell}, \hyperpage{74} + \subitem {toggle\_lock}, \hyperpage{74} + \subitem {transpose}, \hyperpage{74} + \subitem {visited}, \hyperpage{75} + \subitem {zero\_col}, \hyperpage{74} + \subitem {zero\_row}, \hyperpage{74} \item {barray-\/meat-\/operators.hpp} - \subitem {BARRAY\_TEMPLATE}, \hyperpage{252--254} - \subitem {BARRAY\_TEMPLATE\_ARGS}, \hyperpage{253}, \hyperpage{255} - \subitem {BARRAY\_TYPE}, \hyperpage{253}, \hyperpage{255} - \subitem {COL}, \hyperpage{253} - \subitem {for}, \hyperpage{255} - \subitem {operator()}, \hyperpage{255} - \subitem {rhs}, \hyperpage{255} - \subitem {ROW}, \hyperpage{253} - \subitem {this}, \hyperpage{256} + \subitem {BARRAY\_TEMPLATE}, \hyperpage{254--256} + \subitem {BARRAY\_TEMPLATE\_ARGS}, \hyperpage{255}, \hyperpage{257} + \subitem {BARRAY\_TYPE}, \hyperpage{255}, \hyperpage{257} + \subitem {COL}, \hyperpage{255} + \subitem {for}, \hyperpage{257} + \subitem {operator()}, \hyperpage{257} + \subitem {rhs}, \hyperpage{257} + \subitem {ROW}, \hyperpage{255} + \subitem {this}, \hyperpage{258} \item {barray-\/meat.hpp} - \subitem {COL}, \hyperpage{256} - \subitem {ROW}, \hyperpage{257} + \subitem {COL}, \hyperpage{258} + \subitem {ROW}, \hyperpage{259} \item {BARRAY\_TEMPLATE} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{252--254} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{254--256} \item {BARRAY\_TEMPLATE\_ARGS} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253}, - \hyperpage{255} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255}, + \hyperpage{257} \item {BARRAY\_TYPE} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253}, - \hyperpage{255} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255}, + \hyperpage{257} \item {BArrayCell} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} - \item {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} - \subitem {$\sim$BArrayCell}, \hyperpage{74} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} - \subitem {BArrayCell}, \hyperpage{74} - \subitem {operator Cell\_Type}, \hyperpage{75} - \subitem {operator$\ast$=}, \hyperpage{75} - \subitem {operator+=}, \hyperpage{75} - \subitem {operator-\/=}, \hyperpage{75} - \subitem {operator/=}, \hyperpage{75} - \subitem {operator=}, \hyperpage{75} - \subitem {operator==}, \hyperpage{76} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} + \item {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} + \subitem {$\sim$BArrayCell}, \hyperpage{76} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArrayCell}, \hyperpage{76} + \subitem {operator Cell\_Type}, \hyperpage{77} + \subitem {operator$\ast$=}, \hyperpage{77} + \subitem {operator+=}, \hyperpage{77} + \subitem {operator-\/=}, \hyperpage{77} + \subitem {operator/=}, \hyperpage{77} + \subitem {operator=}, \hyperpage{77} + \subitem {operator==}, \hyperpage{78} \item {BArrayCell\_const} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{77} + \hyperpage{79} \item {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{76} - \subitem {$\sim$BArrayCell\_const}, \hyperpage{77} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} - \subitem {BArrayCell\_const}, \hyperpage{77} - \subitem {operator Cell\_Type}, \hyperpage{77} - \subitem {operator!=}, \hyperpage{77} - \subitem {operator$<$}, \hyperpage{77} - \subitem {operator$<$=}, \hyperpage{78} - \subitem {operator$>$}, \hyperpage{78} - \subitem {operator$>$=}, \hyperpage{78} - \subitem {operator==}, \hyperpage{78} + \hyperpage{78} + \subitem {$\sim$BArrayCell\_const}, \hyperpage{79} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArrayCell\_const}, \hyperpage{79} + \subitem {operator Cell\_Type}, \hyperpage{79} + \subitem {operator!=}, \hyperpage{79} + \subitem {operator$<$}, \hyperpage{79} + \subitem {operator$<$=}, \hyperpage{80} + \subitem {operator$>$}, \hyperpage{80} + \subitem {operator$>$=}, \hyperpage{80} + \subitem {operator==}, \hyperpage{80} \item {BArrayDense} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{82, 83} - \item {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{79} - \subitem {$\sim$BArrayDense}, \hyperpage{83} - \subitem {BArrayDense}, \hyperpage{82, 83} + \hyperpage{84, 85} + \item {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{81} + \subitem {$\sim$BArrayDense}, \hyperpage{85} + \subitem {BArrayDense}, \hyperpage{84, 85} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{99} + \hyperpage{97}, \hyperpage{101} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{102} + \hyperpage{97}, \hyperpage{104} \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95} + \hyperpage{97} \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{106} + \hyperpage{97}, \hyperpage{108} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95} - \subitem {clear}, \hyperpage{83} - \subitem {col}, \hyperpage{84} - \subitem {colsum}, \hyperpage{84} - \subitem {D}, \hyperpage{84} - \subitem {D\_ptr}, \hyperpage{85} - \subitem {default\_val}, \hyperpage{85} - \subitem {get\_cell}, \hyperpage{85} - \subitem {get\_col\_vec}, \hyperpage{85, 86} - \subitem {get\_data}, \hyperpage{86} - \subitem {get\_entries}, \hyperpage{86} - \subitem {get\_row\_vec}, \hyperpage{86, 87} - \subitem {insert\_cell}, \hyperpage{87} - \subitem {is\_dense}, \hyperpage{87} - \subitem {is\_empty}, \hyperpage{88} - \subitem {ncol}, \hyperpage{88} - \subitem {nnozero}, \hyperpage{88} - \subitem {nrow}, \hyperpage{88} - \subitem {operator$\ast$=}, \hyperpage{89} - \subitem {operator()}, \hyperpage{88, 89} - \subitem {operator+=}, \hyperpage{89} - \subitem {operator-\/=}, \hyperpage{90} - \subitem {operator/=}, \hyperpage{90} - \subitem {operator=}, \hyperpage{90, 91} - \subitem {operator==}, \hyperpage{91} - \subitem {out\_of\_range}, \hyperpage{91} - \subitem {print}, \hyperpage{91} - \subitem {reserve}, \hyperpage{91} - \subitem {resize}, \hyperpage{92} - \subitem {rm\_cell}, \hyperpage{92} - \subitem {row}, \hyperpage{92} - \subitem {rowsum}, \hyperpage{92} - \subitem {set\_data}, \hyperpage{93} - \subitem {swap\_cells}, \hyperpage{93} - \subitem {swap\_cols}, \hyperpage{93} - \subitem {swap\_rows}, \hyperpage{93} - \subitem {toggle\_cell}, \hyperpage{94} - \subitem {toggle\_lock}, \hyperpage{94} - \subitem {transpose}, \hyperpage{94} - \subitem {visited}, \hyperpage{96} - \subitem {zero\_col}, \hyperpage{94} - \subitem {zero\_row}, \hyperpage{94} + \hyperpage{97} + \subitem {clear}, \hyperpage{85} + \subitem {col}, \hyperpage{86} + \subitem {colsum}, \hyperpage{86} + \subitem {D}, \hyperpage{86} + \subitem {D\_ptr}, \hyperpage{87} + \subitem {default\_val}, \hyperpage{87} + \subitem {get\_cell}, \hyperpage{87} + \subitem {get\_col\_vec}, \hyperpage{87, 88} + \subitem {get\_data}, \hyperpage{88} + \subitem {get\_entries}, \hyperpage{88} + \subitem {get\_row\_vec}, \hyperpage{88, 89} + \subitem {insert\_cell}, \hyperpage{89} + \subitem {is\_dense}, \hyperpage{89} + \subitem {is\_empty}, \hyperpage{90} + \subitem {ncol}, \hyperpage{90} + \subitem {nnozero}, \hyperpage{90} + \subitem {nrow}, \hyperpage{90} + \subitem {operator$\ast$=}, \hyperpage{91} + \subitem {operator()}, \hyperpage{90, 91} + \subitem {operator+=}, \hyperpage{91} + \subitem {operator-\/=}, \hyperpage{92} + \subitem {operator/=}, \hyperpage{92} + \subitem {operator=}, \hyperpage{92, 93} + \subitem {operator==}, \hyperpage{93} + \subitem {out\_of\_range}, \hyperpage{93} + \subitem {print}, \hyperpage{93} + \subitem {reserve}, \hyperpage{93} + \subitem {resize}, \hyperpage{94} + \subitem {rm\_cell}, \hyperpage{94} + \subitem {row}, \hyperpage{94} + \subitem {rowsum}, \hyperpage{94} + \subitem {set\_data}, \hyperpage{95} + \subitem {swap\_cells}, \hyperpage{95} + \subitem {swap\_cols}, \hyperpage{95} + \subitem {swap\_rows}, \hyperpage{95} + \subitem {toggle\_cell}, \hyperpage{96} + \subitem {toggle\_lock}, \hyperpage{96} + \subitem {transpose}, \hyperpage{96} + \subitem {visited}, \hyperpage{98} + \subitem {zero\_col}, \hyperpage{96} + \subitem {zero\_row}, \hyperpage{96} \item {barraydense-\/meat-\/operators.hpp} - \subitem {BDENSE\_TEMPLATE}, \hyperpage{259}, \hyperpage{261} - \subitem {BDENSE\_TEMPLATE\_ARGS}, \hyperpage{259}, \hyperpage{261} - \subitem {BDENSE\_TYPE}, \hyperpage{260}, \hyperpage{262} - \subitem {COL}, \hyperpage{260} - \subitem {POS}, \hyperpage{260} - \subitem {POS\_N}, \hyperpage{260} - \subitem {ROW}, \hyperpage{260} - \item {barraydense-\/meat.hpp} + \subitem {BDENSE\_TEMPLATE}, \hyperpage{261}, \hyperpage{263} + \subitem {BDENSE\_TEMPLATE\_ARGS}, \hyperpage{261}, \hyperpage{263} + \subitem {BDENSE\_TYPE}, \hyperpage{262}, \hyperpage{264} \subitem {COL}, \hyperpage{262} \subitem {POS}, \hyperpage{262} - \subitem {POS\_N}, \hyperpage{263} - \subitem {ROW}, \hyperpage{263} - \subitem {ZERO\_CELL}, \hyperpage{263} + \subitem {POS\_N}, \hyperpage{262} + \subitem {ROW}, \hyperpage{262} + \item {barraydense-\/meat.hpp} + \subitem {COL}, \hyperpage{264} + \subitem {POS}, \hyperpage{264} + \subitem {POS\_N}, \hyperpage{265} + \subitem {ROW}, \hyperpage{265} + \subitem {ZERO\_CELL}, \hyperpage{265} \item {BArrayDenseCell} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{97} - \item {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{96} - \subitem {$\sim$BArrayDenseCell}, \hyperpage{97} + \hyperpage{99} + \item {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{98} + \subitem {$\sim$BArrayDenseCell}, \hyperpage{99} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{99} - \subitem {BArrayDenseCell}, \hyperpage{97} + \hyperpage{97}, \hyperpage{101} + \subitem {BArrayDenseCell}, \hyperpage{99} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{99}, \hyperpage{102} + \hyperpage{101}, \hyperpage{104} \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{99}, \hyperpage{104} + \hyperpage{101}, \hyperpage{106} \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{106} + \hyperpage{108} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{109} - \subitem {operator Cell\_Type}, \hyperpage{97} - \subitem {operator$\ast$=}, \hyperpage{97} - \subitem {operator+=}, \hyperpage{98} - \subitem {operator-\/=}, \hyperpage{98} - \subitem {operator/=}, \hyperpage{98} - \subitem {operator=}, \hyperpage{98} - \subitem {operator==}, \hyperpage{99} + \hyperpage{111} + \subitem {operator Cell\_Type}, \hyperpage{99} + \subitem {operator$\ast$=}, \hyperpage{99} + \subitem {operator+=}, \hyperpage{100} + \subitem {operator-\/=}, \hyperpage{100} + \subitem {operator/=}, \hyperpage{100} + \subitem {operator=}, \hyperpage{100} + \subitem {operator==}, \hyperpage{101} \item {barraydensecell-\/bones.hpp} - \subitem {POS}, \hyperpage{264} + \subitem {POS}, \hyperpage{266} \item {barraydensecell-\/meat.hpp} - \subitem {POS}, \hyperpage{264} + \subitem {POS}, \hyperpage{266} \item {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{100} - \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{102} - \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, + \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{104} - \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{106} + \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{108} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{109} + \hyperpage{111} \item {BArrayDenseCol} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{100} - \item {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{100} - \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{102} - \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{99}, \hyperpage{102} - \subitem {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{102} - \subitem {BArrayDenseCol}, \hyperpage{100} - \subitem {begin}, \hyperpage{101} - \subitem {end}, \hyperpage{101} - \subitem {operator()}, \hyperpage{101} - \subitem {size}, \hyperpage{101} - \item {barraydensecol-\/bones.hpp} - \subitem {POS}, \hyperpage{265} - \subitem {POS\_N}, \hyperpage{265} - \subitem {ZERO\_CELL}, \hyperpage{266} - \item {BArrayDenseCol\_const} - \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{103} - \item {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{102} + \item {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{102} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95} + \hyperpage{97}, \hyperpage{104} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{99}, \hyperpage{104} + \hyperpage{101}, \hyperpage{104} \subitem {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{104} - \subitem {BArrayDenseCol\_const}, \hyperpage{103} + \subitem {BArrayDenseCol}, \hyperpage{102} \subitem {begin}, \hyperpage{103} \subitem {end}, \hyperpage{103} \subitem {operator()}, \hyperpage{103} - \subitem {size}, \hyperpage{104} - \item {BArrayDenseRow} - \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \subitem {size}, \hyperpage{103} + \item {barraydensecol-\/bones.hpp} + \subitem {POS}, \hyperpage{267} + \subitem {POS\_N}, \hyperpage{267} + \subitem {ZERO\_CELL}, \hyperpage{268} + \item {BArrayDenseCol\_const} + \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{105} - \item {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{104} + \item {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{104} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95}, \hyperpage{106} + \hyperpage{97} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{106} + \hyperpage{101}, \hyperpage{106} \subitem {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{106} - \subitem {BArrayDenseRow}, \hyperpage{105} + \subitem {BArrayDenseCol\_const}, \hyperpage{105} \subitem {begin}, \hyperpage{105} \subitem {end}, \hyperpage{105} - \subitem {operator()}, \hyperpage{106} + \subitem {operator()}, \hyperpage{105} \subitem {size}, \hyperpage{106} + \item {BArrayDenseRow} + \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{107} + \item {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{106} + \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{97}, \hyperpage{108} + \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{108} + \subitem {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{108} + \subitem {BArrayDenseRow}, \hyperpage{107} + \subitem {begin}, \hyperpage{107} + \subitem {end}, \hyperpage{107} + \subitem {operator()}, \hyperpage{108} + \subitem {size}, \hyperpage{108} \item {barraydenserow-\/bones.hpp} - \subitem {POS}, \hyperpage{267} - \subitem {POS\_N}, \hyperpage{267} - \subitem {ZERO\_CELL}, \hyperpage{267} + \subitem {POS}, \hyperpage{269} + \subitem {POS\_N}, \hyperpage{269} + \subitem {ZERO\_CELL}, \hyperpage{269} \item {BArrayDenseRow\_const} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{107} + \hyperpage{109} \item {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{107} + \hyperpage{109} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{95} + \hyperpage{97} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{109} + \hyperpage{111} \subitem {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{109} - \subitem {BArrayDenseRow\_const}, \hyperpage{107} - \subitem {begin}, \hyperpage{108} - \subitem {end}, \hyperpage{108} - \subitem {operator()}, \hyperpage{108} - \subitem {size}, \hyperpage{108} + \hyperpage{111} + \subitem {BArrayDenseRow\_const}, \hyperpage{109} + \subitem {begin}, \hyperpage{110} + \subitem {end}, \hyperpage{110} + \subitem {operator()}, \hyperpage{110} + \subitem {size}, \hyperpage{110} \item {BArrayRow} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} - \item {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{109} - \subitem {$\sim$BArrayRow}, \hyperpage{110} - \subitem {BArrayRow}, \hyperpage{110} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} + \item {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{111} + \subitem {$\sim$BArrayRow}, \hyperpage{112} + \subitem {BArrayRow}, \hyperpage{112} \subitem {operator BArrayRow$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{110} - \subitem {operator$\ast$=}, \hyperpage{110} - \subitem {operator+=}, \hyperpage{110} - \subitem {operator-\/=}, \hyperpage{110} - \subitem {operator/=}, \hyperpage{111} - \subitem {operator=}, \hyperpage{111} - \subitem {operator==}, \hyperpage{111} + \hyperpage{112} + \subitem {operator$\ast$=}, \hyperpage{112} + \subitem {operator+=}, \hyperpage{112} + \subitem {operator-\/=}, \hyperpage{112} + \subitem {operator/=}, \hyperpage{113} + \subitem {operator=}, \hyperpage{113} + \subitem {operator==}, \hyperpage{113} \item {barrayrow-\/meat.hpp} - \subitem {BROW\_TEMPLATE}, \hyperpage{268, 269} - \subitem {BROW\_TEMPLATE\_ARGS}, \hyperpage{268} - \subitem {BROW\_TYPE}, \hyperpage{268} + \subitem {BROW\_TEMPLATE}, \hyperpage{270, 271} + \subitem {BROW\_TEMPLATE\_ARGS}, \hyperpage{270} + \subitem {BROW\_TYPE}, \hyperpage{270} \item {BArrayRow\_const} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} + \hyperpage{114} \item {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{111} - \subitem {$\sim$BArrayRow\_const}, \hyperpage{112} - \subitem {BArrayRow\_const}, \hyperpage{112} + \hyperpage{113} + \subitem {$\sim$BArrayRow\_const}, \hyperpage{114} + \subitem {BArrayRow\_const}, \hyperpage{114} \subitem {operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} - \subitem {operator!=}, \hyperpage{112} - \subitem {operator$<$}, \hyperpage{112} - \subitem {operator$<$=}, \hyperpage{113} - \subitem {operator$>$}, \hyperpage{113} - \subitem {operator$>$=}, \hyperpage{113} - \subitem {operator==}, \hyperpage{113} + \hyperpage{114} + \subitem {operator!=}, \hyperpage{114} + \subitem {operator$<$}, \hyperpage{114} + \subitem {operator$<$=}, \hyperpage{115} + \subitem {operator$>$}, \hyperpage{115} + \subitem {operator$>$=}, \hyperpage{115} + \subitem {operator==}, \hyperpage{115} \item {BArrayVector} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{114} - \item {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{113} - \subitem {$\sim$BArrayVector}, \hyperpage{115} - \subitem {BArrayVector}, \hyperpage{114} - \subitem {begin}, \hyperpage{115} - \subitem {end}, \hyperpage{115} - \subitem {is\_col}, \hyperpage{115} - \subitem {is\_row}, \hyperpage{115} - \subitem {operator std::vector$<$ Cell\_Type $>$}, \hyperpage{116} - \subitem {operator$\ast$=}, \hyperpage{116} - \subitem {operator+=}, \hyperpage{116} - \subitem {operator-\/=}, \hyperpage{116} - \subitem {operator/=}, \hyperpage{116} - \subitem {operator=}, \hyperpage{117} - \subitem {operator==}, \hyperpage{117} - \subitem {size}, \hyperpage{117} + \hyperpage{116} + \item {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{115} + \subitem {$\sim$BArrayVector}, \hyperpage{117} + \subitem {BArrayVector}, \hyperpage{116} + \subitem {begin}, \hyperpage{117} + \subitem {end}, \hyperpage{117} + \subitem {is\_col}, \hyperpage{117} + \subitem {is\_row}, \hyperpage{117} + \subitem {operator std::vector$<$ Cell\_Type $>$}, \hyperpage{118} + \subitem {operator$\ast$=}, \hyperpage{118} + \subitem {operator+=}, \hyperpage{118} + \subitem {operator-\/=}, \hyperpage{118} + \subitem {operator/=}, \hyperpage{118} + \subitem {operator=}, \hyperpage{119} + \subitem {operator==}, \hyperpage{119} + \subitem {size}, \hyperpage{119} \item {BArrayVector\_const} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{118} + \hyperpage{120} \item {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{117} - \subitem {$\sim$BArrayVector\_const}, \hyperpage{118} - \subitem {BArrayVector\_const}, \hyperpage{118} - \subitem {begin}, \hyperpage{119} - \subitem {end}, \hyperpage{119} - \subitem {is\_col}, \hyperpage{119} - \subitem {is\_row}, \hyperpage{119} - \subitem {operator std::vector$<$ Cell\_Type $>$}, \hyperpage{119} - \subitem {operator!=}, \hyperpage{119} - \subitem {operator$<$}, \hyperpage{120} - \subitem {operator$<$=}, \hyperpage{120} - \subitem {operator$>$}, \hyperpage{120} - \subitem {operator$>$=}, \hyperpage{120} - \subitem {operator==}, \hyperpage{120} - \subitem {size}, \hyperpage{121} - \item {barry}, \hyperpage{55} + \hyperpage{119} + \subitem {$\sim$BArrayVector\_const}, \hyperpage{120} + \subitem {BArrayVector\_const}, \hyperpage{120} + \subitem {begin}, \hyperpage{121} + \subitem {end}, \hyperpage{121} + \subitem {is\_col}, \hyperpage{121} + \subitem {is\_row}, \hyperpage{121} + \subitem {operator std::vector$<$ Cell\_Type $>$}, \hyperpage{121} + \subitem {operator!=}, \hyperpage{121} + \subitem {operator$<$}, \hyperpage{122} + \subitem {operator$<$=}, \hyperpage{122} + \subitem {operator$>$}, \hyperpage{122} + \subitem {operator$>$=}, \hyperpage{122} + \subitem {operator==}, \hyperpage{122} + \subitem {size}, \hyperpage{123} + \item {barry}, \hyperpage{57} \item {barry-\/configuration.hpp} - \subitem {BARRY\_CHECK\_SUPPORT}, \hyperpage{271} - \subitem {BARRY\_ISFINITE}, \hyperpage{271} - \subitem {BARRY\_MAX\_NUM\_ELEMENTS}, \hyperpage{271} - \subitem {BARRY\_SAFE\_EXP}, \hyperpage{271} - \subitem {Map}, \hyperpage{272} - \subitem {printf\_barry}, \hyperpage{271} + \subitem {BARRY\_CHECK\_SUPPORT}, \hyperpage{273} + \subitem {BARRY\_ISFINITE}, \hyperpage{273} + \subitem {BARRY\_MAX\_NUM\_ELEMENTS}, \hyperpage{273} + \subitem {BARRY\_SAFE\_EXP}, \hyperpage{273} + \subitem {Map}, \hyperpage{274} + \subitem {printf\_barry}, \hyperpage{273} \item {barry-\/debug.hpp} - \subitem {BARRY\_DEBUG\_LEVEL}, \hyperpage{272} + \subitem {BARRY\_DEBUG\_LEVEL}, \hyperpage{274} \item {barry-\/macros.hpp} - \subitem {BARRY\_NCORES\_ARG}, \hyperpage{273} - \subitem {BARRY\_ONE}, \hyperpage{273} - \subitem {BARRY\_ONE\_DENSE}, \hyperpage{273} - \subitem {BARRY\_UNUSED}, \hyperpage{274} - \subitem {BARRY\_ZERO}, \hyperpage{274} - \subitem {BARRY\_ZERO\_DENSE}, \hyperpage{274} + \subitem {BARRY\_NCORES\_ARG}, \hyperpage{275} + \subitem {BARRY\_ONE}, \hyperpage{275} + \subitem {BARRY\_ONE\_DENSE}, \hyperpage{275} + \subitem {BARRY\_UNUSED}, \hyperpage{276} + \subitem {BARRY\_ZERO}, \hyperpage{276} + \subitem {BARRY\_ZERO\_DENSE}, \hyperpage{276} \item {barry.hpp} - \subitem {BARRY\_HPP}, \hyperpage{276} - \subitem {BARRY\_VERSION}, \hyperpage{276} - \subitem {BARRY\_VERSION\_MAYOR}, \hyperpage{276} - \subitem {BARRY\_VERSION\_MINOR}, \hyperpage{276} - \subitem {COUNTER\_FUNCTION}, \hyperpage{276} - \subitem {COUNTER\_LAMBDA}, \hyperpage{276} - \subitem {RULE\_FUNCTION}, \hyperpage{277} - \subitem {RULE\_LAMBDA}, \hyperpage{277} - \item {barry::counters}, \hyperpage{55} - \item {barry::counters::network}, \hyperpage{56} + \subitem {BARRY\_HPP}, \hyperpage{278} + \subitem {BARRY\_VERSION}, \hyperpage{278} + \subitem {BARRY\_VERSION\_MAYOR}, \hyperpage{278} + \subitem {BARRY\_VERSION\_MINOR}, \hyperpage{278} + \subitem {COUNTER\_FUNCTION}, \hyperpage{278} + \subitem {COUNTER\_LAMBDA}, \hyperpage{278} + \subitem {RULE\_FUNCTION}, \hyperpage{279} + \subitem {RULE\_LAMBDA}, \hyperpage{279} + \item {barry::counters}, \hyperpage{57} + \item {barry::counters::network}, \hyperpage{58} \item {BARRY\_CHECK\_SUPPORT} - \subitem {barry-\/configuration.hpp}, \hyperpage{271} + \subitem {barry-\/configuration.hpp}, \hyperpage{273} \item {BARRY\_DEBUG\_LEVEL} - \subitem {barry-\/debug.hpp}, \hyperpage{272} + \subitem {barry-\/debug.hpp}, \hyperpage{274} \item {BARRY\_HPP} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {BARRY\_ISFINITE} - \subitem {barry-\/configuration.hpp}, \hyperpage{271} + \subitem {barry-\/configuration.hpp}, \hyperpage{273} \item {BARRY\_MAX\_NUM\_ELEMENTS} - \subitem {barry-\/configuration.hpp}, \hyperpage{271} + \subitem {barry-\/configuration.hpp}, \hyperpage{273} \item {BARRY\_NCORES\_ARG} - \subitem {barry-\/macros.hpp}, \hyperpage{273} + \subitem {barry-\/macros.hpp}, \hyperpage{275} \item {BARRY\_ONE} - \subitem {barry-\/macros.hpp}, \hyperpage{273} + \subitem {barry-\/macros.hpp}, \hyperpage{275} \item {BARRY\_ONE\_DENSE} - \subitem {barry-\/macros.hpp}, \hyperpage{273} + \subitem {barry-\/macros.hpp}, \hyperpage{275} \item {BARRY\_PROGRESS\_BAR\_WIDTH} - \subitem {progress.hpp}, \hyperpage{333} + \subitem {progress.hpp}, \hyperpage{335} \item {BARRY\_SAFE\_EXP} - \subitem {barry-\/configuration.hpp}, \hyperpage{271} + \subitem {barry-\/configuration.hpp}, \hyperpage{273} \item {BARRY\_SUPPORT\_MEAT\_HPP} - \subitem {support-\/meat.hpp}, \hyperpage{341} + \subitem {support-\/meat.hpp}, \hyperpage{343} \item {BARRY\_UNUSED} - \subitem {barry-\/macros.hpp}, \hyperpage{274} + \subitem {barry-\/macros.hpp}, \hyperpage{276} \item {BARRY\_VERSION} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {BARRY\_VERSION\_MAYOR} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {BARRY\_VERSION\_MINOR} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {BARRY\_ZERO} - \subitem {barry-\/macros.hpp}, \hyperpage{274} + \subitem {barry-\/macros.hpp}, \hyperpage{276} \item {BARRY\_ZERO\_DENSE} - \subitem {barry-\/macros.hpp}, \hyperpage{274} + \subitem {barry-\/macros.hpp}, \hyperpage{276} \item {BARRY\_ZERO\_NETWORK} - \subitem {network.hpp}, \hyperpage{302} + \subitem {network.hpp}, \hyperpage{304} \item {BARRY\_ZERO\_NETWORK\_DENSE} - \subitem {network.hpp}, \hyperpage{302} + \subitem {network.hpp}, \hyperpage{304} \item {BDENSE\_TEMPLATE} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{259}, - \hyperpage{261} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{261}, + \hyperpage{263} \item {BDENSE\_TEMPLATE\_ARGS} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{259}, - \hyperpage{261} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{261}, + \hyperpage{263} \item {BDENSE\_TYPE} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260}, - \hyperpage{262} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262}, + \hyperpage{264} \item {begin} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{101} - \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} - \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{105} + \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{107} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{108} + \hyperpage{110} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{115} + \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} - \subitem {PhyloCounterData}, \hyperpage{215} + \hyperpage{121} + \subitem {PhyloCounterData}, \hyperpage{217} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{221} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \hyperpage{223} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \item {blengths} - \subitem {NodeData}, \hyperpage{212} + \subitem {NodeData}, \hyperpage{214} \item {BOTH} - \subitem {CHECK}, \hyperpage{56} - \subitem {EXISTS}, \hyperpage{57} + \subitem {CHECK}, \hyperpage{58} + \subitem {EXISTS}, \hyperpage{59} \item {BROW\_TEMPLATE} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{268, 269} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{270, 271} \item {BROW\_TEMPLATE\_ARGS} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{268} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{270} \item {BROW\_TYPE} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{268} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{270} \indexspace \item {calc} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{221} + \hyperpage{223} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{241} + \hyperpage{243} \item {calc\_reduced\_sequence} - \subitem {Geese}, \hyperpage{164} + \subitem {Geese}, \hyperpage{166} \item {calc\_sequence} - \subitem {Geese}, \hyperpage{165} + \subitem {Geese}, \hyperpage{167} \item {Cell} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{122, 123} - \item {Cell$<$ Cell\_Type $>$}, \hyperpage{121} - \subitem {$\sim$Cell}, \hyperpage{122} - \subitem {active}, \hyperpage{125} - \subitem {add}, \hyperpage{123, 124} - \subitem {Cell}, \hyperpage{122, 123} - \subitem {operator Cell\_Type}, \hyperpage{124} - \subitem {operator!=}, \hyperpage{124} - \subitem {operator=}, \hyperpage{124, 125} - \subitem {operator==}, \hyperpage{125} - \subitem {value}, \hyperpage{125} - \subitem {visited}, \hyperpage{125} - \item {Cell\_const$<$ Cell\_Type $>$}, \hyperpage{126} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124, 125} + \item {Cell$<$ Cell\_Type $>$}, \hyperpage{123} + \subitem {$\sim$Cell}, \hyperpage{124} + \subitem {active}, \hyperpage{127} + \subitem {add}, \hyperpage{125, 126} + \subitem {Cell}, \hyperpage{124, 125} + \subitem {operator Cell\_Type}, \hyperpage{126} + \subitem {operator!=}, \hyperpage{126} + \subitem {operator=}, \hyperpage{126, 127} + \subitem {operator==}, \hyperpage{127} + \subitem {value}, \hyperpage{127} + \subitem {visited}, \hyperpage{127} + \item {Cell\_const$<$ Cell\_Type $>$}, \hyperpage{128} \item {change\_stats} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} - \item {CHECK}, \hyperpage{56} - \subitem {BOTH}, \hyperpage{56} - \subitem {NONE}, \hyperpage{56} - \subitem {ONE}, \hyperpage{56} - \subitem {TWO}, \hyperpage{56} + \hyperpage{247} + \item {CHECK}, \hyperpage{58} + \subitem {BOTH}, \hyperpage{58} + \subitem {NONE}, \hyperpage{58} + \subitem {ONE}, \hyperpage{58} + \subitem {TWO}, \hyperpage{58} \item {clear} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{63} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{83} - \subitem {FreqTable$<$ T $>$}, \hyperpage{158} - \subitem {statscounter-\/meat.hpp}, \hyperpage{336} + \hyperpage{85} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338} \item {COL} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253} - \subitem {barray-\/meat.hpp}, \hyperpage{256} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260} - \subitem {barraydense-\/meat.hpp}, \hyperpage{262} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} + \subitem {barray-\/meat.hpp}, \hyperpage{258} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262} + \subitem {barraydense-\/meat.hpp}, \hyperpage{264} \item {col} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{63} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{84} + \hyperpage{86} \item {Col\_type} - \subitem {typedefs.hpp}, \hyperpage{344} + \subitem {typedefs.hpp}, \hyperpage{346} \item {colnames} - \subitem {Flock}, \hyperpage{152} - \subitem {Geese}, \hyperpage{165} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{167} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{182} + \hyperpage{184} \item {colsum} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{84} + \hyperpage{86} \item {conditional\_prob} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{182} + \hyperpage{184} \item {ConstBArrayRowIter} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{127} + \hyperpage{129} \item {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{126} - \subitem {$\sim$ConstBArrayRowIter}, \hyperpage{127} - \subitem {Array}, \hyperpage{127} - \subitem {ConstBArrayRowIter}, \hyperpage{127} - \subitem {current\_col}, \hyperpage{128} - \subitem {current\_row}, \hyperpage{128} - \subitem {iter}, \hyperpage{128} + \hyperpage{128} + \subitem {$\sim$ConstBArrayRowIter}, \hyperpage{129} + \subitem {Array}, \hyperpage{129} + \subitem {ConstBArrayRowIter}, \hyperpage{129} + \subitem {current\_col}, \hyperpage{130} + \subitem {current\_row}, \hyperpage{130} + \subitem {iter}, \hyperpage{130} \item {coordiantes\_n\_free} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{247} \item {coordiantes\_n\_locked} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{248} \item {coordinates\_free} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{225} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{248} \item {coordinates\_locked} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{225} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{248} \item {count} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{131} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} \item {count\_all} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{235} + \hyperpage{237} \item {count\_current} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \item {count\_fun} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} - \subitem {counters-\/meat.hpp}, \hyperpage{282} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} + \subitem {counters-\/meat.hpp}, \hyperpage{284} \item {count\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {count\_init} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \item {Counter} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{130} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} \item {counter} - \subitem {counters-\/meat.hpp}, \hyperpage{288} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338} - \item {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{128} - \subitem {$\sim$Counter}, \hyperpage{130} - \subitem {count}, \hyperpage{131} - \subitem {count\_fun}, \hyperpage{132} - \subitem {Counter}, \hyperpage{130} - \subitem {data}, \hyperpage{132} - \subitem {desc}, \hyperpage{133} - \subitem {get\_description}, \hyperpage{131} - \subitem {get\_hasher}, \hyperpage{131} - \subitem {get\_name}, \hyperpage{131} - \subitem {hasher\_fun}, \hyperpage{133} - \subitem {init}, \hyperpage{131} - \subitem {init\_fun}, \hyperpage{133} - \subitem {name}, \hyperpage{133} - \subitem {operator=}, \hyperpage{131, 132} - \subitem {set\_hasher}, \hyperpage{132} + \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {statscounter-\/meat.hpp}, \hyperpage{340} + \item {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{130} + \subitem {$\sim$Counter}, \hyperpage{132} + \subitem {count}, \hyperpage{133} + \subitem {count\_fun}, \hyperpage{134} + \subitem {Counter}, \hyperpage{132} + \subitem {data}, \hyperpage{134} + \subitem {desc}, \hyperpage{135} + \subitem {get\_description}, \hyperpage{133} + \subitem {get\_hasher}, \hyperpage{133} + \subitem {get\_name}, \hyperpage{133} + \subitem {hasher\_fun}, \hyperpage{135} + \subitem {init}, \hyperpage{133} + \subitem {init\_fun}, \hyperpage{135} + \subitem {name}, \hyperpage{135} + \subitem {operator=}, \hyperpage{133, 134} + \subitem {set\_hasher}, \hyperpage{134} \item {counter\_} - \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {counter\_absdiff} \subitem {Network counters}, \hyperpage{26} \item {counter\_co\_opt} \subitem {Counting}, \hyperpage{18} - \subitem {Phylo counters}, \hyperpage{48} + \subitem {Phylo counters}, \hyperpage{49} \item {counter\_cogain} \subitem {Counting}, \hyperpage{18} \subitem {Phylo counters}, \hyperpage{49} \item {counter\_css\_census01} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_census02} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_census03} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_census04} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_census05} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_census06} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_census07} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_census08} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{299} \item {counter\_css\_census09} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{299} \item {counter\_css\_census10} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{299} \item {counter\_css\_completely\_false\_recip\_comiss} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{299} \item {counter\_css\_completely\_false\_recip\_omiss} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{300} \item {counter\_css\_mixed\_recip} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{300} \item {counter\_css\_partially\_false\_recip\_commi} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{300} \item {counter\_css\_partially\_false\_recip\_omiss} - \subitem {network-\/css.hpp}, \hyperpage{299} + \subitem {network-\/css.hpp}, \hyperpage{301} \item {counter\_ctriads} \subitem {Network counters}, \hyperpage{27} \item {counter\_degree} \subitem {Network counters}, \hyperpage{27} \item {counter\_deleted} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} + \subitem {statscounter-\/meat.hpp}, \hyperpage{341} \item {counter\_density} \subitem {Network counters}, \hyperpage{27} \item {counter\_diff} @@ -769,11 +769,11 @@ \subitem {Network counters}, \hyperpage{28} \item {counter\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{197} \item {Counter\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{344} + \subitem {typedefs.hpp}, \hyperpage{346} \item {COUNTER\_FUNCTION} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {counter\_gains} \subitem {Counting}, \hyperpage{18} \subitem {Phylo counters}, \hyperpage{49} @@ -782,7 +782,7 @@ \subitem {Phylo counters}, \hyperpage{49} \item {counter\_gains\_k\_offspring} \subitem {Counting}, \hyperpage{19} - \subitem {Phylo counters}, \hyperpage{49} + \subitem {Phylo counters}, \hyperpage{50} \item {counter\_genes\_changing} \subitem {Counting}, \hyperpage{19} \subitem {Phylo counters}, \hyperpage{50} @@ -798,7 +798,7 @@ \subitem {Counting}, \hyperpage{19} \subitem {Phylo counters}, \hyperpage{50} \item {COUNTER\_LAMBDA} - \subitem {barry.hpp}, \hyperpage{276} + \subitem {barry.hpp}, \hyperpage{278} \item {counter\_less\_than\_p\_prop\_genes\_changing} \subitem {Counting}, \hyperpage{19} \subitem {Phylo counters}, \hyperpage{50} @@ -806,7 +806,7 @@ \subitem {Network counters}, \hyperpage{30} \item {counter\_longest} \subitem {Counting}, \hyperpage{20} - \subitem {Phylo counters}, \hyperpage{50} + \subitem {Phylo counters}, \hyperpage{51} \item {counter\_loss} \subitem {Counting}, \hyperpage{20} \subitem {Phylo counters}, \hyperpage{51} @@ -814,13 +814,13 @@ \subitem {Counting}, \hyperpage{20} \subitem {Phylo counters}, \hyperpage{51} \item {counter\_mutual} - \subitem {Network counters}, \hyperpage{30} + \subitem {Network counters}, \hyperpage{31} \item {counter\_neofun} \subitem {Counting}, \hyperpage{20} \subitem {Phylo counters}, \hyperpage{51} \item {counter\_neofun\_a2b} \subitem {Counting}, \hyperpage{21} - \subitem {Phylo counters}, \hyperpage{51} + \subitem {Phylo counters}, \hyperpage{52} \item {counter\_nodecov} \subitem {Network counters}, \hyperpage{31} \item {counter\_nodeicov} @@ -828,13 +828,13 @@ \item {counter\_nodematch} \subitem {Network counters}, \hyperpage{31} \item {counter\_nodeocov} - \subitem {Network counters}, \hyperpage{31} + \subitem {Network counters}, \hyperpage{32} \item {counter\_odegree} - \subitem {Network counters}, \hyperpage{31, 32} + \subitem {Network counters}, \hyperpage{32} \item {counter\_odegree15} \subitem {Network counters}, \hyperpage{32} \item {counter\_ones} - \subitem {Network counters}, \hyperpage{32} + \subitem {Network counters}, \hyperpage{33} \item {counter\_ostar2} \subitem {Network counters}, \hyperpage{33} \item {counter\_overall\_changes} @@ -848,7 +848,7 @@ \subitem {Phylo counters}, \hyperpage{52} \item {counter\_overall\_loss} \subitem {Counting}, \hyperpage{22} - \subitem {Phylo counters}, \hyperpage{52} + \subitem {Phylo counters}, \hyperpage{53} \item {counter\_pairwise\_first\_gain} \subitem {Counting}, \hyperpage{22} \subitem {Phylo counters}, \hyperpage{53} @@ -860,7 +860,7 @@ \subitem {Phylo counters}, \hyperpage{53} \item {counter\_pairwise\_preserving} \subitem {Counting}, \hyperpage{23} - \subitem {Phylo counters}, \hyperpage{53} + \subitem {Phylo counters}, \hyperpage{54} \item {counter\_preserve\_pseudogene} \subitem {Counting}, \hyperpage{23} \subitem {Phylo counters}, \hyperpage{54} @@ -871,86 +871,86 @@ \subitem {Counting}, \hyperpage{23} \subitem {Phylo counters}, \hyperpage{54} \item {COUNTER\_TEMPLATE} - \subitem {counters-\/meat.hpp}, \hyperpage{280}, - \hyperpage{282, 283} + \subitem {counters-\/meat.hpp}, \hyperpage{282}, + \hyperpage{284, 285} \item {COUNTER\_TEMPLATE\_ARGS} - \subitem {counters-\/meat.hpp}, \hyperpage{280} + \subitem {counters-\/meat.hpp}, \hyperpage{282} \item {counter\_transition} \subitem {Network counters}, \hyperpage{33} \item {counter\_transition\_formula} \subitem {Network counters}, \hyperpage{34} \item {counter\_ttriads} - \subitem {Network counters}, \hyperpage{34} + \subitem {Network counters}, \hyperpage{34, 35} \item {COUNTER\_TYPE} - \subitem {counters-\/meat.hpp}, \hyperpage{281} + \subitem {counters-\/meat.hpp}, \hyperpage{283} \item {Counters} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{134, 135} + \hyperpage{136, 137} \item {counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} - \item {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} - \subitem {$\sim$Counters}, \hyperpage{135} - \subitem {add\_counter}, \hyperpage{135, 136} - \subitem {add\_hash}, \hyperpage{136} - \subitem {Counters}, \hyperpage{134, 135} - \subitem {gen\_hash}, \hyperpage{136} - \subitem {get\_descriptions}, \hyperpage{136} - \subitem {get\_names}, \hyperpage{137} - \subitem {operator=}, \hyperpage{137} - \subitem {operator[]}, \hyperpage{138} - \subitem {size}, \hyperpage{138} + \hyperpage{197} + \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \item {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136} + \subitem {$\sim$Counters}, \hyperpage{137} + \subitem {add\_counter}, \hyperpage{137, 138} + \subitem {add\_hash}, \hyperpage{138} + \subitem {Counters}, \hyperpage{136, 137} + \subitem {gen\_hash}, \hyperpage{138} + \subitem {get\_descriptions}, \hyperpage{138} + \subitem {get\_names}, \hyperpage{139} + \subitem {operator=}, \hyperpage{139} + \subitem {operator[]}, \hyperpage{140} + \subitem {size}, \hyperpage{140} \item {counters-\/meat.hpp} - \subitem {add\_dims}, \hyperpage{287} - \subitem {count\_fun}, \hyperpage{282} - \subitem {count\_fun\_}, \hyperpage{287} - \subitem {counter}, \hyperpage{288} - \subitem {counter\_}, \hyperpage{288} - \subitem {COUNTER\_TEMPLATE}, \hyperpage{280}, \hyperpage{282, 283} - \subitem {COUNTER\_TEMPLATE\_ARGS}, \hyperpage{280} - \subitem {COUNTER\_TYPE}, \hyperpage{281} - \subitem {COUNTERS\_TEMPLATE}, \hyperpage{281}, - \hyperpage{283--285} - \subitem {COUNTERS\_TEMPLATE\_ARGS}, \hyperpage{281} - \subitem {COUNTERS\_TYPE}, \hyperpage{281} - \subitem {data}, \hyperpage{285} - \subitem {data\_}, \hyperpage{288} - \subitem {desc}, \hyperpage{285} - \subitem {desc\_}, \hyperpage{288} - \subitem {for}, \hyperpage{285} - \subitem {fun}, \hyperpage{289} - \subitem {fun\_}, \hyperpage{289} - \subitem {hasher}, \hyperpage{285, 286} - \subitem {hasher\_fun}, \hyperpage{286} - \subitem {hasher\_fun\_}, \hyperpage{289} - \subitem {i}, \hyperpage{289} - \subitem {if}, \hyperpage{286} - \subitem {init\_fun}, \hyperpage{287} - \subitem {init\_fun\_}, \hyperpage{290} - \subitem {j}, \hyperpage{290} - \subitem {name}, \hyperpage{287} - \subitem {name\_}, \hyperpage{290} - \subitem {noexcept}, \hyperpage{290} - \subitem {res}, \hyperpage{290} - \subitem {return}, \hyperpage{291} - \subitem {TMP\_HASHER\_CALL}, \hyperpage{281} + \subitem {add\_dims}, \hyperpage{289} + \subitem {count\_fun}, \hyperpage{284} + \subitem {count\_fun\_}, \hyperpage{289} + \subitem {counter}, \hyperpage{290} + \subitem {counter\_}, \hyperpage{290} + \subitem {COUNTER\_TEMPLATE}, \hyperpage{282}, \hyperpage{284, 285} + \subitem {COUNTER\_TEMPLATE\_ARGS}, \hyperpage{282} + \subitem {COUNTER\_TYPE}, \hyperpage{283} + \subitem {COUNTERS\_TEMPLATE}, \hyperpage{283}, + \hyperpage{285--287} + \subitem {COUNTERS\_TEMPLATE\_ARGS}, \hyperpage{283} + \subitem {COUNTERS\_TYPE}, \hyperpage{283} + \subitem {data}, \hyperpage{287} + \subitem {data\_}, \hyperpage{290} + \subitem {desc}, \hyperpage{287} + \subitem {desc\_}, \hyperpage{290} + \subitem {for}, \hyperpage{287} + \subitem {fun}, \hyperpage{291} + \subitem {fun\_}, \hyperpage{291} + \subitem {hasher}, \hyperpage{287, 288} + \subitem {hasher\_fun}, \hyperpage{288} + \subitem {hasher\_fun\_}, \hyperpage{291} + \subitem {i}, \hyperpage{291} + \subitem {if}, \hyperpage{288} + \subitem {init\_fun}, \hyperpage{289} + \subitem {init\_fun\_}, \hyperpage{292} + \subitem {j}, \hyperpage{292} + \subitem {name}, \hyperpage{289} + \subitem {name\_}, \hyperpage{292} + \subitem {noexcept}, \hyperpage{292} + \subitem {res}, \hyperpage{292} + \subitem {return}, \hyperpage{293} + \subitem {TMP\_HASHER\_CALL}, \hyperpage{283} \item {counters.hpp} - \subitem {DEFM\_COUNTER}, \hyperpage{310} - \subitem {DEFM\_COUNTER\_LAMBDA}, \hyperpage{311} - \subitem {DEFM\_RULE}, \hyperpage{311} - \subitem {DEFM\_RULE\_LAMBDA}, \hyperpage{311} - \subitem {DEFM\_RULEDYN\_LAMBDA}, \hyperpage{311} - \subitem {UNI\_SUB}, \hyperpage{312} + \subitem {DEFM\_COUNTER}, \hyperpage{312} + \subitem {DEFM\_COUNTER\_LAMBDA}, \hyperpage{313} + \subitem {DEFM\_RULE}, \hyperpage{313} + \subitem {DEFM\_RULE\_LAMBDA}, \hyperpage{313} + \subitem {DEFM\_RULEDYN\_LAMBDA}, \hyperpage{313} + \subitem {UNI\_SUB}, \hyperpage{314} \item {counters\_} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} + \subitem {statscounter-\/meat.hpp}, \hyperpage{341} \item {COUNTERS\_TEMPLATE} - \subitem {counters-\/meat.hpp}, \hyperpage{281}, - \hyperpage{283--285} + \subitem {counters-\/meat.hpp}, \hyperpage{283}, + \hyperpage{285--287} \item {COUNTERS\_TEMPLATE\_ARGS} - \subitem {counters-\/meat.hpp}, \hyperpage{281} + \subitem {counters-\/meat.hpp}, \hyperpage{283} \item {COUNTERS\_TYPE} - \subitem {counters-\/meat.hpp}, \hyperpage{281} + \subitem {counters-\/meat.hpp}, \hyperpage{283} \item {Counting}, \hyperpage{13} \subitem {counter\_co\_opt}, \hyperpage{18} \subitem {counter\_cogain}, \hyperpage{18} @@ -991,919 +991,919 @@ \subitem {PHYLO\_RULE\_LAMBDA}, \hyperpage{17} \item {counts} \subitem {Phylo rules}, \hyperpage{44} - \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {PhyloRuleDynData}, \hyperpage{220} \item {Counts\_type} - \subitem {typedefs.hpp}, \hyperpage{344} + \subitem {typedefs.hpp}, \hyperpage{346} \item {covar\_sort} \subitem {Phylo rules}, \hyperpage{44} \item {covar\_used} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Phylo rules}, \hyperpage{45} \item {covariates} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Phylo rules}, \hyperpage{45} \item {CSS\_APPEND} - \subitem {network-\/css.hpp}, \hyperpage{292} + \subitem {network-\/css.hpp}, \hyperpage{294} \item {CSS\_CASE\_ELSE} - \subitem {network-\/css.hpp}, \hyperpage{293} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {CSS\_CASE\_PERCEIVED} - \subitem {network-\/css.hpp}, \hyperpage{293} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {CSS\_CASE\_TRUTH} - \subitem {network-\/css.hpp}, \hyperpage{293} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {CSS\_CHECK\_SIZE} - \subitem {network-\/css.hpp}, \hyperpage{293} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {CSS\_CHECK\_SIZE\_INIT} - \subitem {network-\/css.hpp}, \hyperpage{293} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {CSS\_MATCH\_TYPE} - \subitem {network-\/css.hpp}, \hyperpage{294} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {CSS\_NET\_COUNTER\_LAMBDA\_INIT} - \subitem {network-\/css.hpp}, \hyperpage{294} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {CSS\_PERCEIVED\_CELLS} - \subitem {network-\/css.hpp}, \hyperpage{294} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {CSS\_SIZE} - \subitem {network-\/css.hpp}, \hyperpage{294} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {CSS\_TRUE\_CELLS} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {current\_col} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{128} + \hyperpage{130} \item {current\_row} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{128} + \hyperpage{130} \item {current\_stats} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} + \subitem {statscounter-\/meat.hpp}, \hyperpage{341} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{248} \indexspace \item {D} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{84} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} + \hyperpage{86} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} \item {D\_ptr} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{85} + \hyperpage{87} \item {dat} - \subitem {Flock}, \hyperpage{156} + \subitem {Flock}, \hyperpage{158} \item {data} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} - \subitem {counters-\/meat.hpp}, \hyperpage{285} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{225} \item {data\_} - \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {default\_val} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{85} - \item {DEFM}, \hyperpage{139} - \subitem {DEFM}, \hyperpage{140} - \subitem {get\_column\_major}, \hyperpage{140} - \subitem {get\_ID}, \hyperpage{140} - \subitem {get\_m\_order}, \hyperpage{140} - \subitem {get\_model}, \hyperpage{141} - \subitem {get\_n\_covars}, \hyperpage{141} - \subitem {get\_n\_obs}, \hyperpage{141} - \subitem {get\_n\_rows}, \hyperpage{141} - \subitem {get\_n\_y}, \hyperpage{141} - \subitem {get\_X}, \hyperpage{141} - \subitem {get\_X\_names}, \hyperpage{142} - \subitem {get\_Y}, \hyperpage{142} - \subitem {get\_Y\_names}, \hyperpage{142} - \subitem {init}, \hyperpage{142} - \subitem {is\_motif}, \hyperpage{142} - \subitem {logodds}, \hyperpage{142} - \subitem {motif\_census}, \hyperpage{143} - \subitem {print}, \hyperpage{143} - \subitem {set\_names}, \hyperpage{143} - \subitem {simulate}, \hyperpage{143} - \item {defm}, \hyperpage{57} + \hyperpage{87} + \item {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{142} + \subitem {get\_column\_major}, \hyperpage{142} + \subitem {get\_ID}, \hyperpage{142} + \subitem {get\_m\_order}, \hyperpage{142} + \subitem {get\_model}, \hyperpage{143} + \subitem {get\_n\_covars}, \hyperpage{143} + \subitem {get\_n\_obs}, \hyperpage{143} + \subitem {get\_n\_rows}, \hyperpage{143} + \subitem {get\_n\_y}, \hyperpage{143} + \subitem {get\_X}, \hyperpage{143} + \subitem {get\_X\_names}, \hyperpage{144} + \subitem {get\_Y}, \hyperpage{144} + \subitem {get\_Y\_names}, \hyperpage{144} + \subitem {init}, \hyperpage{144} + \subitem {is\_motif}, \hyperpage{144} + \subitem {logodds}, \hyperpage{144} + \subitem {motif\_census}, \hyperpage{145} + \subitem {print}, \hyperpage{145} + \subitem {set\_names}, \hyperpage{145} + \subitem {simulate}, \hyperpage{145} + \item {defm}, \hyperpage{59} \item {defm-\/meat.hpp} - \subitem {DEFM\_LOOP\_ARRAYS}, \hyperpage{315} - \subitem {DEFM\_RANGES}, \hyperpage{315} - \subitem {keygen\_defm}, \hyperpage{316} + \subitem {DEFM\_LOOP\_ARRAYS}, \hyperpage{317} + \subitem {DEFM\_RANGES}, \hyperpage{317} + \subitem {keygen\_defm}, \hyperpage{318} \item {defm-\/types.hpp} - \subitem {DEFMArray}, \hyperpage{317} + \subitem {DEFMArray}, \hyperpage{319} \item {DEFM\_COUNTER} - \subitem {counters.hpp}, \hyperpage{310} + \subitem {counters.hpp}, \hyperpage{312} \item {DEFM\_COUNTER\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{311} + \subitem {counters.hpp}, \hyperpage{313} \item {DEFM\_LOOP\_ARRAYS} - \subitem {defm-\/meat.hpp}, \hyperpage{315} + \subitem {defm-\/meat.hpp}, \hyperpage{317} \item {defm\_motif\_parser} - \subitem {formula.hpp}, \hyperpage{317} + \subitem {formula.hpp}, \hyperpage{319} \item {DEFM\_RANGES} - \subitem {defm-\/meat.hpp}, \hyperpage{315} + \subitem {defm-\/meat.hpp}, \hyperpage{317} \item {DEFM\_RULE} - \subitem {counters.hpp}, \hyperpage{311} + \subitem {counters.hpp}, \hyperpage{313} \item {DEFM\_RULE\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{311} + \subitem {counters.hpp}, \hyperpage{313} \item {DEFM\_RULEDYN\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{311} + \subitem {counters.hpp}, \hyperpage{313} \item {DEFMArray} - \subitem {defm-\/types.hpp}, \hyperpage{317} + \subitem {defm-\/types.hpp}, \hyperpage{319} \item {DEFMCounter} - \subitem {Phylo rules}, \hyperpage{37} - \item {DEFMCounterData}, \hyperpage{144} + \subitem {Phylo rules}, \hyperpage{38} + \item {DEFMCounterData}, \hyperpage{146} \subitem {Phylo rules}, \hyperpage{39} \item {DEFMCounters} - \subitem {Phylo rules}, \hyperpage{37} - \item {DEFMData}, \hyperpage{144} - \subitem {Phylo rules}, \hyperpage{39} + \subitem {Phylo rules}, \hyperpage{38} + \item {DEFMData}, \hyperpage{146} + \subitem {Phylo rules}, \hyperpage{40} \item {DEFMModel} - \subitem {Phylo rules}, \hyperpage{37} + \subitem {Phylo rules}, \hyperpage{38} \item {DEFMRule} \subitem {Phylo rules}, \hyperpage{38} - \item {DEFMRuleData}, \hyperpage{146} - \subitem {Phylo rules}, \hyperpage{40} + \item {DEFMRuleData}, \hyperpage{148} + \subitem {Phylo rules}, \hyperpage{40, 41} \item {DEFMRuleDyn} \subitem {Phylo rules}, \hyperpage{38} - \item {DEFMRuleDynData}, \hyperpage{147} - \subitem {Phylo rules}, \hyperpage{40} + \item {DEFMRuleDynData}, \hyperpage{149} + \subitem {Phylo rules}, \hyperpage{41} \item {DEFMRules} \subitem {Phylo rules}, \hyperpage{38} \item {DEFMRulesDyn} - \subitem {Phylo rules}, \hyperpage{38} + \subitem {Phylo rules}, \hyperpage{39} \item {DEFMStatsCounter} - \subitem {Phylo rules}, \hyperpage{38} + \subitem {Phylo rules}, \hyperpage{39} \item {DEFMSupport} - \subitem {Phylo rules}, \hyperpage{38} + \subitem {Phylo rules}, \hyperpage{39} \item {delete\_counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{197} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{248} \item {delete\_rengine} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{174} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{197} \item {delete\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{198} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{249} \item {delete\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{198} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{249} \item {delete\_support} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{174} \item {desc} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {counters-\/meat.hpp}, \hyperpage{285} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \item {desc\_} - \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {directed} - \subitem {NetworkData}, \hyperpage{205} + \subitem {NetworkData}, \hyperpage{207} \item {duplication} - \subitem {Node}, \hyperpage{210} - \subitem {NodeData}, \hyperpage{213} - \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {Node}, \hyperpage{212} + \subitem {NodeData}, \hyperpage{215} + \subitem {PhyloRuleDynData}, \hyperpage{220} \indexspace \item {empty} - \subitem {PhyloCounterData}, \hyperpage{215} + \subitem {PhyloCounterData}, \hyperpage{217} \item {EmptyArray} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} + \hyperpage{226} + \subitem {statscounter-\/meat.hpp}, \hyperpage{341} \item {end} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{101} - \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} - \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{105} + \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{107} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{108} + \hyperpage{110} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{115} + \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} - \subitem {PhyloCounterData}, \hyperpage{215} + \hyperpage{121} + \subitem {PhyloCounterData}, \hyperpage{217} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} - \subitem {Progress}, \hyperpage{226} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \hyperpage{224} + \subitem {Progress}, \hyperpage{228} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \item {Entries} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{148} - \item {Entries$<$ Cell\_Type $>$}, \hyperpage{148} - \subitem {$\sim$Entries}, \hyperpage{149} - \subitem {Entries}, \hyperpage{148} - \subitem {resize}, \hyperpage{149} - \subitem {source}, \hyperpage{149} - \subitem {target}, \hyperpage{149} - \subitem {val}, \hyperpage{149} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} + \item {Entries$<$ Cell\_Type $>$}, \hyperpage{150} + \subitem {$\sim$Entries}, \hyperpage{151} + \subitem {Entries}, \hyperpage{150} + \subitem {resize}, \hyperpage{151} + \subitem {source}, \hyperpage{151} + \subitem {target}, \hyperpage{151} + \subitem {val}, \hyperpage{151} \item {etype\_default} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{174} \item {etype\_duplication} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{174} \item {etype\_either} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{174} \item {etype\_speciation} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{175} \item {eval\_rules\_dyn} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} - \item {EXISTS}, \hyperpage{57} - \subitem {AS\_ONE}, \hyperpage{57} - \subitem {AS\_ZERO}, \hyperpage{57} - \subitem {BOTH}, \hyperpage{57} - \subitem {NONE}, \hyperpage{58} - \subitem {ONE}, \hyperpage{58} - \subitem {TWO}, \hyperpage{58} - \subitem {UKNOWN}, \hyperpage{58} + \hyperpage{244} + \item {EXISTS}, \hyperpage{59} + \subitem {AS\_ONE}, \hyperpage{59} + \subitem {AS\_ZERO}, \hyperpage{59} + \subitem {BOTH}, \hyperpage{59} + \subitem {NONE}, \hyperpage{60} + \subitem {ONE}, \hyperpage{60} + \subitem {TWO}, \hyperpage{60} + \subitem {UKNOWN}, \hyperpage{60} \indexspace \item {f\_} - \subitem {statscounter-\/meat.hpp}, \hyperpage{340} + \subitem {statscounter-\/meat.hpp}, \hyperpage{342} \item {first\_calc\_done} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} - \item {Flock}, \hyperpage{150} - \subitem {$\sim$Flock}, \hyperpage{151} - \subitem {add\_data}, \hyperpage{151} - \subitem {colnames}, \hyperpage{152} - \subitem {dat}, \hyperpage{156} - \subitem {Flock}, \hyperpage{151} - \subitem {get\_counters}, \hyperpage{152} - \subitem {get\_model}, \hyperpage{152} - \subitem {get\_stats\_support}, \hyperpage{152} - \subitem {get\_stats\_target}, \hyperpage{152} - \subitem {get\_support\_fun}, \hyperpage{153} - \subitem {init}, \hyperpage{153} - \subitem {initialized}, \hyperpage{156} - \subitem {likelihood\_joint}, \hyperpage{153} - \subitem {model}, \hyperpage{156} - \subitem {nfunctions}, \hyperpage{156} - \subitem {nfuns}, \hyperpage{153} - \subitem {nleafs}, \hyperpage{154} - \subitem {nnodes}, \hyperpage{154} - \subitem {nterms}, \hyperpage{154} - \subitem {ntrees}, \hyperpage{154} - \subitem {operator()}, \hyperpage{154} - \subitem {parse\_polytomies}, \hyperpage{155} - \subitem {print}, \hyperpage{155} - \subitem {rengine}, \hyperpage{156} - \subitem {set\_seed}, \hyperpage{155} - \subitem {support\_size}, \hyperpage{155} + \hyperpage{198} + \item {Flock}, \hyperpage{152} + \subitem {$\sim$Flock}, \hyperpage{153} + \subitem {add\_data}, \hyperpage{153} + \subitem {colnames}, \hyperpage{154} + \subitem {dat}, \hyperpage{158} + \subitem {Flock}, \hyperpage{153} + \subitem {get\_counters}, \hyperpage{154} + \subitem {get\_model}, \hyperpage{154} + \subitem {get\_stats\_support}, \hyperpage{154} + \subitem {get\_stats\_target}, \hyperpage{154} + \subitem {get\_support\_fun}, \hyperpage{155} + \subitem {init}, \hyperpage{155} + \subitem {initialized}, \hyperpage{158} + \subitem {likelihood\_joint}, \hyperpage{155} + \subitem {model}, \hyperpage{158} + \subitem {nfunctions}, \hyperpage{158} + \subitem {nfuns}, \hyperpage{155} + \subitem {nleafs}, \hyperpage{156} + \subitem {nnodes}, \hyperpage{156} + \subitem {nterms}, \hyperpage{156} + \subitem {ntrees}, \hyperpage{156} + \subitem {operator()}, \hyperpage{156} + \subitem {parse\_polytomies}, \hyperpage{157} + \subitem {print}, \hyperpage{157} + \subitem {rengine}, \hyperpage{158} + \subitem {set\_seed}, \hyperpage{157} + \subitem {support\_size}, \hyperpage{157} \item {flush\_data} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \item {for} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} - \subitem {counters-\/meat.hpp}, \hyperpage{285} - \subitem {statscounter-\/meat.hpp}, \hyperpage{336} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} + \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338} \item {formula.hpp} - \subitem {defm\_motif\_parser}, \hyperpage{317} + \subitem {defm\_motif\_parser}, \hyperpage{319} \item {FreqTable} - \subitem {FreqTable$<$ T $>$}, \hyperpage{158} - \item {FreqTable$<$ T $>$}, \hyperpage{157} - \subitem {$\sim$FreqTable}, \hyperpage{158} - \subitem {add}, \hyperpage{158} - \subitem {as\_vector}, \hyperpage{158} - \subitem {clear}, \hyperpage{158} - \subitem {FreqTable}, \hyperpage{158} - \subitem {get\_data}, \hyperpage{159} - \subitem {get\_index}, \hyperpage{159} - \subitem {make\_hash}, \hyperpage{159} - \subitem {print}, \hyperpage{159} - \subitem {reserve}, \hyperpage{159} - \subitem {size}, \hyperpage{160} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \item {FreqTable$<$ T $>$}, \hyperpage{159} + \subitem {$\sim$FreqTable}, \hyperpage{160} + \subitem {add}, \hyperpage{160} + \subitem {as\_vector}, \hyperpage{160} + \subitem {clear}, \hyperpage{160} + \subitem {FreqTable}, \hyperpage{160} + \subitem {get\_data}, \hyperpage{161} + \subitem {get\_index}, \hyperpage{161} + \subitem {make\_hash}, \hyperpage{161} + \subitem {print}, \hyperpage{161} + \subitem {reserve}, \hyperpage{161} + \subitem {size}, \hyperpage{162} \item {fun} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{291} \item {fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{291} \indexspace - \item {Geese}, \hyperpage{160} - \subitem {$\sim$Geese}, \hyperpage{164} - \subitem {calc\_reduced\_sequence}, \hyperpage{164} - \subitem {calc\_sequence}, \hyperpage{165} - \subitem {colnames}, \hyperpage{165} - \subitem {delete\_rengine}, \hyperpage{172} - \subitem {delete\_support}, \hyperpage{172} - \subitem {etype\_default}, \hyperpage{172} - \subitem {etype\_duplication}, \hyperpage{172} - \subitem {etype\_either}, \hyperpage{172} - \subitem {etype\_speciation}, \hyperpage{173} - \subitem {Geese}, \hyperpage{163, 164} - \subitem {get\_annotated\_nodes}, \hyperpage{165} - \subitem {get\_annotations}, \hyperpage{165} - \subitem {get\_counters}, \hyperpage{165} - \subitem {get\_model}, \hyperpage{166} - \subitem {get\_probabilities}, \hyperpage{166} - \subitem {get\_rengine}, \hyperpage{166} - \subitem {get\_states}, \hyperpage{166} - \subitem {get\_support\_fun}, \hyperpage{166} - \subitem {inherit\_support}, \hyperpage{167} - \subitem {init}, \hyperpage{167} - \subitem {init\_node}, \hyperpage{167} - \subitem {initialized}, \hyperpage{173} - \subitem {likelihood}, \hyperpage{167} - \subitem {likelihood\_exhaust}, \hyperpage{167} - \subitem {map\_to\_state\_id}, \hyperpage{173} - \subitem {nannotations}, \hyperpage{168} - \subitem {nfunctions}, \hyperpage{173} - \subitem {nfuns}, \hyperpage{168} - \subitem {nleafs}, \hyperpage{168} - \subitem {nnodes}, \hyperpage{168} - \subitem {nodes}, \hyperpage{173} - \subitem {nterms}, \hyperpage{168} - \subitem {observed\_counts}, \hyperpage{169} - \subitem {operator=}, \hyperpage{169} - \subitem {parse\_polytomies}, \hyperpage{169} - \subitem {predict}, \hyperpage{169} - \subitem {predict\_backend}, \hyperpage{170} - \subitem {predict\_exhaust}, \hyperpage{170} - \subitem {predict\_exhaust\_backend}, \hyperpage{170} - \subitem {predict\_sim}, \hyperpage{170} - \subitem {print}, \hyperpage{170} - \subitem {print\_nodes}, \hyperpage{171} - \subitem {print\_observed\_counts}, \hyperpage{171} - \subitem {pset\_loc}, \hyperpage{173} - \subitem {reduced\_sequence}, \hyperpage{174} - \subitem {sequence}, \hyperpage{174} - \subitem {set\_seed}, \hyperpage{171} - \subitem {simulate}, \hyperpage{171} - \subitem {support\_size}, \hyperpage{171} - \subitem {update\_annotations}, \hyperpage{171} - \item {geese}, \hyperpage{58} + \item {Geese}, \hyperpage{162} + \subitem {$\sim$Geese}, \hyperpage{166} + \subitem {calc\_reduced\_sequence}, \hyperpage{166} + \subitem {calc\_sequence}, \hyperpage{167} + \subitem {colnames}, \hyperpage{167} + \subitem {delete\_rengine}, \hyperpage{174} + \subitem {delete\_support}, \hyperpage{174} + \subitem {etype\_default}, \hyperpage{174} + \subitem {etype\_duplication}, \hyperpage{174} + \subitem {etype\_either}, \hyperpage{174} + \subitem {etype\_speciation}, \hyperpage{175} + \subitem {Geese}, \hyperpage{165, 166} + \subitem {get\_annotated\_nodes}, \hyperpage{167} + \subitem {get\_annotations}, \hyperpage{167} + \subitem {get\_counters}, \hyperpage{167} + \subitem {get\_model}, \hyperpage{168} + \subitem {get\_probabilities}, \hyperpage{168} + \subitem {get\_rengine}, \hyperpage{168} + \subitem {get\_states}, \hyperpage{168} + \subitem {get\_support\_fun}, \hyperpage{168} + \subitem {inherit\_support}, \hyperpage{169} + \subitem {init}, \hyperpage{169} + \subitem {init\_node}, \hyperpage{169} + \subitem {initialized}, \hyperpage{175} + \subitem {likelihood}, \hyperpage{169} + \subitem {likelihood\_exhaust}, \hyperpage{169} + \subitem {map\_to\_state\_id}, \hyperpage{175} + \subitem {nannotations}, \hyperpage{170} + \subitem {nfunctions}, \hyperpage{175} + \subitem {nfuns}, \hyperpage{170} + \subitem {nleafs}, \hyperpage{170} + \subitem {nnodes}, \hyperpage{170} + \subitem {nodes}, \hyperpage{175} + \subitem {nterms}, \hyperpage{170} + \subitem {observed\_counts}, \hyperpage{171} + \subitem {operator=}, \hyperpage{171} + \subitem {parse\_polytomies}, \hyperpage{171} + \subitem {predict}, \hyperpage{171} + \subitem {predict\_backend}, \hyperpage{172} + \subitem {predict\_exhaust}, \hyperpage{172} + \subitem {predict\_exhaust\_backend}, \hyperpage{172} + \subitem {predict\_sim}, \hyperpage{172} + \subitem {print}, \hyperpage{172} + \subitem {print\_nodes}, \hyperpage{173} + \subitem {print\_observed\_counts}, \hyperpage{173} + \subitem {pset\_loc}, \hyperpage{175} + \subitem {reduced\_sequence}, \hyperpage{176} + \subitem {sequence}, \hyperpage{176} + \subitem {set\_seed}, \hyperpage{173} + \subitem {simulate}, \hyperpage{173} + \subitem {support\_size}, \hyperpage{173} + \subitem {update\_annotations}, \hyperpage{173} + \item {geese}, \hyperpage{60} \item {geese-\/bones.hpp} - \subitem {INITIALIZED}, \hyperpage{321} - \subitem {keygen\_full}, \hyperpage{321} - \subitem {RULE\_FUNCTION}, \hyperpage{321} - \subitem {vec\_diff}, \hyperpage{321} - \subitem {vector\_caster}, \hyperpage{322} + \subitem {INITIALIZED}, \hyperpage{323} + \subitem {keygen\_full}, \hyperpage{323} + \subitem {RULE\_FUNCTION}, \hyperpage{323} + \subitem {vec\_diff}, \hyperpage{323} + \subitem {vector\_caster}, \hyperpage{324} \item {geese-\/meat-\/likelihood.hpp} - \subitem {pset\_loop}, \hyperpage{323} + \subitem {pset\_loop}, \hyperpage{325} \item {geese-\/types.hpp} - \subitem {PhyloArray}, \hyperpage{329} - \subitem {PhyloCounter}, \hyperpage{329} - \subitem {PhyloCounters}, \hyperpage{329} - \subitem {PhyloModel}, \hyperpage{329} - \subitem {PhyloPowerSet}, \hyperpage{329} - \subitem {PhyloRule}, \hyperpage{330} - \subitem {PhyloRuleData}, \hyperpage{330} - \subitem {PhyloRuleDyn}, \hyperpage{330} - \subitem {PhyloRules}, \hyperpage{330} - \subitem {PhyloRulesDyn}, \hyperpage{330} - \subitem {PhyloStatsCounter}, \hyperpage{330} - \subitem {PhyloSupport}, \hyperpage{331} - \subitem {POS}, \hyperpage{328} + \subitem {PhyloArray}, \hyperpage{331} + \subitem {PhyloCounter}, \hyperpage{331} + \subitem {PhyloCounters}, \hyperpage{331} + \subitem {PhyloModel}, \hyperpage{331} + \subitem {PhyloPowerSet}, \hyperpage{331} + \subitem {PhyloRule}, \hyperpage{332} + \subitem {PhyloRuleData}, \hyperpage{332} + \subitem {PhyloRuleDyn}, \hyperpage{332} + \subitem {PhyloRules}, \hyperpage{332} + \subitem {PhyloRulesDyn}, \hyperpage{332} + \subitem {PhyloStatsCounter}, \hyperpage{332} + \subitem {PhyloSupport}, \hyperpage{333} + \subitem {POS}, \hyperpage{330} \item {gen\_hash} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} \item {gen\_key} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{183} + \hyperpage{185} \item {get\_annotated\_nodes} - \subitem {Geese}, \hyperpage{165} + \subitem {Geese}, \hyperpage{167} \item {get\_annotations} - \subitem {Geese}, \hyperpage{165} + \subitem {Geese}, \hyperpage{167} \item {get\_arrays2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{183} + \hyperpage{185} \item {get\_cell} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{64} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{85} + \hyperpage{87} \item {get\_col\_vec} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{85, 86} + \hyperpage{87, 88} \item {get\_column\_major} - \subitem {DEFM}, \hyperpage{140} + \subitem {DEFM}, \hyperpage{142} \item {get\_counters} - \subitem {Flock}, \hyperpage{152} - \subitem {Geese}, \hyperpage{165} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{167} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{183} - \subitem {PhyloCounterData}, \hyperpage{215} + \hyperpage{185} + \subitem {PhyloCounterData}, \hyperpage{217} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} + \hyperpage{244} \item {get\_counts} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} + \hyperpage{244} \item {get\_current\_stats} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} + \hyperpage{244} \item {get\_data} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{86} - \subitem {FreqTable$<$ T $>$}, \hyperpage{159} + \hyperpage{88} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} + \hyperpage{224} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{245} \item {get\_data\_ptr} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} + \hyperpage{224} \item {get\_description} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{131} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} \item {get\_descriptions} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \item {get\_entries} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{86} + \hyperpage{88} \item {get\_hasher} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{131} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} \item {get\_ID} - \subitem {DEFM}, \hyperpage{140} + \subitem {DEFM}, \hyperpage{142} \item {get\_index} - \subitem {FreqTable$<$ T $>$}, \hyperpage{159} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} \item {get\_last\_name} \subitem {Counting}, \hyperpage{24} \item {get\_likelihoods} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{186} \item {get\_m\_order} - \subitem {DEFM}, \hyperpage{140} + \subitem {DEFM}, \hyperpage{142} \item {get\_model} - \subitem {DEFM}, \hyperpage{141} - \subitem {Flock}, \hyperpage{152} - \subitem {Geese}, \hyperpage{166} + \subitem {DEFM}, \hyperpage{143} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{168} \item {get\_n\_covars} - \subitem {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{143} \item {get\_n\_obs} - \subitem {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{143} \item {get\_n\_rows} - \subitem {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{143} \item {get\_n\_y} - \subitem {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{143} \item {get\_name} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{131} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} \item {get\_names} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{137} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{139} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \item {get\_normalizing\_constants} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{186} \item {get\_parent} - \subitem {Node}, \hyperpage{208} + \subitem {Node}, \hyperpage{210} \item {get\_probabilities} - \subitem {Geese}, \hyperpage{166} + \subitem {Geese}, \hyperpage{168} \item {get\_pset} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{186} \item {get\_pset\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{186} \item {get\_pset\_locations} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{186} \item {get\_pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{185} + \hyperpage{187} \item {get\_pset\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{185} + \hyperpage{187} \item {get\_pset\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{185} + \hyperpage{187} \item {get\_rengine} - \subitem {Geese}, \hyperpage{166} + \subitem {Geese}, \hyperpage{168} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{188} \item {get\_row\_vec} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{86, 87} + \hyperpage{88, 89} \item {get\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{188} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{245} \item {get\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{188} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{245} \item {get\_seq} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} \item {get\_states} - \subitem {Geese}, \hyperpage{166} + \subitem {Geese}, \hyperpage{168} \item {get\_stats\_support} - \subitem {Flock}, \hyperpage{152} + \subitem {Flock}, \hyperpage{154} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{188} \item {get\_stats\_support\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{188} \item {get\_stats\_support\_sizes\_acc} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{189} \item {get\_stats\_target} - \subitem {Flock}, \hyperpage{152} + \subitem {Flock}, \hyperpage{154} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{189} \item {get\_support\_fun} - \subitem {Flock}, \hyperpage{153} - \subitem {Geese}, \hyperpage{166} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{168} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{189} \item {get\_X} - \subitem {DEFM}, \hyperpage{141} + \subitem {DEFM}, \hyperpage{143} \item {get\_X\_names} - \subitem {DEFM}, \hyperpage{142} + \subitem {DEFM}, \hyperpage{144} \item {get\_Y} - \subitem {DEFM}, \hyperpage{142} + \subitem {DEFM}, \hyperpage{144} \item {get\_Y\_names} - \subitem {DEFM}, \hyperpage{142} + \subitem {DEFM}, \hyperpage{144} \indexspace \item {has\_leaf} - \subitem {NodeData}, \hyperpage{213} + \subitem {NodeData}, \hyperpage{215} \item {hasher} - \subitem {counters-\/meat.hpp}, \hyperpage{285, 286} + \subitem {counters-\/meat.hpp}, \hyperpage{287, 288} \item {hasher\_fun} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {counters-\/meat.hpp}, \hyperpage{286} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} + \subitem {counters-\/meat.hpp}, \hyperpage{288} \item {hasher\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{291} \item {Hasher\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{344} + \subitem {typedefs.hpp}, \hyperpage{346} \item {hashes} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{249} \item {hashes\_initialized} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{249} \indexspace \item {i} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{291} \item {id} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{212} \item {idx} - \subitem {Phylo rules}, \hyperpage{40, 41} + \subitem {Phylo rules}, \hyperpage{41} \item {if} - \subitem {counters-\/meat.hpp}, \hyperpage{286} + \subitem {counters-\/meat.hpp}, \hyperpage{288} \item {IF\_MATCHES} \subitem {Counting}, \hyperpage{15} \item {IF\_NOTMATCHES} \subitem {Counting}, \hyperpage{15} - \item {include/barry/barray-\/bones.hpp}, \hyperpage{251} - \item {include/barry/barray-\/iterator.hpp}, \hyperpage{251} - \item {include/barry/barray-\/meat-\/operators.hpp}, \hyperpage{252} - \item {include/barry/barray-\/meat.hpp}, \hyperpage{256} - \item {include/barry/barraycell-\/bones.hpp}, \hyperpage{257} - \item {include/barry/barraycell-\/meat.hpp}, \hyperpage{258} - \item {include/barry/barraydense-\/bones.hpp}, \hyperpage{258} + \item {include/barry/barray-\/bones.hpp}, \hyperpage{253} + \item {include/barry/barray-\/iterator.hpp}, \hyperpage{253} + \item {include/barry/barray-\/meat-\/operators.hpp}, \hyperpage{254} + \item {include/barry/barray-\/meat.hpp}, \hyperpage{258} + \item {include/barry/barraycell-\/bones.hpp}, \hyperpage{259} + \item {include/barry/barraycell-\/meat.hpp}, \hyperpage{260} + \item {include/barry/barraydense-\/bones.hpp}, \hyperpage{260} \item {include/barry/barraydense-\/meat-\/operators.hpp}, - \hyperpage{259} - \item {include/barry/barraydense-\/meat.hpp}, \hyperpage{262} - \item {include/barry/barraydensecell-\/bones.hpp}, \hyperpage{263} - \item {include/barry/barraydensecell-\/meat.hpp}, \hyperpage{264} - \item {include/barry/barraydensecol-\/bones.hpp}, \hyperpage{265} - \item {include/barry/barraydenserow-\/bones.hpp}, \hyperpage{266} - \item {include/barry/barrayrow-\/bones.hpp}, \hyperpage{267} - \item {include/barry/barrayrow-\/meat.hpp}, \hyperpage{267} - \item {include/barry/barrayvector-\/bones.hpp}, \hyperpage{269} - \item {include/barry/barrayvector-\/meat.hpp}, \hyperpage{270} - \item {include/barry/barry-\/configuration.hpp}, \hyperpage{270} - \item {include/barry/barry-\/debug.hpp}, \hyperpage{272} - \item {include/barry/barry-\/macros.hpp}, \hyperpage{273} - \item {include/barry/barry.hpp}, \hyperpage{274} - \item {include/barry/cell-\/bones.hpp}, \hyperpage{277} - \item {include/barry/cell-\/meat.hpp}, \hyperpage{278} - \item {include/barry/col-\/bones.hpp}, \hyperpage{278} - \item {include/barry/counters-\/bones.hpp}, \hyperpage{278} - \item {include/barry/counters-\/meat.hpp}, \hyperpage{279} - \item {include/barry/counters/network-\/css.hpp}, \hyperpage{291} - \item {include/barry/counters/network.hpp}, \hyperpage{299} - \item {include/barry/freqtable.hpp}, \hyperpage{306} - \item {include/barry/model-\/bones.hpp}, \hyperpage{307} - \item {include/barry/model-\/meat.hpp}, \hyperpage{307} - \item {include/barry/models/defm.hpp}, \hyperpage{308} - \item {include/barry/models/defm/counters.hpp}, \hyperpage{309} - \item {include/barry/models/defm/defm-\/bones.hpp}, \hyperpage{314} - \item {include/barry/models/defm/defm-\/meat.hpp}, \hyperpage{315} - \item {include/barry/models/defm/defm-\/types.hpp}, \hyperpage{316} - \item {include/barry/models/defm/formula.hpp}, \hyperpage{317} - \item {include/barry/models/geese.hpp}, \hyperpage{319} - \item {include/barry/models/geese/counters.hpp}, \hyperpage{312} - \item {include/barry/models/geese/flock-\/bones.hpp}, \hyperpage{319} - \item {include/barry/models/geese/flock-\/meat.hpp}, \hyperpage{320} - \item {include/barry/models/geese/geese-\/bones.hpp}, \hyperpage{320} + \hyperpage{261} + \item {include/barry/barraydense-\/meat.hpp}, \hyperpage{264} + \item {include/barry/barraydensecell-\/bones.hpp}, \hyperpage{265} + \item {include/barry/barraydensecell-\/meat.hpp}, \hyperpage{266} + \item {include/barry/barraydensecol-\/bones.hpp}, \hyperpage{267} + \item {include/barry/barraydenserow-\/bones.hpp}, \hyperpage{268} + \item {include/barry/barrayrow-\/bones.hpp}, \hyperpage{269} + \item {include/barry/barrayrow-\/meat.hpp}, \hyperpage{269} + \item {include/barry/barrayvector-\/bones.hpp}, \hyperpage{271} + \item {include/barry/barrayvector-\/meat.hpp}, \hyperpage{272} + \item {include/barry/barry-\/configuration.hpp}, \hyperpage{272} + \item {include/barry/barry-\/debug.hpp}, \hyperpage{274} + \item {include/barry/barry-\/macros.hpp}, \hyperpage{275} + \item {include/barry/barry.hpp}, \hyperpage{276} + \item {include/barry/cell-\/bones.hpp}, \hyperpage{279} + \item {include/barry/cell-\/meat.hpp}, \hyperpage{280} + \item {include/barry/col-\/bones.hpp}, \hyperpage{280} + \item {include/barry/counters-\/bones.hpp}, \hyperpage{280} + \item {include/barry/counters-\/meat.hpp}, \hyperpage{281} + \item {include/barry/counters/network-\/css.hpp}, \hyperpage{293} + \item {include/barry/counters/network.hpp}, \hyperpage{301} + \item {include/barry/freqtable.hpp}, \hyperpage{308} + \item {include/barry/model-\/bones.hpp}, \hyperpage{309} + \item {include/barry/model-\/meat.hpp}, \hyperpage{309} + \item {include/barry/models/defm.hpp}, \hyperpage{310} + \item {include/barry/models/defm/counters.hpp}, \hyperpage{311} + \item {include/barry/models/defm/defm-\/bones.hpp}, \hyperpage{316} + \item {include/barry/models/defm/defm-\/meat.hpp}, \hyperpage{317} + \item {include/barry/models/defm/defm-\/types.hpp}, \hyperpage{318} + \item {include/barry/models/defm/formula.hpp}, \hyperpage{319} + \item {include/barry/models/geese.hpp}, \hyperpage{321} + \item {include/barry/models/geese/counters.hpp}, \hyperpage{314} + \item {include/barry/models/geese/flock-\/bones.hpp}, \hyperpage{321} + \item {include/barry/models/geese/flock-\/meat.hpp}, \hyperpage{322} + \item {include/barry/models/geese/geese-\/bones.hpp}, \hyperpage{322} \item {include/barry/models/geese/geese-\/meat-\/constructors.hpp}, - \hyperpage{322} + \hyperpage{324} \item {include/barry/models/geese/geese-\/meat-\/likelihood.hpp}, - \hyperpage{323} + \hyperpage{325} \item {include/barry/models/geese/geese-\/meat-\/likelihood\_exhaust.hpp}, - \hyperpage{324} + \hyperpage{326} \item {include/barry/models/geese/geese-\/meat-\/predict.hpp}, - \hyperpage{325} + \hyperpage{327} \item {include/barry/models/geese/geese-\/meat-\/predict\_exhaust.hpp}, - \hyperpage{325} + \hyperpage{327} \item {include/barry/models/geese/geese-\/meat-\/predict\_sim.hpp}, - \hyperpage{326} + \hyperpage{328} \item {include/barry/models/geese/geese-\/meat-\/simulate.hpp}, - \hyperpage{326} - \item {include/barry/models/geese/geese-\/meat.hpp}, \hyperpage{327} + \hyperpage{328} + \item {include/barry/models/geese/geese-\/meat.hpp}, \hyperpage{329} \item {include/barry/models/geese/geese-\/node-\/bones.hpp}, - \hyperpage{327} - \item {include/barry/models/geese/geese-\/types.hpp}, \hyperpage{328} - \item {include/barry/powerset-\/bones.hpp}, \hyperpage{331} - \item {include/barry/powerset-\/meat.hpp}, \hyperpage{332} - \item {include/barry/progress.hpp}, \hyperpage{332} - \item {include/barry/rules-\/bones.hpp}, \hyperpage{333} - \item {include/barry/rules-\/meat.hpp}, \hyperpage{334} - \item {include/barry/statscounter-\/bones.hpp}, \hyperpage{334} - \item {include/barry/statscounter-\/meat.hpp}, \hyperpage{335} - \item {include/barry/support-\/bones.hpp}, \hyperpage{340} - \item {include/barry/support-\/meat.hpp}, \hyperpage{341} - \item {include/barry/typedefs.hpp}, \hyperpage{342} + \hyperpage{329} + \item {include/barry/models/geese/geese-\/types.hpp}, \hyperpage{330} + \item {include/barry/powerset-\/bones.hpp}, \hyperpage{333} + \item {include/barry/powerset-\/meat.hpp}, \hyperpage{334} + \item {include/barry/progress.hpp}, \hyperpage{334} + \item {include/barry/rules-\/bones.hpp}, \hyperpage{335} + \item {include/barry/rules-\/meat.hpp}, \hyperpage{336} + \item {include/barry/statscounter-\/bones.hpp}, \hyperpage{336} + \item {include/barry/statscounter-\/meat.hpp}, \hyperpage{337} + \item {include/barry/support-\/bones.hpp}, \hyperpage{342} + \item {include/barry/support-\/meat.hpp}, \hyperpage{343} + \item {include/barry/typedefs.hpp}, \hyperpage{344} \item {indices} - \subitem {NetCounterData}, \hyperpage{203} + \subitem {NetCounterData}, \hyperpage{205} \subitem {Phylo rules}, \hyperpage{45} \item {inherit\_support} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{169} \item {init} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{131} - \subitem {DEFM}, \hyperpage{142} - \subitem {Flock}, \hyperpage{153} - \subitem {Geese}, \hyperpage{167} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} + \subitem {DEFM}, \hyperpage{144} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{169} \subitem {Phylo rules}, \hyperpage{45} \item {init\_fun} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {init\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{292} \item {init\_node} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{169} \item {init\_support} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} + \hyperpage{224} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{245} \item {INITIALIZED} - \subitem {geese-\/bones.hpp}, \hyperpage{321} + \subitem {geese-\/bones.hpp}, \hyperpage{323} \item {initialized} - \subitem {Flock}, \hyperpage{156} - \subitem {Geese}, \hyperpage{173} + \subitem {Flock}, \hyperpage{158} + \subitem {Geese}, \hyperpage{175} \item {insert\_cell} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{87} + \hyperpage{89} \item {is\_col} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{115} + \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} + \hyperpage{121} \item {is\_dense} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{87} + \hyperpage{89} \item {IS\_DUPLICATION} \subitem {Counting}, \hyperpage{15} \item {IS\_EITHER} \subitem {Counting}, \hyperpage{15} \item {is\_empty} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{88} + \hyperpage{90} \item {is\_leaf} - \subitem {Node}, \hyperpage{209} + \subitem {Node}, \hyperpage{211} \item {is\_motif} - \subitem {DEFM}, \hyperpage{142} + \subitem {DEFM}, \hyperpage{144} \subitem {Phylo rules}, \hyperpage{45} \item {is\_row} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{115} + \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} + \hyperpage{121} \item {IS\_SPECIATION} \subitem {Counting}, \hyperpage{16} \item {is\_true} - \subitem {Phylo rules}, \hyperpage{41} + \subitem {Phylo rules}, \hyperpage{41, 42} \item {iter} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{128} + \hyperpage{130} \indexspace \item {j} - \subitem {counters-\/meat.hpp}, \hyperpage{290} - \subitem {statscounter-\/meat.hpp}, \hyperpage{340} + \subitem {counters-\/meat.hpp}, \hyperpage{292} + \subitem {statscounter-\/meat.hpp}, \hyperpage{342} \indexspace \item {keygen\_defm} - \subitem {defm-\/meat.hpp}, \hyperpage{316} + \subitem {defm-\/meat.hpp}, \hyperpage{318} \item {keygen\_full} - \subitem {geese-\/bones.hpp}, \hyperpage{321} + \subitem {geese-\/bones.hpp}, \hyperpage{323} \item {keys2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{198} \indexspace \item {lb} - \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {PhyloRuleDynData}, \hyperpage{220} \item {likelihood} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{169} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187, 188} + \hyperpage{189, 190} \item {likelihood\_} - \subitem {model-\/meat.hpp}, \hyperpage{308} + \subitem {model-\/meat.hpp}, \hyperpage{310} \item {likelihood\_exhaust} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{169} \item {likelihood\_joint} - \subitem {Flock}, \hyperpage{153} + \subitem {Flock}, \hyperpage{155} \item {likelihood\_total} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{191} \item {logical} - \subitem {Phylo rules}, \hyperpage{45} + \subitem {Phylo rules}, \hyperpage{46} \item {logodds} - \subitem {DEFM}, \hyperpage{142} + \subitem {DEFM}, \hyperpage{144} \indexspace \item {M} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{226} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{249} \item {MAKE\_DEFM\_HASHER} \subitem {Counting}, \hyperpage{16} \item {MAKE\_DUPL\_VARS} \subitem {Counting}, \hyperpage{16} \item {make\_hash} - \subitem {FreqTable$<$ T $>$}, \hyperpage{159} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} \item {Map} - \subitem {barry-\/configuration.hpp}, \hyperpage{272} + \subitem {barry-\/configuration.hpp}, \hyperpage{274} \item {map\_to\_state\_id} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{175} \item {MapVec\_type} - \subitem {typedefs.hpp}, \hyperpage{345} + \subitem {typedefs.hpp}, \hyperpage{347} \item {max\_num\_elements} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{250} \item {Model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{179, 180} + \hyperpage{181, 182} \item {model} - \subitem {Flock}, \hyperpage{156} + \subitem {Flock}, \hyperpage{158} \item {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{175} - \subitem {$\sim$Model}, \hyperpage{180} - \subitem {add\_array}, \hyperpage{180} - \subitem {add\_counter}, \hyperpage{181} - \subitem {add\_hasher}, \hyperpage{181} - \subitem {add\_rule}, \hyperpage{181, 182} - \subitem {add\_rule\_dyn}, \hyperpage{182} - \subitem {arrays2support}, \hyperpage{195} - \subitem {colnames}, \hyperpage{182} - \subitem {conditional\_prob}, \hyperpage{182} - \subitem {counter\_fun}, \hyperpage{195} - \subitem {counters}, \hyperpage{195} - \subitem {delete\_counters}, \hyperpage{195} - \subitem {delete\_rengine}, \hyperpage{195} - \subitem {delete\_rules}, \hyperpage{196} - \subitem {delete\_rules\_dyn}, \hyperpage{196} - \subitem {first\_calc\_done}, \hyperpage{196} - \subitem {gen\_key}, \hyperpage{183} - \subitem {get\_arrays2support}, \hyperpage{183} - \subitem {get\_counters}, \hyperpage{183} - \subitem {get\_likelihoods}, \hyperpage{184} - \subitem {get\_normalizing\_constants}, \hyperpage{184} - \subitem {get\_pset}, \hyperpage{184} - \subitem {get\_pset\_arrays}, \hyperpage{184} - \subitem {get\_pset\_locations}, \hyperpage{184} - \subitem {get\_pset\_probs}, \hyperpage{185} - \subitem {get\_pset\_sizes}, \hyperpage{185} - \subitem {get\_pset\_stats}, \hyperpage{185} - \subitem {get\_rengine}, \hyperpage{186} - \subitem {get\_rules}, \hyperpage{186} - \subitem {get\_rules\_dyn}, \hyperpage{186} - \subitem {get\_stats\_support}, \hyperpage{186} - \subitem {get\_stats\_support\_sizes}, \hyperpage{186} - \subitem {get\_stats\_support\_sizes\_acc}, \hyperpage{187} - \subitem {get\_stats\_target}, \hyperpage{187} - \subitem {get\_support\_fun}, \hyperpage{187} - \subitem {keys2support}, \hyperpage{196} - \subitem {likelihood}, \hyperpage{187, 188} - \subitem {likelihood\_total}, \hyperpage{189} - \subitem {Model}, \hyperpage{179, 180} - \subitem {normalizing\_constants}, \hyperpage{196} - \subitem {nrules}, \hyperpage{189} - \subitem {nrules\_dyn}, \hyperpage{189} - \subitem {nterms}, \hyperpage{189} - \subitem {operator=}, \hyperpage{190} - \subitem {params\_last}, \hyperpage{197} - \subitem {print}, \hyperpage{190} - \subitem {print\_stats}, \hyperpage{190} - \subitem {pset\_arrays}, \hyperpage{197} - \subitem {pset\_locations}, \hyperpage{197} - \subitem {pset\_probs}, \hyperpage{197} - \subitem {pset\_sizes}, \hyperpage{198} - \subitem {pset\_stats}, \hyperpage{198} - \subitem {rengine}, \hyperpage{198} - \subitem {rules}, \hyperpage{198} - \subitem {rules\_dyn}, \hyperpage{199} - \subitem {sample}, \hyperpage{190, 191} - \subitem {set\_counters}, \hyperpage{191} - \subitem {set\_rengine}, \hyperpage{191} - \subitem {set\_rules}, \hyperpage{191} - \subitem {set\_rules\_dyn}, \hyperpage{192} - \subitem {set\_seed}, \hyperpage{192} - \subitem {set\_transform\_model}, \hyperpage{192} - \subitem {size}, \hyperpage{193} - \subitem {size\_unique}, \hyperpage{193} - \subitem {stats\_likelihood}, \hyperpage{199} - \subitem {stats\_support}, \hyperpage{199} - \subitem {stats\_support\_n\_arrays}, \hyperpage{199} - \subitem {stats\_support\_sizes}, \hyperpage{200} - \subitem {stats\_support\_sizes\_acc}, \hyperpage{200} - \subitem {stats\_target}, \hyperpage{200} - \subitem {store\_psets}, \hyperpage{193} - \subitem {support\_fun}, \hyperpage{200} - \subitem {support\_size}, \hyperpage{193} - \subitem {transform\_model}, \hyperpage{193} - \subitem {transform\_model\_fun}, \hyperpage{201} - \subitem {transform\_model\_term\_names}, \hyperpage{201} - \subitem {update\_likelihoods}, \hyperpage{194} - \subitem {update\_normalizing\_constants}, \hyperpage{194} - \subitem {update\_pset\_probs}, \hyperpage{194} - \subitem {with\_pset}, \hyperpage{201} + \hyperpage{177} + \subitem {$\sim$Model}, \hyperpage{182} + \subitem {add\_array}, \hyperpage{182} + \subitem {add\_counter}, \hyperpage{183} + \subitem {add\_hasher}, \hyperpage{183} + \subitem {add\_rule}, \hyperpage{183, 184} + \subitem {add\_rule\_dyn}, \hyperpage{184} + \subitem {arrays2support}, \hyperpage{197} + \subitem {colnames}, \hyperpage{184} + \subitem {conditional\_prob}, \hyperpage{184} + \subitem {counter\_fun}, \hyperpage{197} + \subitem {counters}, \hyperpage{197} + \subitem {delete\_counters}, \hyperpage{197} + \subitem {delete\_rengine}, \hyperpage{197} + \subitem {delete\_rules}, \hyperpage{198} + \subitem {delete\_rules\_dyn}, \hyperpage{198} + \subitem {first\_calc\_done}, \hyperpage{198} + \subitem {gen\_key}, \hyperpage{185} + \subitem {get\_arrays2support}, \hyperpage{185} + \subitem {get\_counters}, \hyperpage{185} + \subitem {get\_likelihoods}, \hyperpage{186} + \subitem {get\_normalizing\_constants}, \hyperpage{186} + \subitem {get\_pset}, \hyperpage{186} + \subitem {get\_pset\_arrays}, \hyperpage{186} + \subitem {get\_pset\_locations}, \hyperpage{186} + \subitem {get\_pset\_probs}, \hyperpage{187} + \subitem {get\_pset\_sizes}, \hyperpage{187} + \subitem {get\_pset\_stats}, \hyperpage{187} + \subitem {get\_rengine}, \hyperpage{188} + \subitem {get\_rules}, \hyperpage{188} + \subitem {get\_rules\_dyn}, \hyperpage{188} + \subitem {get\_stats\_support}, \hyperpage{188} + \subitem {get\_stats\_support\_sizes}, \hyperpage{188} + \subitem {get\_stats\_support\_sizes\_acc}, \hyperpage{189} + \subitem {get\_stats\_target}, \hyperpage{189} + \subitem {get\_support\_fun}, \hyperpage{189} + \subitem {keys2support}, \hyperpage{198} + \subitem {likelihood}, \hyperpage{189, 190} + \subitem {likelihood\_total}, \hyperpage{191} + \subitem {Model}, \hyperpage{181, 182} + \subitem {normalizing\_constants}, \hyperpage{198} + \subitem {nrules}, \hyperpage{191} + \subitem {nrules\_dyn}, \hyperpage{191} + \subitem {nterms}, \hyperpage{191} + \subitem {operator=}, \hyperpage{192} + \subitem {params\_last}, \hyperpage{199} + \subitem {print}, \hyperpage{192} + \subitem {print\_stats}, \hyperpage{192} + \subitem {pset\_arrays}, \hyperpage{199} + \subitem {pset\_locations}, \hyperpage{199} + \subitem {pset\_probs}, \hyperpage{199} + \subitem {pset\_sizes}, \hyperpage{200} + \subitem {pset\_stats}, \hyperpage{200} + \subitem {rengine}, \hyperpage{200} + \subitem {rules}, \hyperpage{200} + \subitem {rules\_dyn}, \hyperpage{201} + \subitem {sample}, \hyperpage{192, 193} + \subitem {set\_counters}, \hyperpage{193} + \subitem {set\_rengine}, \hyperpage{193} + \subitem {set\_rules}, \hyperpage{193} + \subitem {set\_rules\_dyn}, \hyperpage{194} + \subitem {set\_seed}, \hyperpage{194} + \subitem {set\_transform\_model}, \hyperpage{194} + \subitem {size}, \hyperpage{195} + \subitem {size\_unique}, \hyperpage{195} + \subitem {stats\_likelihood}, \hyperpage{201} + \subitem {stats\_support}, \hyperpage{201} + \subitem {stats\_support\_n\_arrays}, \hyperpage{201} + \subitem {stats\_support\_sizes}, \hyperpage{202} + \subitem {stats\_support\_sizes\_acc}, \hyperpage{202} + \subitem {stats\_target}, \hyperpage{202} + \subitem {store\_psets}, \hyperpage{195} + \subitem {support\_fun}, \hyperpage{202} + \subitem {support\_size}, \hyperpage{195} + \subitem {transform\_model}, \hyperpage{195} + \subitem {transform\_model\_fun}, \hyperpage{203} + \subitem {transform\_model\_term\_names}, \hyperpage{203} + \subitem {update\_likelihoods}, \hyperpage{196} + \subitem {update\_normalizing\_constants}, \hyperpage{196} + \subitem {update\_pset\_probs}, \hyperpage{196} + \subitem {with\_pset}, \hyperpage{203} \item {model-\/meat.hpp} - \subitem {likelihood\_}, \hyperpage{308} - \subitem {update\_normalizing\_constant}, \hyperpage{308} + \subitem {likelihood\_}, \hyperpage{310} + \subitem {update\_normalizing\_constant}, \hyperpage{310} \item {motif\_census} - \subitem {DEFM}, \hyperpage{143} + \subitem {DEFM}, \hyperpage{145} \indexspace \item {N} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{226} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{250} \item {n\_counters} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{250} \item {n\_free} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{226} \item {n\_locked} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{226} \item {name} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {name\_} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{292} \item {nannotations} - \subitem {Geese}, \hyperpage{168} + \subitem {Geese}, \hyperpage{170} \item {narray} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{212} \item {ncol} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{88} - \subitem {Phylo rules}, \hyperpage{41} + \hyperpage{90} + \subitem {Phylo rules}, \hyperpage{42} \item {NET\_C\_DATA\_IDX} - \subitem {network.hpp}, \hyperpage{303} + \subitem {network.hpp}, \hyperpage{305} \item {NET\_C\_DATA\_NUM} - \subitem {network.hpp}, \hyperpage{303} + \subitem {network.hpp}, \hyperpage{305} \item {NetCounter} - \subitem {network.hpp}, \hyperpage{304} - \item {NetCounterData}, \hyperpage{202} - \subitem {$\sim$NetCounterData}, \hyperpage{203} - \subitem {indices}, \hyperpage{203} - \subitem {NetCounterData}, \hyperpage{202} - \subitem {numbers}, \hyperpage{203} + \subitem {network.hpp}, \hyperpage{306} + \item {NetCounterData}, \hyperpage{204} + \subitem {$\sim$NetCounterData}, \hyperpage{205} + \subitem {indices}, \hyperpage{205} + \subitem {NetCounterData}, \hyperpage{204} + \subitem {numbers}, \hyperpage{205} \item {NetCounters} - \subitem {network.hpp}, \hyperpage{304} + \subitem {network.hpp}, \hyperpage{306} \item {NetModel} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {NetRule} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {NetRules} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {NetStatsCounter} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {NetSupport} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {Network} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{307} \item {Network counters}, \hyperpage{24} \subitem {counter\_absdiff}, \hyperpage{26} \subitem {counter\_ctriads}, \hyperpage{27} @@ -1917,166 +1917,166 @@ \subitem {counter\_isolates}, \hyperpage{29, 30} \subitem {counter\_istar2}, \hyperpage{30} \subitem {counter\_logit\_intercept}, \hyperpage{30} - \subitem {counter\_mutual}, \hyperpage{30} + \subitem {counter\_mutual}, \hyperpage{31} \subitem {counter\_nodecov}, \hyperpage{31} \subitem {counter\_nodeicov}, \hyperpage{31} \subitem {counter\_nodematch}, \hyperpage{31} - \subitem {counter\_nodeocov}, \hyperpage{31} - \subitem {counter\_odegree}, \hyperpage{31, 32} + \subitem {counter\_nodeocov}, \hyperpage{32} + \subitem {counter\_odegree}, \hyperpage{32} \subitem {counter\_odegree15}, \hyperpage{32} - \subitem {counter\_ones}, \hyperpage{32} + \subitem {counter\_ones}, \hyperpage{33} \subitem {counter\_ostar2}, \hyperpage{33} \subitem {counter\_transition}, \hyperpage{33} \subitem {counter\_transition\_formula}, \hyperpage{34} - \subitem {counter\_ttriads}, \hyperpage{34} - \subitem {NETWORK\_COUNTER}, \hyperpage{34} - \subitem {rules\_dont\_become\_zero}, \hyperpage{34} + \subitem {counter\_ttriads}, \hyperpage{34, 35} + \subitem {NETWORK\_COUNTER}, \hyperpage{35} + \subitem {rules\_dont\_become\_zero}, \hyperpage{35} \subitem {rules\_markov\_fixed}, \hyperpage{35} \item {network-\/css.hpp} - \subitem {counter\_css\_census01}, \hyperpage{295} - \subitem {counter\_css\_census02}, \hyperpage{295} - \subitem {counter\_css\_census03}, \hyperpage{295} - \subitem {counter\_css\_census04}, \hyperpage{296} - \subitem {counter\_css\_census05}, \hyperpage{296} - \subitem {counter\_css\_census06}, \hyperpage{296} - \subitem {counter\_css\_census07}, \hyperpage{296} - \subitem {counter\_css\_census08}, \hyperpage{297} - \subitem {counter\_css\_census09}, \hyperpage{297} - \subitem {counter\_css\_census10}, \hyperpage{297} + \subitem {counter\_css\_census01}, \hyperpage{297} + \subitem {counter\_css\_census02}, \hyperpage{297} + \subitem {counter\_css\_census03}, \hyperpage{297} + \subitem {counter\_css\_census04}, \hyperpage{298} + \subitem {counter\_css\_census05}, \hyperpage{298} + \subitem {counter\_css\_census06}, \hyperpage{298} + \subitem {counter\_css\_census07}, \hyperpage{298} + \subitem {counter\_css\_census08}, \hyperpage{299} + \subitem {counter\_css\_census09}, \hyperpage{299} + \subitem {counter\_css\_census10}, \hyperpage{299} \subitem {counter\_css\_completely\_false\_recip\_comiss}, - \hyperpage{297} + \hyperpage{299} \subitem {counter\_css\_completely\_false\_recip\_omiss}, - \hyperpage{298} - \subitem {counter\_css\_mixed\_recip}, \hyperpage{298} + \hyperpage{300} + \subitem {counter\_css\_mixed\_recip}, \hyperpage{300} \subitem {counter\_css\_partially\_false\_recip\_commi}, - \hyperpage{298} + \hyperpage{300} \subitem {counter\_css\_partially\_false\_recip\_omiss}, - \hyperpage{299} - \subitem {CSS\_APPEND}, \hyperpage{292} - \subitem {CSS\_CASE\_ELSE}, \hyperpage{293} - \subitem {CSS\_CASE\_PERCEIVED}, \hyperpage{293} - \subitem {CSS\_CASE\_TRUTH}, \hyperpage{293} - \subitem {CSS\_CHECK\_SIZE}, \hyperpage{293} - \subitem {CSS\_CHECK\_SIZE\_INIT}, \hyperpage{293} - \subitem {CSS\_MATCH\_TYPE}, \hyperpage{294} - \subitem {CSS\_NET\_COUNTER\_LAMBDA\_INIT}, \hyperpage{294} - \subitem {CSS\_PERCEIVED\_CELLS}, \hyperpage{294} - \subitem {CSS\_SIZE}, \hyperpage{294} - \subitem {CSS\_TRUE\_CELLS}, \hyperpage{295} + \hyperpage{301} + \subitem {CSS\_APPEND}, \hyperpage{294} + \subitem {CSS\_CASE\_ELSE}, \hyperpage{295} + \subitem {CSS\_CASE\_PERCEIVED}, \hyperpage{295} + \subitem {CSS\_CASE\_TRUTH}, \hyperpage{295} + \subitem {CSS\_CHECK\_SIZE}, \hyperpage{295} + \subitem {CSS\_CHECK\_SIZE\_INIT}, \hyperpage{295} + \subitem {CSS\_MATCH\_TYPE}, \hyperpage{296} + \subitem {CSS\_NET\_COUNTER\_LAMBDA\_INIT}, \hyperpage{296} + \subitem {CSS\_PERCEIVED\_CELLS}, \hyperpage{296} + \subitem {CSS\_SIZE}, \hyperpage{296} + \subitem {CSS\_TRUE\_CELLS}, \hyperpage{297} \item {network.hpp} - \subitem {BARRY\_ZERO\_NETWORK}, \hyperpage{302} - \subitem {BARRY\_ZERO\_NETWORK\_DENSE}, \hyperpage{302} - \subitem {NET\_C\_DATA\_IDX}, \hyperpage{303} - \subitem {NET\_C\_DATA\_NUM}, \hyperpage{303} - \subitem {NetCounter}, \hyperpage{304} - \subitem {NetCounters}, \hyperpage{304} - \subitem {NetModel}, \hyperpage{305} - \subitem {NetRule}, \hyperpage{305} - \subitem {NetRules}, \hyperpage{305} - \subitem {NetStatsCounter}, \hyperpage{305} - \subitem {NetSupport}, \hyperpage{305} - \subitem {Network}, \hyperpage{305} - \subitem {NETWORK\_COUNTER}, \hyperpage{303} - \subitem {NETWORK\_COUNTER\_LAMBDA}, \hyperpage{303} - \subitem {NETWORK\_RULE}, \hyperpage{303} - \subitem {NETWORK\_RULE\_LAMBDA}, \hyperpage{304} - \subitem {NetworkDense}, \hyperpage{306} - \subitem {NETWORKDENSE\_COUNTER\_LAMBDA}, \hyperpage{304} - \subitem {rules\_zerodiag}, \hyperpage{306} + \subitem {BARRY\_ZERO\_NETWORK}, \hyperpage{304} + \subitem {BARRY\_ZERO\_NETWORK\_DENSE}, \hyperpage{304} + \subitem {NET\_C\_DATA\_IDX}, \hyperpage{305} + \subitem {NET\_C\_DATA\_NUM}, \hyperpage{305} + \subitem {NetCounter}, \hyperpage{306} + \subitem {NetCounters}, \hyperpage{306} + \subitem {NetModel}, \hyperpage{307} + \subitem {NetRule}, \hyperpage{307} + \subitem {NetRules}, \hyperpage{307} + \subitem {NetStatsCounter}, \hyperpage{307} + \subitem {NetSupport}, \hyperpage{307} + \subitem {Network}, \hyperpage{307} + \subitem {NETWORK\_COUNTER}, \hyperpage{305} + \subitem {NETWORK\_COUNTER\_LAMBDA}, \hyperpage{305} + \subitem {NETWORK\_RULE}, \hyperpage{305} + \subitem {NETWORK\_RULE\_LAMBDA}, \hyperpage{306} + \subitem {NetworkDense}, \hyperpage{308} + \subitem {NETWORKDENSE\_COUNTER\_LAMBDA}, \hyperpage{306} + \subitem {rules\_zerodiag}, \hyperpage{308} \item {NETWORK\_COUNTER} - \subitem {Network counters}, \hyperpage{34} - \subitem {network.hpp}, \hyperpage{303} + \subitem {Network counters}, \hyperpage{35} + \subitem {network.hpp}, \hyperpage{305} \item {NETWORK\_COUNTER\_LAMBDA} - \subitem {network.hpp}, \hyperpage{303} + \subitem {network.hpp}, \hyperpage{305} \item {NETWORK\_RULE} - \subitem {network.hpp}, \hyperpage{303} + \subitem {network.hpp}, \hyperpage{305} \item {NETWORK\_RULE\_LAMBDA} - \subitem {network.hpp}, \hyperpage{304} - \item {NetworkData}, \hyperpage{203} - \subitem {$\sim$NetworkData}, \hyperpage{205} - \subitem {directed}, \hyperpage{205} - \subitem {NetworkData}, \hyperpage{204, 205} - \subitem {vertex\_attr}, \hyperpage{205} - \item {NetworkDense} \subitem {network.hpp}, \hyperpage{306} + \item {NetworkData}, \hyperpage{205} + \subitem {$\sim$NetworkData}, \hyperpage{207} + \subitem {directed}, \hyperpage{207} + \subitem {NetworkData}, \hyperpage{206, 207} + \subitem {vertex\_attr}, \hyperpage{207} + \item {NetworkDense} + \subitem {network.hpp}, \hyperpage{308} \item {NETWORKDENSE\_COUNTER\_LAMBDA} - \subitem {network.hpp}, \hyperpage{304} + \subitem {network.hpp}, \hyperpage{306} \item {next} - \subitem {Progress}, \hyperpage{226} + \subitem {Progress}, \hyperpage{228} \item {nfunctions} - \subitem {Flock}, \hyperpage{156} - \subitem {Geese}, \hyperpage{173} + \subitem {Flock}, \hyperpage{158} + \subitem {Geese}, \hyperpage{175} \item {nfuns} - \subitem {Flock}, \hyperpage{153} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{170} \item {nleafs} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{170} \item {nnodes} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{170} \item {nnozero} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{88} - \item {Node}, \hyperpage{206} - \subitem {$\sim$Node}, \hyperpage{208} - \subitem {annotations}, \hyperpage{209} - \subitem {array}, \hyperpage{209} - \subitem {arrays}, \hyperpage{209} - \subitem {duplication}, \hyperpage{210} - \subitem {get\_parent}, \hyperpage{208} - \subitem {id}, \hyperpage{210} - \subitem {is\_leaf}, \hyperpage{209} - \subitem {narray}, \hyperpage{210} - \subitem {Node}, \hyperpage{207, 208} - \subitem {noffspring}, \hyperpage{209} - \subitem {offspring}, \hyperpage{210} - \subitem {ord}, \hyperpage{210} - \subitem {parent}, \hyperpage{211} - \subitem {probability}, \hyperpage{211} - \subitem {subtree\_prob}, \hyperpage{211} - \subitem {visited}, \hyperpage{211} - \item {NodeData}, \hyperpage{212} - \subitem {blengths}, \hyperpage{212} - \subitem {duplication}, \hyperpage{213} - \subitem {has\_leaf}, \hyperpage{213} - \subitem {NodeData}, \hyperpage{212} - \subitem {states}, \hyperpage{213} + \hyperpage{90} + \item {Node}, \hyperpage{208} + \subitem {$\sim$Node}, \hyperpage{210} + \subitem {annotations}, \hyperpage{211} + \subitem {array}, \hyperpage{211} + \subitem {arrays}, \hyperpage{211} + \subitem {duplication}, \hyperpage{212} + \subitem {get\_parent}, \hyperpage{210} + \subitem {id}, \hyperpage{212} + \subitem {is\_leaf}, \hyperpage{211} + \subitem {narray}, \hyperpage{212} + \subitem {Node}, \hyperpage{209, 210} + \subitem {noffspring}, \hyperpage{211} + \subitem {offspring}, \hyperpage{212} + \subitem {ord}, \hyperpage{212} + \subitem {parent}, \hyperpage{213} + \subitem {probability}, \hyperpage{213} + \subitem {subtree\_prob}, \hyperpage{213} + \subitem {visited}, \hyperpage{213} + \item {NodeData}, \hyperpage{214} + \subitem {blengths}, \hyperpage{214} + \subitem {duplication}, \hyperpage{215} + \subitem {has\_leaf}, \hyperpage{215} + \subitem {NodeData}, \hyperpage{214} + \subitem {states}, \hyperpage{215} \item {nodes} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{175} \item {noexcept} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{292} \item {noffspring} - \subitem {Node}, \hyperpage{209} + \subitem {Node}, \hyperpage{211} \item {NONE} - \subitem {CHECK}, \hyperpage{56} - \subitem {EXISTS}, \hyperpage{58} + \subitem {CHECK}, \hyperpage{58} + \subitem {EXISTS}, \hyperpage{60} \item {normalizing\_constants} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{198} \item {nrow} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{88} - \subitem {Phylo rules}, \hyperpage{41} + \hyperpage{90} + \subitem {Phylo rules}, \hyperpage{42} \item {nrules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{191} \item {nrules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{191} \item {nterms} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{170} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{191} \item {ntrees} - \subitem {Flock}, \hyperpage{154} + \subitem {Flock}, \hyperpage{156} \item {num} - \subitem {Phylo rules}, \hyperpage{41, 42} + \subitem {Phylo rules}, \hyperpage{42} \item {numbers} - \subitem {NetCounterData}, \hyperpage{203} + \subitem {NetCounterData}, \hyperpage{205} \subitem {Phylo rules}, \hyperpage{46} \indexspace @@ -2084,248 +2084,248 @@ \item {obs\_start} \subitem {Phylo rules}, \hyperpage{46} \item {observed\_counts} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{171} \item {offspring} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{212} \item {ONE} - \subitem {CHECK}, \hyperpage{56} - \subitem {EXISTS}, \hyperpage{58} + \subitem {CHECK}, \hyperpage{58} + \subitem {EXISTS}, \hyperpage{60} \item {operator BArrayRow$<$ Cell\_Type, Data\_Type $>$} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} \item {operator BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} + \hyperpage{114} \item {operator Cell\_Type} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{77} + \hyperpage{79} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{97} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124} + \hyperpage{99} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{126} \item {operator std::vector$<$ Cell\_Type $>$} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{116} + \hyperpage{118} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} + \hyperpage{121} \item {operator!=} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{77} + \hyperpage{79} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} + \hyperpage{114} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{119} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124} + \hyperpage{121} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{126} \item {operator$<$} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{77} + \hyperpage{79} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{112} + \hyperpage{114} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{120} + \hyperpage{122} \item {operator$<$=} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{78} + \hyperpage{80} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{113} + \hyperpage{115} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{120} + \hyperpage{122} \item {operator$>$} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{78} + \hyperpage{80} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{113} + \hyperpage{115} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{120} + \hyperpage{122} \item {operator$>$=} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{78} + \hyperpage{80} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{113} + \hyperpage{115} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{120} + \hyperpage{122} \item {operator$\ast$=} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{89} + \hyperpage{91} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{97} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} + \hyperpage{99} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{116} + \hyperpage{118} \item {operator()} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{88, 89} + \hyperpage{90, 91} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{101} - \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} + \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{105} \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{106} - \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{108} - \subitem {Flock}, \hyperpage{154} + \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{110} + \subitem {Flock}, \hyperpage{156} \subitem {Phylo rules}, \hyperpage{42} - \subitem {PhyloCounterData}, \hyperpage{215} - \subitem {PhyloRuleDynData}, \hyperpage{217} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} - \subitem {vecHasher$<$ T $>$}, \hyperpage{249} + \subitem {PhyloCounterData}, \hyperpage{217} + \subitem {PhyloRuleDynData}, \hyperpage{219} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} + \subitem {vecHasher$<$ T $>$}, \hyperpage{251} \item {operator+=} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{89} + \hyperpage{91} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{98} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} + \hyperpage{100} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{116} + \hyperpage{118} \item {operator-\/=} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{90} + \hyperpage{92} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{98} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} + \hyperpage{100} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{112} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{116} + \hyperpage{118} \item {operator/=} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{90} + \hyperpage{92} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{98} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{111} + \hyperpage{100} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{113} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{116} + \hyperpage{118} \item {operator=} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{90, 91} + \hyperpage{92, 93} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{98} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{111} + \hyperpage{100} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{113} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{117} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124, 125} + \hyperpage{119} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{126, 127} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{131, 132} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{137} - \subitem {Geese}, \hyperpage{169} + \hyperpage{133, 134} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{139} + \subitem {Geese}, \hyperpage{171} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{190} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \hyperpage{192} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{235} \item {operator==} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} - \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{78} \subitem {BArrayCell\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{78} + \hyperpage{80} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{91} + \hyperpage{93} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{99} - \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{111} + \hyperpage{101} + \subitem {BArrayRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{113} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{113} + \hyperpage{115} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{117} + \hyperpage{119} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{120} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125} + \hyperpage{122} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {operator[]} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} - \subitem {PhyloCounterData}, \hyperpage{215} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{140} + \subitem {PhyloCounterData}, \hyperpage{217} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} + \hyperpage{224} \item {ord} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{212} \item {out\_of\_range} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{91} + \hyperpage{93} \indexspace \item {params\_last} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{199} \item {parent} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{213} \item {parse\_polytomies} - \subitem {Flock}, \hyperpage{155} - \subitem {Geese}, \hyperpage{169} + \subitem {Flock}, \hyperpage{157} + \subitem {Geese}, \hyperpage{171} \item {Phylo counters}, \hyperpage{47} - \subitem {counter\_co\_opt}, \hyperpage{48} + \subitem {counter\_co\_opt}, \hyperpage{49} \subitem {counter\_cogain}, \hyperpage{49} \subitem {counter\_gains}, \hyperpage{49} \subitem {counter\_gains\_from\_0}, \hyperpage{49} - \subitem {counter\_gains\_k\_offspring}, \hyperpage{49} + \subitem {counter\_gains\_k\_offspring}, \hyperpage{50} \subitem {counter\_genes\_changing}, \hyperpage{50} \subitem {counter\_k\_genes\_changing}, \hyperpage{50} \subitem {counter\_less\_than\_p\_prop\_genes\_changing}, \hyperpage{50} - \subitem {counter\_longest}, \hyperpage{50} + \subitem {counter\_longest}, \hyperpage{51} \subitem {counter\_loss}, \hyperpage{51} \subitem {counter\_maxfuns}, \hyperpage{51} \subitem {counter\_neofun}, \hyperpage{51} - \subitem {counter\_neofun\_a2b}, \hyperpage{51} + \subitem {counter\_neofun\_a2b}, \hyperpage{52} \subitem {counter\_overall\_changes}, \hyperpage{52} \subitem {counter\_overall\_gains}, \hyperpage{52} \subitem {counter\_overall\_gains\_from\_0}, \hyperpage{52} - \subitem {counter\_overall\_loss}, \hyperpage{52} + \subitem {counter\_overall\_loss}, \hyperpage{53} \subitem {counter\_pairwise\_first\_gain}, \hyperpage{53} \subitem {counter\_pairwise\_neofun\_singlefun}, \hyperpage{53} \subitem {counter\_pairwise\_overall\_change}, \hyperpage{53} - \subitem {counter\_pairwise\_preserving}, \hyperpage{53} + \subitem {counter\_pairwise\_preserving}, \hyperpage{54} \subitem {counter\_preserve\_pseudogene}, \hyperpage{54} \subitem {counter\_prop\_genes\_changing}, \hyperpage{54} \subitem {counter\_subfun}, \hyperpage{54} - \item {Phylo rules}, \hyperpage{35} - \subitem {$\sim$DEFMCounterData}, \hyperpage{43} - \subitem {$\sim$DEFMData}, \hyperpage{43} - \subitem {$\sim$DEFMRuleDynData}, \hyperpage{43} + \item {Phylo rules}, \hyperpage{36} + \subitem {$\sim$DEFMCounterData}, \hyperpage{44} + \subitem {$\sim$DEFMData}, \hyperpage{44} + \subitem {$\sim$DEFMRuleDynData}, \hyperpage{44} \subitem {array}, \hyperpage{44} \subitem {at}, \hyperpage{39} \subitem {counts}, \hyperpage{44} \subitem {covar\_sort}, \hyperpage{44} - \subitem {covar\_used}, \hyperpage{44} - \subitem {covariates}, \hyperpage{44} - \subitem {DEFMCounter}, \hyperpage{37} + \subitem {covar\_used}, \hyperpage{45} + \subitem {covariates}, \hyperpage{45} + \subitem {DEFMCounter}, \hyperpage{38} \subitem {DEFMCounterData}, \hyperpage{39} - \subitem {DEFMCounters}, \hyperpage{37} - \subitem {DEFMData}, \hyperpage{39} - \subitem {DEFMModel}, \hyperpage{37} + \subitem {DEFMCounters}, \hyperpage{38} + \subitem {DEFMData}, \hyperpage{40} + \subitem {DEFMModel}, \hyperpage{38} \subitem {DEFMRule}, \hyperpage{38} - \subitem {DEFMRuleData}, \hyperpage{40} + \subitem {DEFMRuleData}, \hyperpage{40, 41} \subitem {DEFMRuleDyn}, \hyperpage{38} - \subitem {DEFMRuleDynData}, \hyperpage{40} + \subitem {DEFMRuleDynData}, \hyperpage{41} \subitem {DEFMRules}, \hyperpage{38} - \subitem {DEFMRulesDyn}, \hyperpage{38} - \subitem {DEFMStatsCounter}, \hyperpage{38} - \subitem {DEFMSupport}, \hyperpage{38} - \subitem {idx}, \hyperpage{40, 41} + \subitem {DEFMRulesDyn}, \hyperpage{39} + \subitem {DEFMStatsCounter}, \hyperpage{39} + \subitem {DEFMSupport}, \hyperpage{39} + \subitem {idx}, \hyperpage{41} \subitem {indices}, \hyperpage{45} \subitem {init}, \hyperpage{45} \subitem {is\_motif}, \hyperpage{45} - \subitem {is\_true}, \hyperpage{41} - \subitem {logical}, \hyperpage{45} - \subitem {ncol}, \hyperpage{41} - \subitem {nrow}, \hyperpage{41} - \subitem {num}, \hyperpage{41, 42} + \subitem {is\_true}, \hyperpage{41, 42} + \subitem {logical}, \hyperpage{46} + \subitem {ncol}, \hyperpage{42} + \subitem {nrow}, \hyperpage{42} + \subitem {num}, \hyperpage{42} \subitem {numbers}, \hyperpage{46} \subitem {obs\_start}, \hyperpage{46} \subitem {operator()}, \hyperpage{42} - \subitem {print}, \hyperpage{42} - \subitem {rule\_dyn\_limit\_changes}, \hyperpage{42} + \subitem {print}, \hyperpage{43} + \subitem {rule\_dyn\_limit\_changes}, \hyperpage{43} \subitem {rule\_leafs}, \hyperpage{43} \subitem {X\_ncol}, \hyperpage{46} - \subitem {X\_nrow}, \hyperpage{46} + \subitem {X\_nrow}, \hyperpage{47} \item {PHYLO\_CHECK\_MISSING} \subitem {Counting}, \hyperpage{16} \item {PHYLO\_COUNTER\_LAMBDA} @@ -2335,592 +2335,592 @@ \item {PHYLO\_RULE\_LAMBDA} \subitem {Counting}, \hyperpage{17} \item {PhyloArray} - \subitem {geese-\/types.hpp}, \hyperpage{329} + \subitem {geese-\/types.hpp}, \hyperpage{331} \item {PhyloCounter} - \subitem {geese-\/types.hpp}, \hyperpage{329} - \item {PhyloCounterData}, \hyperpage{213} - \subitem {at}, \hyperpage{214} - \subitem {begin}, \hyperpage{215} - \subitem {empty}, \hyperpage{215} - \subitem {end}, \hyperpage{215} - \subitem {get\_counters}, \hyperpage{215} - \subitem {operator()}, \hyperpage{215} - \subitem {operator[]}, \hyperpage{215} - \subitem {PhyloCounterData}, \hyperpage{214} - \subitem {push\_back}, \hyperpage{216} - \subitem {reserve}, \hyperpage{216} - \subitem {shrink\_to\_fit}, \hyperpage{216} - \subitem {size}, \hyperpage{216} + \subitem {geese-\/types.hpp}, \hyperpage{331} + \item {PhyloCounterData}, \hyperpage{215} + \subitem {at}, \hyperpage{216} + \subitem {begin}, \hyperpage{217} + \subitem {empty}, \hyperpage{217} + \subitem {end}, \hyperpage{217} + \subitem {get\_counters}, \hyperpage{217} + \subitem {operator()}, \hyperpage{217} + \subitem {operator[]}, \hyperpage{217} + \subitem {PhyloCounterData}, \hyperpage{216} + \subitem {push\_back}, \hyperpage{218} + \subitem {reserve}, \hyperpage{218} + \subitem {shrink\_to\_fit}, \hyperpage{218} + \subitem {size}, \hyperpage{218} \item {PhyloCounters} - \subitem {geese-\/types.hpp}, \hyperpage{329} + \subitem {geese-\/types.hpp}, \hyperpage{331} \item {PhyloModel} - \subitem {geese-\/types.hpp}, \hyperpage{329} + \subitem {geese-\/types.hpp}, \hyperpage{331} \item {PhyloPowerSet} - \subitem {geese-\/types.hpp}, \hyperpage{329} + \subitem {geese-\/types.hpp}, \hyperpage{331} \item {PhyloRule} - \subitem {geese-\/types.hpp}, \hyperpage{330} + \subitem {geese-\/types.hpp}, \hyperpage{332} \item {PhyloRuleData} - \subitem {geese-\/types.hpp}, \hyperpage{330} + \subitem {geese-\/types.hpp}, \hyperpage{332} \item {PhyloRuleDyn} - \subitem {geese-\/types.hpp}, \hyperpage{330} - \item {PhyloRuleDynData}, \hyperpage{216} - \subitem {$\sim$PhyloRuleDynData}, \hyperpage{217} - \subitem {counts}, \hyperpage{218} - \subitem {duplication}, \hyperpage{218} - \subitem {lb}, \hyperpage{218} - \subitem {operator()}, \hyperpage{217} - \subitem {PhyloRuleDynData}, \hyperpage{217} - \subitem {pos}, \hyperpage{218} - \subitem {ub}, \hyperpage{218} + \subitem {geese-\/types.hpp}, \hyperpage{332} + \item {PhyloRuleDynData}, \hyperpage{218} + \subitem {$\sim$PhyloRuleDynData}, \hyperpage{219} + \subitem {counts}, \hyperpage{220} + \subitem {duplication}, \hyperpage{220} + \subitem {lb}, \hyperpage{220} + \subitem {operator()}, \hyperpage{219} + \subitem {PhyloRuleDynData}, \hyperpage{219} + \subitem {pos}, \hyperpage{220} + \subitem {ub}, \hyperpage{220} \item {PhyloRules} - \subitem {geese-\/types.hpp}, \hyperpage{330} + \subitem {geese-\/types.hpp}, \hyperpage{332} \item {PhyloRulesDyn} - \subitem {geese-\/types.hpp}, \hyperpage{330} + \subitem {geese-\/types.hpp}, \hyperpage{332} \item {PhyloStatsCounter} - \subitem {geese-\/types.hpp}, \hyperpage{330} + \subitem {geese-\/types.hpp}, \hyperpage{332} \item {PhyloSupport} - \subitem {geese-\/types.hpp}, \hyperpage{331} + \subitem {geese-\/types.hpp}, \hyperpage{333} \item {POS} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260} - \subitem {barraydense-\/meat.hpp}, \hyperpage{262} - \subitem {barraydensecell-\/bones.hpp}, \hyperpage{264} - \subitem {barraydensecell-\/meat.hpp}, \hyperpage{264} - \subitem {barraydensecol-\/bones.hpp}, \hyperpage{265} - \subitem {barraydenserow-\/bones.hpp}, \hyperpage{267} - \subitem {geese-\/types.hpp}, \hyperpage{328} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262} + \subitem {barraydense-\/meat.hpp}, \hyperpage{264} + \subitem {barraydensecell-\/bones.hpp}, \hyperpage{266} + \subitem {barraydensecell-\/meat.hpp}, \hyperpage{266} + \subitem {barraydensecol-\/bones.hpp}, \hyperpage{267} + \subitem {barraydenserow-\/bones.hpp}, \hyperpage{269} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {pos} - \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {PhyloRuleDynData}, \hyperpage{220} \item {POS\_N} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260} - \subitem {barraydense-\/meat.hpp}, \hyperpage{263} - \subitem {barraydensecol-\/bones.hpp}, \hyperpage{265} - \subitem {barraydenserow-\/bones.hpp}, \hyperpage{267} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262} + \subitem {barraydense-\/meat.hpp}, \hyperpage{265} + \subitem {barraydensecol-\/bones.hpp}, \hyperpage{267} + \subitem {barraydenserow-\/bones.hpp}, \hyperpage{269} \item {PowerSet} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{220} + \hyperpage{222} \item {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{219} - \subitem {$\sim$PowerSet}, \hyperpage{221} - \subitem {add\_rule}, \hyperpage{221} - \subitem {begin}, \hyperpage{221} - \subitem {calc}, \hyperpage{221} - \subitem {coordinates\_free}, \hyperpage{223} - \subitem {coordinates\_locked}, \hyperpage{223} - \subitem {data}, \hyperpage{223} - \subitem {EmptyArray}, \hyperpage{224} - \subitem {end}, \hyperpage{222} - \subitem {get\_data}, \hyperpage{222} - \subitem {get\_data\_ptr}, \hyperpage{222} - \subitem {init\_support}, \hyperpage{222} - \subitem {M}, \hyperpage{224} - \subitem {N}, \hyperpage{224} - \subitem {n\_free}, \hyperpage{224} - \subitem {n\_locked}, \hyperpage{224} - \subitem {operator[]}, \hyperpage{222} - \subitem {PowerSet}, \hyperpage{220} - \subitem {reset}, \hyperpage{223} - \subitem {rules}, \hyperpage{224} - \subitem {rules\_deleted}, \hyperpage{225} - \subitem {size}, \hyperpage{223} + \hyperpage{221} + \subitem {$\sim$PowerSet}, \hyperpage{223} + \subitem {add\_rule}, \hyperpage{223} + \subitem {begin}, \hyperpage{223} + \subitem {calc}, \hyperpage{223} + \subitem {coordinates\_free}, \hyperpage{225} + \subitem {coordinates\_locked}, \hyperpage{225} + \subitem {data}, \hyperpage{225} + \subitem {EmptyArray}, \hyperpage{226} + \subitem {end}, \hyperpage{224} + \subitem {get\_data}, \hyperpage{224} + \subitem {get\_data\_ptr}, \hyperpage{224} + \subitem {init\_support}, \hyperpage{224} + \subitem {M}, \hyperpage{226} + \subitem {N}, \hyperpage{226} + \subitem {n\_free}, \hyperpage{226} + \subitem {n\_locked}, \hyperpage{226} + \subitem {operator[]}, \hyperpage{224} + \subitem {PowerSet}, \hyperpage{222} + \subitem {reset}, \hyperpage{225} + \subitem {rules}, \hyperpage{226} + \subitem {rules\_deleted}, \hyperpage{227} + \subitem {size}, \hyperpage{225} \item {predict} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{171} \item {predict\_backend} - \subitem {Geese}, \hyperpage{170} + \subitem {Geese}, \hyperpage{172} \item {predict\_exhaust} - \subitem {Geese}, \hyperpage{170} + \subitem {Geese}, \hyperpage{172} \item {predict\_exhaust\_backend} - \subitem {Geese}, \hyperpage{170} + \subitem {Geese}, \hyperpage{172} \item {predict\_sim} - \subitem {Geese}, \hyperpage{170} + \subitem {Geese}, \hyperpage{172} \item {print} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{91} - \subitem {DEFM}, \hyperpage{143} - \subitem {Flock}, \hyperpage{155} - \subitem {FreqTable$<$ T $>$}, \hyperpage{159} - \subitem {Geese}, \hyperpage{170} + \hyperpage{93} + \subitem {DEFM}, \hyperpage{145} + \subitem {Flock}, \hyperpage{157} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} + \subitem {Geese}, \hyperpage{172} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{190} - \subitem {Phylo rules}, \hyperpage{42} + \hyperpage{192} + \subitem {Phylo rules}, \hyperpage{43} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{246} \item {print\_n} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \item {print\_nodes} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{173} \item {print\_observed\_counts} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{173} \item {print\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{190} + \hyperpage{192} \item {printf\_barry} - \subitem {barry-\/configuration.hpp}, \hyperpage{271} + \subitem {barry-\/configuration.hpp}, \hyperpage{273} \item {probability} - \subitem {Node}, \hyperpage{211} - \item {Progress}, \hyperpage{225} - \subitem {$\sim$Progress}, \hyperpage{226} - \subitem {end}, \hyperpage{226} - \subitem {next}, \hyperpage{226} - \subitem {Progress}, \hyperpage{225} + \subitem {Node}, \hyperpage{213} + \item {Progress}, \hyperpage{227} + \subitem {$\sim$Progress}, \hyperpage{228} + \subitem {end}, \hyperpage{228} + \subitem {next}, \hyperpage{228} + \subitem {Progress}, \hyperpage{227} \item {progress.hpp} - \subitem {BARRY\_PROGRESS\_BAR\_WIDTH}, \hyperpage{333} + \subitem {BARRY\_PROGRESS\_BAR\_WIDTH}, \hyperpage{335} \item {pset\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{199} \item {pset\_loc} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{175} \item {pset\_locations} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{199} \item {pset\_loop} - \subitem {geese-\/meat-\/likelihood.hpp}, \hyperpage{323} + \subitem {geese-\/meat-\/likelihood.hpp}, \hyperpage{325} \item {pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{199} \item {pset\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{200} \item {pset\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{200} \item {push\_back} - \subitem {PhyloCounterData}, \hyperpage{216} + \subitem {PhyloCounterData}, \hyperpage{218} \indexspace - \item {README.md}, \hyperpage{347} + \item {README.md}, \hyperpage{349} \item {reduced\_sequence} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{176} \item {rengine} - \subitem {Flock}, \hyperpage{156} + \subitem {Flock}, \hyperpage{158} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{200} \item {res} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{292} \item {reserve} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{91} - \subitem {FreqTable$<$ T $>$}, \hyperpage{159} - \subitem {PhyloCounterData}, \hyperpage{216} + \hyperpage{93} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} + \subitem {PhyloCounterData}, \hyperpage{218} \item {reset} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{225} \item {reset\_array} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{236} + \hyperpage{238} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{246} \item {resize} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{92} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} - \subitem {statscounter-\/meat.hpp}, \hyperpage{337} + \hyperpage{94} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \item {return} - \subitem {counters-\/meat.hpp}, \hyperpage{291} - \subitem {statscounter-\/meat.hpp}, \hyperpage{340} + \subitem {counters-\/meat.hpp}, \hyperpage{293} + \subitem {statscounter-\/meat.hpp}, \hyperpage{342} \item {rhs} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} \item {rm\_cell} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{92} + \hyperpage{94} \item {ROW} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253} - \subitem {barray-\/meat.hpp}, \hyperpage{257} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260} - \subitem {barraydense-\/meat.hpp}, \hyperpage{263} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} + \subitem {barray-\/meat.hpp}, \hyperpage{259} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262} + \subitem {barraydense-\/meat.hpp}, \hyperpage{265} \item {row} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{92} + \hyperpage{94} \item {Row\_type} - \subitem {typedefs.hpp}, \hyperpage{345} + \subitem {typedefs.hpp}, \hyperpage{347} \item {rowsum} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{92} + \hyperpage{94} \item {Rule} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{227} - \item {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{226} - \subitem {$\sim$Rule}, \hyperpage{227} - \subitem {D}, \hyperpage{228} - \subitem {get\_description}, \hyperpage{228} - \subitem {get\_name}, \hyperpage{228} - \subitem {operator()}, \hyperpage{229} - \subitem {Rule}, \hyperpage{227} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} + \item {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} + \subitem {$\sim$Rule}, \hyperpage{229} + \subitem {D}, \hyperpage{230} + \subitem {get\_description}, \hyperpage{230} + \subitem {get\_name}, \hyperpage{230} + \subitem {operator()}, \hyperpage{231} + \subitem {Rule}, \hyperpage{229} \item {rule\_dyn\_limit\_changes} - \subitem {Phylo rules}, \hyperpage{42} + \subitem {Phylo rules}, \hyperpage{43} \item {rule\_fun\_default} - \subitem {rules-\/bones.hpp}, \hyperpage{333} + \subitem {rules-\/bones.hpp}, \hyperpage{335} \item {Rule\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{345} + \subitem {typedefs.hpp}, \hyperpage{347} \item {RULE\_FUNCTION} - \subitem {barry.hpp}, \hyperpage{277} - \subitem {geese-\/bones.hpp}, \hyperpage{321} + \subitem {barry.hpp}, \hyperpage{279} + \subitem {geese-\/bones.hpp}, \hyperpage{323} \item {RULE\_LAMBDA} - \subitem {barry.hpp}, \hyperpage{277} + \subitem {barry.hpp}, \hyperpage{279} \item {rule\_leafs} \subitem {Phylo rules}, \hyperpage{43} \item {Rules} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \item {rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{200} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} - \item {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} - \subitem {$\sim$Rules}, \hyperpage{230} - \subitem {add\_rule}, \hyperpage{231} - \subitem {begin}, \hyperpage{231} - \subitem {end}, \hyperpage{231} - \subitem {get\_descriptions}, \hyperpage{231} - \subitem {get\_names}, \hyperpage{232} - \subitem {get\_seq}, \hyperpage{232} - \subitem {operator()}, \hyperpage{232} - \subitem {operator=}, \hyperpage{233} - \subitem {Rules}, \hyperpage{230} - \subitem {size}, \hyperpage{233} + \hyperpage{226} + \item {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} + \subitem {$\sim$Rules}, \hyperpage{232} + \subitem {add\_rule}, \hyperpage{233} + \subitem {begin}, \hyperpage{233} + \subitem {end}, \hyperpage{233} + \subitem {get\_descriptions}, \hyperpage{233} + \subitem {get\_names}, \hyperpage{234} + \subitem {get\_seq}, \hyperpage{234} + \subitem {operator()}, \hyperpage{234} + \subitem {operator=}, \hyperpage{235} + \subitem {Rules}, \hyperpage{232} + \subitem {size}, \hyperpage{235} \item {rules-\/bones.hpp} - \subitem {rule\_fun\_default}, \hyperpage{333} + \subitem {rule\_fun\_default}, \hyperpage{335} \item {rules\_deleted} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} + \hyperpage{227} \item {rules\_dont\_become\_zero} - \subitem {Network counters}, \hyperpage{34} + \subitem {Network counters}, \hyperpage{35} \item {rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{201} \item {rules\_markov\_fixed} \subitem {Network counters}, \hyperpage{35} \item {rules\_zerodiag} - \subitem {network.hpp}, \hyperpage{306} + \subitem {network.hpp}, \hyperpage{308} \indexspace \item {sample} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{190, 191} + \hyperpage{192, 193} \item {sequence} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{176} \item {set\_counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{193} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{237} + \hyperpage{239} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{246} \item {set\_data} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{93} + \hyperpage{95} \item {set\_hasher} - \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} + \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} \item {set\_names} - \subitem {DEFM}, \hyperpage{143} + \subitem {DEFM}, \hyperpage{145} \item {set\_rengine} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{193} \item {set\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{193} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{247} \item {set\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} + \hyperpage{194} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{247} \item {set\_seed} - \subitem {Flock}, \hyperpage{155} - \subitem {Geese}, \hyperpage{171} + \subitem {Flock}, \hyperpage{157} + \subitem {Geese}, \hyperpage{173} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} + \hyperpage{194} \item {set\_transform\_model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} + \hyperpage{194} \item {shrink\_to\_fit} - \subitem {PhyloCounterData}, \hyperpage{216} + \subitem {PhyloCounterData}, \hyperpage{218} \item {simulate} - \subitem {DEFM}, \hyperpage{143} - \subitem {Geese}, \hyperpage{171} + \subitem {DEFM}, \hyperpage{145} + \subitem {Geese}, \hyperpage{173} \item {size} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{101} + \hyperpage{103} \subitem {BArrayDenseCol\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{104} - \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{106} - \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, + \subitem {BArrayDenseRow$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{108} + \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, + \hyperpage{110} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{117} + \hyperpage{119} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{121} - \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} - \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \hyperpage{123} + \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{140} + \subitem {FreqTable$<$ T $>$}, \hyperpage{162} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} - \subitem {PhyloCounterData}, \hyperpage{216} + \hyperpage{195} + \subitem {PhyloCounterData}, \hyperpage{218} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \hyperpage{225} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{235} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{237} + \hyperpage{239} \item {size\_unique} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{195} \item {sort\_array} - \subitem {typedefs.hpp}, \hyperpage{345} + \subitem {typedefs.hpp}, \hyperpage{347} \item {source} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} \item {states} - \subitem {NodeData}, \hyperpage{213} + \subitem {NodeData}, \hyperpage{215} \item {Statistical Models}, \hyperpage{24} \item {stats\_likelihood} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{201} \item {stats\_support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{201} \item {stats\_support\_n\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{201} \item {stats\_support\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{202} \item {stats\_support\_sizes\_acc} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{202} \item {stats\_target} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{202} \item {StatsCounter} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{234, 235} - \item {StatsCounter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} - \subitem {$\sim$StatsCounter}, \hyperpage{235} - \subitem {add\_counter}, \hyperpage{235} - \subitem {count\_all}, \hyperpage{235} - \subitem {count\_current}, \hyperpage{236} - \subitem {count\_init}, \hyperpage{236} - \subitem {get\_counters}, \hyperpage{236} - \subitem {get\_descriptions}, \hyperpage{236} - \subitem {get\_names}, \hyperpage{236} - \subitem {reset\_array}, \hyperpage{236} - \subitem {set\_counters}, \hyperpage{237} - \subitem {size}, \hyperpage{237} - \subitem {StatsCounter}, \hyperpage{234, 235} + \hyperpage{236, 237} + \item {StatsCounter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{235} + \subitem {$\sim$StatsCounter}, \hyperpage{237} + \subitem {add\_counter}, \hyperpage{237} + \subitem {count\_all}, \hyperpage{237} + \subitem {count\_current}, \hyperpage{238} + \subitem {count\_init}, \hyperpage{238} + \subitem {get\_counters}, \hyperpage{238} + \subitem {get\_descriptions}, \hyperpage{238} + \subitem {get\_names}, \hyperpage{238} + \subitem {reset\_array}, \hyperpage{238} + \subitem {set\_counters}, \hyperpage{239} + \subitem {size}, \hyperpage{239} + \subitem {StatsCounter}, \hyperpage{236, 237} \item {statscounter-\/meat.hpp} - \subitem {clear}, \hyperpage{336} - \subitem {counter}, \hyperpage{338} - \subitem {counter\_deleted}, \hyperpage{339} - \subitem {counters}, \hyperpage{339} - \subitem {counters\_}, \hyperpage{339} - \subitem {current\_stats}, \hyperpage{339} - \subitem {EmptyArray}, \hyperpage{339} - \subitem {f\_}, \hyperpage{340} - \subitem {for}, \hyperpage{336} - \subitem {j}, \hyperpage{340} - \subitem {resize}, \hyperpage{337} - \subitem {return}, \hyperpage{340} - \subitem {STATSCOUNTER\_TEMPLATE}, \hyperpage{336--338} - \subitem {STATSCOUNTER\_TEMPLATE\_ARGS}, \hyperpage{336} - \subitem {STATSCOUNTER\_TYPE}, \hyperpage{336} + \subitem {clear}, \hyperpage{338} + \subitem {counter}, \hyperpage{340} + \subitem {counter\_deleted}, \hyperpage{341} + \subitem {counters}, \hyperpage{341} + \subitem {counters\_}, \hyperpage{341} + \subitem {current\_stats}, \hyperpage{341} + \subitem {EmptyArray}, \hyperpage{341} + \subitem {f\_}, \hyperpage{342} + \subitem {for}, \hyperpage{338} + \subitem {j}, \hyperpage{342} + \subitem {resize}, \hyperpage{339} + \subitem {return}, \hyperpage{342} + \subitem {STATSCOUNTER\_TEMPLATE}, \hyperpage{338--340} + \subitem {STATSCOUNTER\_TEMPLATE\_ARGS}, \hyperpage{338} + \subitem {STATSCOUNTER\_TYPE}, \hyperpage{338} \item {STATSCOUNTER\_TEMPLATE} - \subitem {statscounter-\/meat.hpp}, \hyperpage{336--338} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338--340} \item {STATSCOUNTER\_TEMPLATE\_ARGS} - \subitem {statscounter-\/meat.hpp}, \hyperpage{336} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338} \item {STATSCOUNTER\_TYPE} - \subitem {statscounter-\/meat.hpp}, \hyperpage{336} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338} \item {store\_psets} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{195} \item {subtree\_prob} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{213} \item {Support} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{239, 240} + \hyperpage{241, 242} \item {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{237} - \subitem {$\sim$Support}, \hyperpage{240} - \subitem {add\_counter}, \hyperpage{240} - \subitem {add\_rule}, \hyperpage{240, 241} - \subitem {add\_rule\_dyn}, \hyperpage{241} - \subitem {calc}, \hyperpage{241} - \subitem {change\_stats}, \hyperpage{245} - \subitem {coordiantes\_n\_free}, \hyperpage{245} - \subitem {coordiantes\_n\_locked}, \hyperpage{246} - \subitem {coordinates\_free}, \hyperpage{246} - \subitem {coordinates\_locked}, \hyperpage{246} - \subitem {current\_stats}, \hyperpage{246} - \subitem {delete\_counters}, \hyperpage{246} - \subitem {delete\_rules}, \hyperpage{247} - \subitem {delete\_rules\_dyn}, \hyperpage{247} - \subitem {eval\_rules\_dyn}, \hyperpage{242} - \subitem {get\_counters}, \hyperpage{242} - \subitem {get\_counts}, \hyperpage{242} - \subitem {get\_current\_stats}, \hyperpage{242} - \subitem {get\_data}, \hyperpage{243} - \subitem {get\_rules}, \hyperpage{243} - \subitem {get\_rules\_dyn}, \hyperpage{243} - \subitem {hashes}, \hyperpage{247} - \subitem {hashes\_initialized}, \hyperpage{247} - \subitem {init\_support}, \hyperpage{243} - \subitem {M}, \hyperpage{247} - \subitem {max\_num\_elements}, \hyperpage{248} - \subitem {N}, \hyperpage{248} - \subitem {n\_counters}, \hyperpage{248} - \subitem {print}, \hyperpage{244} - \subitem {reset\_array}, \hyperpage{244} - \subitem {set\_counters}, \hyperpage{244} - \subitem {set\_rules}, \hyperpage{245} - \subitem {set\_rules\_dyn}, \hyperpage{245} - \subitem {Support}, \hyperpage{239, 240} + \hyperpage{239} + \subitem {$\sim$Support}, \hyperpage{242} + \subitem {add\_counter}, \hyperpage{242} + \subitem {add\_rule}, \hyperpage{242, 243} + \subitem {add\_rule\_dyn}, \hyperpage{243} + \subitem {calc}, \hyperpage{243} + \subitem {change\_stats}, \hyperpage{247} + \subitem {coordiantes\_n\_free}, \hyperpage{247} + \subitem {coordiantes\_n\_locked}, \hyperpage{248} + \subitem {coordinates\_free}, \hyperpage{248} + \subitem {coordinates\_locked}, \hyperpage{248} + \subitem {current\_stats}, \hyperpage{248} + \subitem {delete\_counters}, \hyperpage{248} + \subitem {delete\_rules}, \hyperpage{249} + \subitem {delete\_rules\_dyn}, \hyperpage{249} + \subitem {eval\_rules\_dyn}, \hyperpage{244} + \subitem {get\_counters}, \hyperpage{244} + \subitem {get\_counts}, \hyperpage{244} + \subitem {get\_current\_stats}, \hyperpage{244} + \subitem {get\_data}, \hyperpage{245} + \subitem {get\_rules}, \hyperpage{245} + \subitem {get\_rules\_dyn}, \hyperpage{245} + \subitem {hashes}, \hyperpage{249} + \subitem {hashes\_initialized}, \hyperpage{249} + \subitem {init\_support}, \hyperpage{245} + \subitem {M}, \hyperpage{249} + \subitem {max\_num\_elements}, \hyperpage{250} + \subitem {N}, \hyperpage{250} + \subitem {n\_counters}, \hyperpage{250} + \subitem {print}, \hyperpage{246} + \subitem {reset\_array}, \hyperpage{246} + \subitem {set\_counters}, \hyperpage{246} + \subitem {set\_rules}, \hyperpage{247} + \subitem {set\_rules\_dyn}, \hyperpage{247} + \subitem {Support}, \hyperpage{241, 242} \item {support-\/meat.hpp} - \subitem {BARRY\_SUPPORT\_MEAT\_HPP}, \hyperpage{341} + \subitem {BARRY\_SUPPORT\_MEAT\_HPP}, \hyperpage{343} \item {support\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{202} \item {support\_size} - \subitem {Flock}, \hyperpage{155} - \subitem {Geese}, \hyperpage{171} + \subitem {Flock}, \hyperpage{157} + \subitem {Geese}, \hyperpage{173} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{195} \item {swap\_cells} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{93} + \hyperpage{95} \item {swap\_cols} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{93} + \hyperpage{95} \item {swap\_rows} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{93} + \hyperpage{95} \indexspace \item {target} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} \item {this} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{256} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{258} \item {TMP\_HASHER\_CALL} - \subitem {counters-\/meat.hpp}, \hyperpage{281} + \subitem {counters-\/meat.hpp}, \hyperpage{283} \item {toggle\_cell} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{94} + \hyperpage{96} \item {toggle\_lock} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{94} + \hyperpage{96} \item {transform\_model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{195} \item {transform\_model\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{203} \item {transform\_model\_term\_names} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{203} \item {transpose} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{94} + \hyperpage{96} \item {TWO} - \subitem {CHECK}, \hyperpage{56} - \subitem {EXISTS}, \hyperpage{58} + \subitem {CHECK}, \hyperpage{58} + \subitem {EXISTS}, \hyperpage{60} \item {typedefs.hpp} - \subitem {Col\_type}, \hyperpage{344} - \subitem {Counter\_fun\_type}, \hyperpage{344} - \subitem {Counts\_type}, \hyperpage{344} - \subitem {Hasher\_fun\_type}, \hyperpage{344} - \subitem {MapVec\_type}, \hyperpage{345} - \subitem {Row\_type}, \hyperpage{345} - \subitem {Rule\_fun\_type}, \hyperpage{345} - \subitem {sort\_array}, \hyperpage{345} - \subitem {vec\_equal}, \hyperpage{346} - \subitem {vec\_equal\_approx}, \hyperpage{346} - \subitem {vec\_inner\_prod}, \hyperpage{346, 347} + \subitem {Col\_type}, \hyperpage{346} + \subitem {Counter\_fun\_type}, \hyperpage{346} + \subitem {Counts\_type}, \hyperpage{346} + \subitem {Hasher\_fun\_type}, \hyperpage{346} + \subitem {MapVec\_type}, \hyperpage{347} + \subitem {Row\_type}, \hyperpage{347} + \subitem {Rule\_fun\_type}, \hyperpage{347} + \subitem {sort\_array}, \hyperpage{347} + \subitem {vec\_equal}, \hyperpage{348} + \subitem {vec\_equal\_approx}, \hyperpage{348} + \subitem {vec\_inner\_prod}, \hyperpage{348, 349} \indexspace \item {ub} - \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {PhyloRuleDynData}, \hyperpage{220} \item {UKNOWN} - \subitem {EXISTS}, \hyperpage{58} + \subitem {EXISTS}, \hyperpage{60} \item {UNI\_SUB} - \subitem {counters.hpp}, \hyperpage{312} + \subitem {counters.hpp}, \hyperpage{314} \item {update\_annotations} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{173} \item {update\_likelihoods} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{196} \item {update\_normalizing\_constant} - \subitem {model-\/meat.hpp}, \hyperpage{308} + \subitem {model-\/meat.hpp}, \hyperpage{310} \item {update\_normalizing\_constants} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{196} \item {update\_pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{196} \indexspace \item {val} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} \item {value} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {vec\_diff} - \subitem {geese-\/bones.hpp}, \hyperpage{321} + \subitem {geese-\/bones.hpp}, \hyperpage{323} \item {vec\_equal} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{348} \item {vec\_equal\_approx} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{348} \item {vec\_inner\_prod} - \subitem {typedefs.hpp}, \hyperpage{346, 347} - \item {vecHasher$<$ T $>$}, \hyperpage{248} - \subitem {operator()}, \hyperpage{249} + \subitem {typedefs.hpp}, \hyperpage{348, 349} + \item {vecHasher$<$ T $>$}, \hyperpage{250} + \subitem {operator()}, \hyperpage{251} \item {vector\_caster} - \subitem {geese-\/bones.hpp}, \hyperpage{322} + \subitem {geese-\/bones.hpp}, \hyperpage{324} \item {vertex\_attr} - \subitem {NetworkData}, \hyperpage{205} + \subitem {NetworkData}, \hyperpage{207} \item {visited} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{96} - \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125} - \subitem {Node}, \hyperpage{211} + \hyperpage{98} + \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} + \subitem {Node}, \hyperpage{213} \indexspace \item {with\_pset} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{203} \indexspace \item {X\_ncol} \subitem {Phylo rules}, \hyperpage{46} \item {X\_nrow} - \subitem {Phylo rules}, \hyperpage{46} + \subitem {Phylo rules}, \hyperpage{47} \indexspace \item {ZERO\_CELL} - \subitem {barraydense-\/meat.hpp}, \hyperpage{263} - \subitem {barraydensecol-\/bones.hpp}, \hyperpage{266} - \subitem {barraydenserow-\/bones.hpp}, \hyperpage{267} + \subitem {barraydense-\/meat.hpp}, \hyperpage{265} + \subitem {barraydensecol-\/bones.hpp}, \hyperpage{268} + \subitem {barraydenserow-\/bones.hpp}, \hyperpage{269} \item {zero\_col} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{94} + \hyperpage{96} \item {zero\_row} - \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} + \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, - \hyperpage{94} + \hyperpage{96} \end{theindex} diff --git a/latex/refman.log b/latex/refman.log index 7084e4e4f..6497cbbf9 100644 --- a/latex/refman.log +++ b/latex/refman.log @@ -1,4 +1,4 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Alpine Linux) (preloaded format=pdflatex 2023.10.25) 25 OCT 2023 22:41 +This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Alpine Linux) (preloaded format=pdflatex 2023.11.1) 1 NOV 2023 23:08 entering extended mode restricted \write18 enabled. %&-line parsing enabled. @@ -1176,7 +1176,7 @@ LaTeX Font Info: Font shape `T1/pcr/m/it' in size <8> not available (Font) Font shape `T1/pcr/m/sl' tried instead on input line 167. [16] LaTeX Font Info: Font shape `T1/pcr/m/it' in size <7> not available -(Font) Font shape `T1/pcr/m/sl' tried instead on input line 280. +(Font) Font shape `T1/pcr/m/sl' tried instead on input line 287. [17] [18] [19] [20] [21] [22] [23]) (./group__stat-models.tex) (./group__counters-network.tex [24] [25] [26] LaTeX Font Info: Font shape `T1/phv/b/n' will be @@ -1185,18 +1185,18 @@ LaTeX Font Info: Font shape `T1/phv/b/n' will be Overfull \vbox (5.5016pt too high) has occurred while \output is active [] -[28] [29] [30] [31] [32] [33] [34]) (./group__rules-phylo.tex <./group__rules-p -hylo.pdf +[28] [29] [30] [31] [32] [33] [34]) (./group__rules-phylo.tex [35] <./group__ru +les-phylo.pdf pdfTeX warning: pdflatex (file ./group__rules-phylo.pdf): PDF inclusion: multip le pdfs with page group included in a single page > - + File: group__rules-phylo.pdf Graphic file (type pdf) Package pdftex.def Info: group__rules-phylo.pdf used on input line 13. (pdftex.def) Requested size: 260.0pt x 99.00102pt. - [35] + Underfull \hbox (badness 5147) in paragraph at lines 70--71 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 support, size []_[]t pos, size[]_[]t lb, size[]_[]t ub, size[]_[] @@ -1214,32 +1214,32 @@ Underfull \hbox (badness 10000) in paragraph at lines 118--120 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[37] [38] +[37] [38] [39] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 covariates[] [] -[39] [40] [41] +[40] [41] [42] Underfull \hbox (badness 10000) detected at line 434 [][][] [] -[42] + Underfull \hbox (badness 10000) detected at line 472 [][][] [] -[43] [44] [45]) (./group__counters-phylo.tex <./group__counters-phylo.pdf +[43] [44] [45] [46]) (./group__counters-phylo.tex <./group__counters-phylo.pdf pdfTeX warning: pdflatex (file ./group__counters-phylo.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page > - + File: group__counters-phylo.pdf Graphic file (type pdf) Package pdftex.def Info: group__counters-phylo.pdf used on input line 13. (pdftex.def) Requested size: 260.0pt x 99.00102pt. - [46] + Overfull \hbox (23.90007pt too wide) in paragraph at lines 25--26 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$[]\T1/phv/m/n/10 , std[]::ve ctor$\OML/cmm/m/it/10 <$ \T1/phv/m/n/10 size[]_[]t $\OML/cmm/m/it/10 >$ \T1/phv @@ -1259,7 +1259,7 @@ ctor$\OML/cmm/m/it/10 <$ \T1/phv/m/n/10 size[]_[]t $\OML/cmm/m/it/10 >$ \T1/phv /m/n/10 nfun, size[]_[]t duplication=[]) [] - +[47] Overfull \hbox (27.65639pt too wide) in paragraph at lines 43--44 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$[]\T1/phv/m/n/10 , size[]_[] t nfunA, size[]_[]t nfunB, size[]_[]t duplication=[]) @@ -1295,7 +1295,7 @@ Overfull \hbox (27.65639pt too wide) in paragraph at lines 55--56 t nfunA, size[]_[]t nfunB, size[]_[]t duplication=[]) [] -[47] + Overfull \hbox (74.95236pt too wide) in paragraph at lines 59--60 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$[]\T1/phv/m/n/10 , dou-ble p , size[]_[]t duplication=[]) @@ -1320,15 +1320,15 @@ Underfull \hbox (badness 7576) in paragraph at lines 69--70 t nfunA, size[]_[]t nfunB, size[]_[] [] -pdfTeX warning (ext4): destination with the same identifier (name{group__counti -ng_ga39768a8cbb21e6b775c382568a4f98f9}) has been already used, duplicate ignore -d +[48]pdfTeX warning (ext4): destination with the same identifier (name{group__co +unting_ga39768a8cbb21e6b775c382568a4f98f9}) has been already used, duplicate ig +nored \relax l.84 ...nting_ga39768a8cbb21e6b775c382568a4f98f9}} - [48]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_ga9d57bfb85ca8ab5a943 -e46b461e42aea}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_ga9d57bfb85ca8ab5a943e46b4 +61e42aea}) has been already used, duplicate ignored \relax l.98 ...nting_ga9d57bfb85ca8ab5a943e46b461e42aea}} @@ -1344,9 +1344,9 @@ d2f99d52}) has been already used, duplicate ignored \relax l.126 ...ting_ga8f28f78a8170fcd27f8888bfd2f99d52}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_gac5bf2141645db356fbd1333d -56ce8444}) has been already used, duplicate ignored + [49]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_gac5bf2141645db356fbd +1333d56ce8444}) has been already used, duplicate ignored \relax l.140 ...ting_gac5bf2141645db356fbd1333d56ce8444}} @@ -1356,9 +1356,9 @@ ation with the same identifier (name{group__counting_ga347aabd9065d9ff8352e58fb \relax l.154 ...ting_ga347aabd9065d9ff8352e58fb282b8fd2}} - [49]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_ga1f7678ddbb9f9084cb5 -fe1c79f205558}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_ga1f7678ddbb9f9084cb5fe1c7 +9f205558}) has been already used, duplicate ignored \relax l.168 ...ting_ga1f7678ddbb9f9084cb5fe1c79f205558}} @@ -1374,15 +1374,15 @@ ation with the same identifier (name{group__counting_gac356c5c159d2f37088b162ed \relax l.196 ...ting_gac356c5c159d2f37088b162ed04c362ad}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_ga6de412cdee1ec990e62edcb2 -9c118824}) has been already used, duplicate ignored + [50]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_ga6de412cdee1ec990e62 +edcb29c118824}) has been already used, duplicate ignored \relax l.210 ...ting_ga6de412cdee1ec990e62edcb29c118824}} - [50]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_gae0453a90fb7c8668a68 -45fe850477cc7}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_gae0453a90fb7c8668a6845fe8 +50477cc7}) has been already used, duplicate ignored \relax l.224 ...ting_gae0453a90fb7c8668a6845fe850477cc7}} @@ -1416,9 +1416,9 @@ acfc656c}) has been already used, duplicate ignored \relax l.294 ...ting_gac2eb4b7941b56f783eff66f5acfc656c}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_ga8f65b1cc27fb2f27eb5525b5 -b36c19f8}) has been already used, duplicate ignored + [52]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_ga8f65b1cc27fb2f27eb5 +525b5b36c19f8}) has been already used, duplicate ignored \relax l.308 ...ting_ga8f65b1cc27fb2f27eb5525b5b36c19f8}} @@ -1428,9 +1428,9 @@ ation with the same identifier (name{group__counting_gaf3bb2dd1c9db36df1d010cc6 \relax l.322 ...ting_gaf3bb2dd1c9db36df1d010cc691573243}} - [52]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_gaa7de3c183a65a0701cb -ce03545421c7d}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_gaa7de3c183a65a0701cbce035 +45421c7d}) has been already used, duplicate ignored \relax l.336 ...ting_gaa7de3c183a65a0701cbce03545421c7d}} @@ -1464,14 +1464,14 @@ ation with the same identifier (name{group__counting_ga23c694532337cb12a77a64f3 \relax l.406 ...ting_ga23c694532337cb12a77a64f3202a14cf}} - ) [54] + ) [54] [55] [56 + +] Chapter 7. (./namespacebarry.tex) (./namespacebarry_1_1counters.tex) (./namespacebarry_1_1counters_1_1network.tex) (./namespace_c_h_e_c_k.tex -[55 - -]) (./namespacedefm.tex) (./namespace_e_x_i_s_t_s.tex [56] [57]) -(./namespacegeese.tex) [58] +[57]) (./namespacedefm.tex) (./namespace_e_x_i_s_t_s.tex [58] [59]) +(./namespacegeese.tex) [60] Chapter 8. (./class_b_array.tex @@ -1494,9 +1494,9 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Overfull \vbox (29.19507pt too high) has occurred while \output is active [] -[59 +[61 -] [60] +] [62] Underfull \hbox (badness 1082) in paragraph at lines 149--151 []\T1/phv/m/n/10 void [] (size[]_[]t i0, size[]_[]t j0, size[]_[]t i1, size[]_[ ]t j1, bool check[]_[]bounds=true, int check[]_[] @@ -1508,12 +1508,12 @@ LaTeX Font Info: Font shape `T1/phv/bc/n' will be Overfull \vbox (7.14642pt too high) has occurred while \output is active [] -[61] [62] [63] [64] +[63] [64] [65] [66] Underfull \hbox (badness 10000) detected at line 394 [][][] [] -[65] [66] [67] [68] [69] [70] [71] [72]) (./class_b_array_cell.tex +[67] [68] [69] [70] [71] [72] [73] [74]) (./class_b_array_cell.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1530,7 +1530,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[73] [74] [75]) (./class_b_array_cell__const.tex +[75] [76] [77]) (./class_b_array_cell__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1547,7 +1547,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[76] [77]) (./class_b_array_dense.tex +[78] [79]) (./class_b_array_dense.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1564,18 +1564,18 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[78] [79] +[80] [81] Underfull \hbox (badness 1082) in paragraph at lines 155--157 []\T1/phv/m/n/10 void [] (size[]_[]t i0, size[]_[]t j0, size[]_[]t i1, size[]_[ ]t j1, bool check[]_[]bounds=true, int check[]_[] [] -[80] [81] [82] [83] [84] [85] +[82] [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) detected at line 492 [][][] [] -[86] [87] [88] [89] [90] [91] [92] [93] [94] [95]) +[88] [89] [90] [91] [92] [93] [94] [95] [96] [97]) (./class_b_array_dense_cell.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): @@ -1593,14 +1593,14 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[96] [97] +[98] [99] Underfull \hbox (badness 10000) in paragraph at lines 136--138 []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type, Data[]_[][]Type $\OML/cmm/ m/it/8 >$ \T1/pcr/m/n/8 & []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type, Data[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::operator= [] -[98]) (./class_b_array_dense_cell__const.tex +[100]) (./class_b_array_dense_cell__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1617,7 +1617,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[99]) (./class_b_array_dense_col.tex +[101]) (./class_b_array_dense_col.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1634,7 +1634,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[100] [101]) (./class_b_array_dense_col__const.tex +[102] [103]) (./class_b_array_dense_col__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1651,7 +1651,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[102] [103]) (./class_b_array_dense_row.tex +[104] [105]) (./class_b_array_dense_row.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1668,7 +1668,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[104] [105]) (./class_b_array_dense_row__const.tex +[106] [107]) (./class_b_array_dense_row__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1685,14 +1685,14 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[106] +[108] Underfull \hbox (badness 10000) in paragraph at lines 58--60 []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pc r/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Typ e, Data[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::begin ( ) [] -[107] +[109] Underfull \hbox (badness 10000) in paragraph at lines 69--71 []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pc r/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Typ @@ -1706,7 +1706,7 @@ OML/cmm/m/it/8 <$\T1/pcr/m/n/8 Cell[]_[][]Type$\OML/cmm/m/it/8 >$ $>$ []$<$ \T1 /pcr/m/n/8 Cell[]_[][]Type, Data[]_[][]Type $\OML/cmm/m/it/8 >$[] [] -[108]) (./class_b_array_row.tex +[110]) (./class_b_array_row.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1723,7 +1723,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[109] [110]) (./class_b_array_row__const.tex +[111] [112]) (./class_b_array_row__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1740,14 +1740,14 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[111] +[113] Underfull \hbox (badness 10000) in paragraph at lines 70--72 []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type, Data[]_[][]Type $\OML/cmm/ m/it/8 >$[]\T1/pcr/m/n/8 ::operator []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_ [][]Type, Data[]_[][]Type $\OML/cmm/m/it/8 >$ \T1/pcr/m/n/8 ( ) [] -[112]) (./class_b_array_vector.tex +[114]) (./class_b_array_vector.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1764,11 +1764,11 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[113] +[115] Overfull \vbox (46.09114pt too high) has occurred while \output is active [] -[114] +[116] Underfull \hbox (badness 10000) in paragraph at lines 120--122 \T1/pcr/m/n/8 std[]::vector$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type $\ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 @@ -1776,7 +1776,7 @@ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 ::end [inline], [] -[115] [116]) (./class_b_array_vector__const.tex +[117] [118]) (./class_b_array_vector__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1793,7 +1793,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[117] +[119] Underfull \hbox (badness 10000) in paragraph at lines 80--82 \T1/pcr/m/n/8 std[]::vector$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type $\ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 @@ -1801,7 +1801,7 @@ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 ::begin ( [] -[118] +[120] Underfull \hbox (badness 10000) in paragraph at lines 87--89 \T1/pcr/m/n/8 std[]::vector$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Cell[]_[][]Type $\ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 @@ -1809,7 +1809,7 @@ OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::const[]_[]iterator []$\OML/cmm/m/it/8 <$ \T1 ::end ( ) [] -[119] [120]) (./class_cell.tex +[121] [122]) (./class_cell.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1826,7 +1826,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[121] [122] [123] [124]) (./class_cell__const.tex +[123] [124] [125] [126]) (./class_cell__const.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1843,7 +1843,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[125]) (./class_const_b_array_row_iter.tex +[127]) (./class_const_b_array_row_iter.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1865,14 +1865,14 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): pdfTeX warning: pdflatex (file ./class_const_b_array_row_iter__coll__graph.pdf) : PDF inclusion: multiple pdfs with page group included in a single page > - File: class_const_b_array_row_iter__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_const_b_array_row_iter__coll__graph.pdf used on input line 14. (pdftex.def) Requested size: 208.0pt x 189.01065pt. - [126] [127]) (./class_counter.tex + [128] [129]) (./class_counter.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1889,7 +1889,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[128] [129] [130] [131] [132]) (./class_counters.tex +[130] [131] [132] [133] [134]) (./class_counters.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -1906,7 +1906,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[133] [134] +[135] [136] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 counter[] [] @@ -1916,12 +1916,12 @@ Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 counters[] [] -[135] +[137] Underfull \hbox (badness 10000) detected at line 150 [][][] [] -[136] +[138] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 counter[] [] @@ -1936,7 +1936,7 @@ Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 counter[] [] -[137] +[139] Underfull \hbox (badness 10000) detected at line 202 [][][] [] @@ -1956,51 +1956,51 @@ Underfull \hbox (badness 10000) detected at line 235 pdfTeX warning: pdflatex (file ./class_d_e_f_m__inherit__graph.pdf): PDF inclus ion: multiple pdfs with page group included in a single page > - + File: class_d_e_f_m__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_d_e_f_m__inherit__graph.pdf used on input line 14. (pdftex.def) Requested size: 150.0pt x 156.01357pt. - [138] <./class_d_e_f_m__coll__graph.pdf + [140] <./class_d_e_f_m__coll__graph.pdf pdfTeX warning: pdflatex (file ./class_d_e_f_m__coll__graph.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: class_d_e_f_m__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_d_e_f_m__coll__graph.pdf used on input line 24. (pdftex.def) Requested size: 150.0pt x 156.01357pt. - [139] [140] [141] [142]) (./class_d_e_f_m_counter_data.tex [143]) -(./class_d_e_f_m_data.tex [144]) (./class_d_e_f_m_rule_data.tex <./class_d_e_f_ + [141] [142] [143] [144]) (./class_d_e_f_m_counter_data.tex [145]) +(./class_d_e_f_m_data.tex [146]) (./class_d_e_f_m_rule_data.tex <./class_d_e_f_ m_rule_data__inherit__graph.pdf pdfTeX warning: pdflatex (file ./class_d_e_f_m_rule_data__inherit__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: class_d_e_f_m_rule_data__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_d_e_f_m_rule_data__inherit__graph.pdf used on i nput line 14. (pdftex.def) Requested size: 180.0pt x 156.00162pt. - [145]) (./class_d_e_f_m_rule_dyn_data.tex <./class_d_e_f_m_rule_dyn_data__inhe + [147]) (./class_d_e_f_m_rule_dyn_data.tex <./class_d_e_f_m_rule_dyn_data__inhe rit__graph.pdf pdfTeX warning: pdflatex (file ./class_d_e_f_m_rule_dyn_data__inherit__graph.pd f): PDF inclusion: multiple pdfs with page group included in a single page > - File: class_d_e_f_m_rule_dyn_data__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_d_e_f_m_rule_dyn_data__inherit__graph.pdf used on input line 14. (pdftex.def) Requested size: 180.0pt x 156.00162pt. - [146] <./class_d_e_f_m_rule_dyn_data__coll__graph.pdf> - + [148] <./class_d_e_f_m_rule_dyn_data__coll__graph.pdf> + File: class_d_e_f_m_rule_dyn_data__coll__graph.pdf Graphic file (type pdf) @@ -2024,29 +2024,29 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[147] [148]) (./class_flock.tex [149] +[149] [150]) (./class_flock.tex [151] Underfull \hbox (badness 1348) in paragraph at lines 35--36 []\T1/phv/m/n/10 double [] (const std[]::vector$\OML/cmm/m/it/10 <$ \T1/phv/m/n /10 dou-ble $\OML/cmm/m/it/10 >$ \T1/phv/m/n/10 &par, bool as[]_[]log=false, bo ol use[]_[]reduced[]_[] [] -[150] [151] +[152] [153] Underfull \hbox (badness 10000) detected at line 130 [][][] [] -[152] +[154] Underfull \hbox (badness 10000) detected at line 226 [][][] [] -[153] [154] +[155] [156] Underfull \hbox (badness 10000) detected at line 300 [][][] [] -[155]) (./class_freq_table.tex +[157]) (./class_freq_table.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -2063,7 +2063,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[156] [157] [158] [159] +[158] [159] [160] [161] Underfull \hbox (badness 10000) detected at line 187 [][][] [] @@ -2073,7 +2073,7 @@ LaTeX Font Info: Font shape `TS1/phv/m/it' in size <9> not available (Font) Font shape `TS1/phv/m/sl' tried instead on input line 48. LaTeX Font Info: Font shape `TS1/phv/m/sl' will be (Font) scaled to size 8.09995pt on input line 48. - [160] [161] + [162] [163] Underfull \hbox (badness 10000) detected at line 127 [][][] [] @@ -2083,17 +2083,17 @@ Underfull \hbox (badness 10000) detected at line 146 [][][] [] -[162] +[164] Underfull \hbox (badness 10000) detected at line 215 [][][] [] -[163] [164] [165] +[165] [166] [167] Underfull \hbox (badness 10000) detected at line 392 [][][] [] -[166] [167] [168] [169] [170] [171] [172] [173]) (./class_model.tex +[168] [169] [170] [171] [172] [173] [174] [175]) (./class_model.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -2115,37 +2115,37 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): pdfTeX warning: pdflatex (file ./class_model__coll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: class_model__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model__coll__graph.pdf used on input line 19. (pdftex.def) Requested size: 350.0pt x 212.75758pt. - [174] + [176] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 22.16548pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. -[175] +[177] Overfull \hbox (18.25592pt too wide) in paragraph at lines 119--120 []\T1/phv/m/n/10 double [] (const std[]::vector$\OML/cmm/m/it/10 <$ \T1/phv/m/n /10 dou-ble $\OML/cmm/m/it/10 >$ \T1/phv/m/n/10 ¶ms, bool as[]_[]log=false, [](=2), [] -[176] +[178] Underfull \hbox (badness 10000) detected at line 148 [][][] [] -[177] +[179] Underfull \hbox (badness 1436) in paragraph at lines 234--235 []\T1/pcr/m/sl/10 stats[]_[]target \T1/phv/m/sl/10 holds the ob-served suf-fi-c ient statis-tics for each ar-ray in the dataset. \T1/pcr/m/sl/10 array[]_[] [] -[178] +[180] LaTeX Font Info: Font shape `T1/phv/m/n' will be (Font) scaled to size 4.49997pt on input line 298. @@ -2155,7 +2155,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[179] +[181] Underfull \hbox (badness 10000) in paragraph at lines 333--335 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2198,7 +2198,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[180] +[182] Underfull \hbox (badness 10000) detected at line 383 [][][] [] @@ -2238,7 +2238,7 @@ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ ][]Type = bool, typename Data[]_[][] [] -[181] +[183] Underfull \hbox (badness 10000) in paragraph at lines 445--447 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2287,7 +2287,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[182] +[184] Underfull \hbox (badness 10000) detected at line 498 [][][] [] @@ -2335,7 +2335,7 @@ Type $\OML/cmm/m/it/8 >$ $\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/ n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[] [] -[183] +[185] Underfull \hbox (badness 10000) in paragraph at lines 542--544 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2400,7 +2400,7 @@ mm/m/it/8 >$ $\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_ ]Rule[]_[][]Dyn[] [] -[184] +[186] Underfull \hbox (badness 10000) in paragraph at lines 597--599 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2473,7 +2473,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 645--647 ]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][]Type [] -[185] +[187] Underfull \hbox (badness 10000) in paragraph at lines 656--658 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2532,7 +2532,7 @@ mm/m/it/8 >$ $\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_ ]Rule[]_[][]Dyn[] [] -[186] +[188] Underfull \hbox (badness 10000) in paragraph at lines 708--710 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2590,7 +2590,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 749--751 n[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::likelihood [] -[187] +[189] Underfull \hbox (badness 10000) in paragraph at lines 760--762 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2639,7 +2639,7 @@ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ ][]Type = bool, typename Data[]_[][] [] -[188] +[190] Underfull \hbox (badness 10000) in paragraph at lines 804--806 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2702,7 +2702,7 @@ ta[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][] Dyn[]_[][]Type $\OML/cmm/m/it/8 >$ [] -[189] +[191] Underfull \hbox (badness 10000) in paragraph at lines 848--850 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2744,7 +2744,7 @@ Type, Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rul e[]_[][]Dyn[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::sample [] -[190] +[192] Underfull \hbox (badness 10000) in paragraph at lines 896--898 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2786,7 +2786,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::set[]_[]rules[]_[]dyn [] -[191] +[193] Underfull \hbox (badness 10000) in paragraph at lines 940--942 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -2804,7 +2804,7 @@ e , typename Overfull \vbox (21.45195pt too high) has occurred while \output is active [] -[192] +[194] Underfull \hbox (badness 10000) in paragraph at lines 979--981 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2888,7 +2888,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::update[]_[] [] -[193] +[195] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -2930,7 +2930,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[194] +[196] Underfull \hbox (badness 10000) in paragraph at lines 1081--1083 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3000,7 +3000,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::delete[]_[]rules [] -[195] +[197] Underfull \hbox (badness 10000) in paragraph at lines 1136--1138 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3056,7 +3056,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 1173--1175 ata[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[196] +[198] Underfull \hbox (badness 10000) in paragraph at lines 1184--1186 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3127,7 +3127,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[197] +[199] Underfull \hbox (badness 10000) in paragraph at lines 1259--1261 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3177,7 +3177,7 @@ _[][]Type$\OML/cmm/m/it/8 >$$\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr ype, [] -[198] +[200] Underfull \hbox (badness 10000) in paragraph at lines 1307--1309 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3233,7 +3233,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[199] +[201] Underfull \hbox (badness 10000) in paragraph at lines 1363--1365 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3290,7 +3290,7 @@ S/cmsy/m/n/8 ^^C$\T1/pcr/m/n/8 , size[]_[]t k)$\OML/cmm/m/it/8 >$ []$<$ \T1/pcr /m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Type, [] -[200] +[202] Underfull \hbox (badness 10000) detected at line 1419 [][][] [] @@ -3323,20 +3323,20 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::with[]_[]pset = [] -) (./class_net_counter_data.tex [201] [202]) (./class_network_data.tex [203] -[204]) (./class_node.tex [205] <./class_node__coll__graph.pdf +) (./class_net_counter_data.tex [203] [204]) (./class_network_data.tex [205] +[206]) (./class_node.tex [207] <./class_node__coll__graph.pdf pdfTeX warning: pdflatex (file ./class_node__coll__graph.pdf): PDF inclusion: m ultiple pdfs with page group included in a single page > - + File: class_node__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_node__coll__graph.pdf used on input line 19. (pdftex.def) Requested size: 168.0pt x 100.00255pt. - [206] [207] [208] [209] [210]) (./class_node_data.tex [211] [212]) -(./class_phylo_counter_data.tex [213] [214] [215]) -(./class_phylo_rule_dyn_data.tex [216] [217]) (./class_power_set.tex + [208] [209] [210] [211] [212]) (./class_node_data.tex [213] [214]) +(./class_phylo_counter_data.tex [215] [216] [217]) +(./class_phylo_rule_dyn_data.tex [218] [219]) (./class_power_set.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3358,13 +3358,13 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): pdfTeX warning: pdflatex (file ./class_power_set__coll__graph.pdf): PDF inclusi on: multiple pdfs with page group included in a single page > - + File: class_power_set__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_power_set__coll__graph.pdf used on input line 1 9. (pdftex.def) Requested size: 202.0pt x 178.00456pt. - [218] [219] [220] [221] + [220] [221] [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 229--231 \T1/pcr/m/n/8 const std[]::vector$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][] Type $\OML/cmm/m/it/8 >$$\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n @@ -3372,7 +3372,7 @@ Type $\OML/cmm/m/it/8 >$$\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n n/8 ::get[]_[]data[]_[]ptr ( ) [] -[222] [223] [224]) (./class_progress.tex [225]) (./class_rule.tex +[224] [225] [226]) (./class_progress.tex [227]) (./class_rule.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3389,7 +3389,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[226] [227] [228]) (./class_rules.tex +[228] [229] [230]) (./class_rules.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3406,7 +3406,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[229] [230] +[231] [232] Underfull \hbox (badness 10000) in paragraph at lines 134--136 \T1/pcr/m/n/8 std[]::vector$\OML/cmm/m/it/8 <$ []$<$\T1/pcr/m/n/8 Array[]_[][]T ype,Data[]_[][]Type$\OML/cmm/m/it/8 >$ $>$[]\T1/pcr/m/n/8 ::iterator []$\OML/cm @@ -3422,12 +3422,12 @@ m/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Type $\OML/cmm/m/it/8 >$ []\T1/pcr/m/n/8 ::end ( ) [] -[231] +[233] Underfull \hbox (badness 10000) detected at line 194 [][][] [] -[232] +[234] Underfull \hbox (badness 10000) detected at line 221 [][][] [] @@ -3449,17 +3449,17 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[233] +[235] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 Array[] [] -[234] [235] +[236] [237] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 Array[] [] -[236]) (./class_support.tex +[238]) (./class_support.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3484,7 +3484,7 @@ y[]_[][]Type $\OML/cmm/m/it/10 >$ $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 array[]_ cmm/m/it/10 >$ $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 stats[]_[] [] -[237] +[239] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/n/10 Array[] [] @@ -3499,7 +3499,7 @@ Overfull \hbox (3.9776pt too wide) in paragraph at lines 3--3 []\T1/phv/m/n/10 counters[] [] -[238] [239] +[240] [241] Underfull \hbox (badness 10000) in paragraph at lines 182--184 []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][] Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][]Type $\OML/cm @@ -3541,7 +3541,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[240] +[242] Underfull \hbox (badness 10000) in paragraph at lines 240--242 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3576,7 +3576,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[241] +[243] Underfull \hbox (badness 10000) in paragraph at lines 286--288 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3647,7 +3647,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 338--340 ]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][] [] -[242] +[244] Underfull \hbox (badness 10000) in paragraph at lines 349--351 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3703,7 +3703,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::print [] -[243] +[245] Underfull \hbox (badness 10000) in paragraph at lines 401--403 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3752,7 +3752,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[244] +[246] Underfull \hbox (badness 10000) in paragraph at lines 445--447 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3787,7 +3787,7 @@ Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[] []Dyn[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::coordiantes[] [] -[245] +[247] Underfull \hbox (badness 10000) in paragraph at lines 492--494 \T1/pcr/m/n/8 std[]::vector$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 size[]_[]t $\OML/c mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ @@ -3815,7 +3815,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::delete[]_[] [] -[246] +[248] Underfull \hbox (badness 10000) in paragraph at lines 536--538 \T1/pcr/m/n/8 bool []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[] _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ @@ -3843,7 +3843,7 @@ t/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Type, Dat a[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[247] +[249] Underfull \hbox (badness 10000) in paragraph at lines 591--593 \T1/pcr/m/n/8 size[]_[]t []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[] @@ -3874,7 +3874,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. -[248]) [249] [250 +[250]) [251] [252 ] Chapter 9. @@ -3883,7 +3883,7 @@ Chapter 9. pdfTeX warning: pdflatex (file ./barray-bones_8hpp__dep__incl.pdf): PDF inclusi on: multiple pdfs with page group included in a single page > - + File: barray-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barray-bones_8hpp__dep__incl.pdf used on input line 8 @@ -3895,28 +3895,28 @@ Package pdftex.def Info: barray-bones_8hpp__dep__incl.pdf used on input line 8 pdfTeX warning: pdflatex (file ./barray-meat-operators_8hpp__dep__incl.pdf): PD F inclusion: multiple pdfs with page group included in a single page > - File: barray-meat-operators_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barray-meat-operators_8hpp__dep__incl.pdf used on inp ut line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [251] [252] [253] [254]) (./barray-meat_8hpp.tex <./barray-meat_8hpp__dep__inc + [253] [254] [255] [256]) (./barray-meat_8hpp.tex <./barray-meat_8hpp__dep__inc l.pdf pdfTeX warning: pdflatex (file ./barray-meat_8hpp__dep__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: barray-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barray-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [255] [256]) (./barraycell-bones_8hpp.tex <./barraycell-bones_8hpp__dep__incl. + [257] [258]) (./barraycell-bones_8hpp.tex <./barraycell-bones_8hpp__dep__incl. pdf> - + File: barraycell-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraycell-bones_8hpp__dep__incl.pdf used on input li @@ -3927,14 +3927,14 @@ ne 8. pdfTeX warning: pdflatex (file ./barraycell-meat_8hpp__dep__incl.pdf): PDF incl usion: multiple pdfs with page group included in a single page > - + File: barraycell-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraycell-meat_8hpp__dep__incl.pdf used on input lin e 8. (pdftex.def) Requested size: 196.0pt x 166.99916pt. -) (./barraydense-bones_8hpp.tex [257] <./barraydense-bones_8hpp__dep__incl.pdf> - +) (./barraydense-bones_8hpp.tex [259] <./barraydense-bones_8hpp__dep__incl.pdf> + File: barraydense-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydense-bones_8hpp__dep__incl.pdf used on input l @@ -3946,37 +3946,37 @@ p__incl.pdf pdfTeX warning: pdflatex (file ./barraydense-meat-operators_8hpp__dep__incl.pdf ): PDF inclusion: multiple pdfs with page group included in a single page > - File: barraydense-meat-operators_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydense-meat-operators_8hpp__dep__incl.pdf used o n input line 8. (pdftex.def) Requested size: 207.0pt x 167.00684pt. - [258] [259] [260]) (./barraydense-meat_8hpp.tex <./barraydense-meat_8hpp__dep_ + [260] [261] [262]) (./barraydense-meat_8hpp.tex <./barraydense-meat_8hpp__dep_ _incl.pdf pdfTeX warning: pdflatex (file ./barraydense-meat_8hpp__dep__incl.pdf): PDF inc lusion: multiple pdfs with page group included in a single page > - + File: barraydense-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydense-meat_8hpp__dep__incl.pdf used on input li ne 8. (pdftex.def) Requested size: 207.0pt x 167.00684pt. - [261] [262]) (./barraydensecell-bones_8hpp.tex <./barraydensecell-bones_8hpp__ + [263] [264]) (./barraydensecell-bones_8hpp.tex <./barraydensecell-bones_8hpp__ dep__incl.pdf> - + File: barraydensecell-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydensecell-bones_8hpp__dep__incl.pdf used on inp ut line 8. (pdftex.def) Requested size: 222.0pt x 167.00172pt. - [263]) (./barraydensecell-meat_8hpp.tex <./barraydensecell-meat_8hpp__dep__inc + [265]) (./barraydensecell-meat_8hpp.tex <./barraydensecell-meat_8hpp__dep__inc l.pdf> - + File: barraydensecell-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydensecell-meat_8hpp__dep__incl.pdf used on inpu @@ -3987,35 +3987,35 @@ t line 8. pdfTeX warning: pdflatex (file ./barraydensecol-bones_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: barraydensecol-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydensecol-bones_8hpp__dep__incl.pdf used on inpu t line 8. (pdftex.def) Requested size: 220.0pt x 167.00684pt. - [264] [265]) (./barraydenserow-bones_8hpp.tex <./barraydenserow-bones_8hpp__de + [266] [267]) (./barraydenserow-bones_8hpp.tex <./barraydenserow-bones_8hpp__de p__incl.pdf> - + File: barraydenserow-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barraydenserow-bones_8hpp__dep__incl.pdf used on inpu t line 8. (pdftex.def) Requested size: 223.0pt x 167.00427pt. - [266]) (./barrayrow-bones_8hpp.tex) (./barrayrow-meat_8hpp.tex -[267] [268]) (./barrayvector-bones_8hpp.tex) (./barrayvector-meat_8hpp.tex) + [268]) (./barrayrow-bones_8hpp.tex) (./barrayrow-meat_8hpp.tex +[269] [270]) (./barrayvector-bones_8hpp.tex) (./barrayvector-meat_8hpp.tex) (./barry-configuration_8hpp.tex <./barry-configuration_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./barry-configuration_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: barry-configuration_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barry-configuration_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 209.0pt x 222.9989pt. - [269] [270] + [271] [272] Underfull \hbox (badness 10000) in paragraph at lines 63--64 \T1/pcr/m/n/8 #define BARRY[]_[][]MAX[]_[][]NUM[]_[][]ELEMENTS static[]_[]cast$ \OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 size[]_[]t $\OML/cmm/m/it/8 >$\T1/pcr/m/n/8 (s @@ -4024,37 +4024,37 @@ m/it/8 >$[]\T1/pcr/m/n/8 ::max() [] ) (./barry-debug_8hpp.tex <./barry-debug_8hpp__dep__incl.pdf> - + File: barry-debug_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barry-debug_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 209.0pt x 222.9989pt. - [271]) + [273]) (./barry-macros_8hpp.tex <./barry-macros_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./barry-macros_8hpp__dep__incl.pdf): PDF inclusi on: multiple pdfs with page group included in a single page > - + File: barry-macros_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barry-macros_8hpp__dep__incl.pdf used on input line 8 . (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [272] [273]) (./barry_8hpp.tex <./barry_8hpp__incl.pdf> - + [274] [275]) (./barry_8hpp.tex <./barry_8hpp__incl.pdf> + File: barry_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: barry_8hpp__incl.pdf used on input line 56. (pdftex.def) Requested size: 350.0pt x 15.16017pt. - [274] [275] [276]) + [276] [277] [278]) (./cell-bones_8hpp.tex <./cell-bones_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./cell-bones_8hpp__dep__incl.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: cell-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: cell-bones_8hpp__dep__incl.pdf used on input line 8. @@ -4064,14 +4064,14 @@ Package pdftex.def Info: cell-bones_8hpp__dep__incl.pdf used on input line 8. pdfTeX warning: pdflatex (file ./cell-meat_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: cell-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: cell-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. -) (./col-bones_8hpp.tex [277]) (./counters-bones_8hpp.tex <./counters-bones_8hp +) (./col-bones_8hpp.tex [279]) (./counters-bones_8hpp.tex <./counters-bones_8hp p__dep__incl.pdf> - + File: counters-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: counters-bones_8hpp__dep__incl.pdf used on input line @@ -4082,18 +4082,18 @@ Package pdftex.def Info: counters-bones_8hpp__dep__incl.pdf used on input line pdfTeX warning: pdflatex (file ./counters-meat_8hpp__dep__incl.pdf): PDF inclus ion: multiple pdfs with page group included in a single page > - + File: counters-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: counters-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [278] + [280] Overfull \hbox (28.03874pt too wide) in paragraph at lines 26--27 []\T1/phv/m/n/10 #define [](a, b) tem-plate []() in-line a []()[] [] -[279] [280] [281] [282] [283] [284] [285] [286] [287] +[281] [282] [283] [284] [285] [286] [287] [288] [289] Underfull \hbox (badness 10000) in paragraph at lines 550--551 \T1/pcr/m/n/8 Data[]_[][]Type []$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 Array[]_[][]Ty pe,Data[]_[][]Type$\OML/cmm/m/it/8 >$ []$<$\T1/pcr/m/n/8 Array[]_[][]Type,Data[ @@ -4107,31 +4107,31 @@ pe,Data[]_[][]Type$\OML/cmm/m/it/8 >$ []$<$\T1/pcr/m/n/8 Array[]_[][]Type,Data[ ]_[][]Type$\OML/cmm/m/it/8 >$ \T1/pcr/m/n/8 Data[] [] -[288] [289] +[290] [291] Underfull \hbox (badness 10000) in paragraph at lines 665--666 \T1/pcr/m/n/8 Data[]_[][]Type []$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 Array[]_[][]Ty pe,Data[]_[][]Type$\OML/cmm/m/it/8 >$ []$<$\T1/pcr/m/n/8 Array[]_[][]Type,Data[ ]_[][]Type$\OML/cmm/m/it/8 >$ \T1/pcr/m/n/8 Data[] [] -[290]) (./network-css_8hpp.tex <./network-css_8hpp__dep__incl.pdf +[292]) (./network-css_8hpp.tex <./network-css_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./network-css_8hpp__dep__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: network-css_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: network-css_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 234.00244pt. - [291] [292] [293] [294] [295] [296] [297] [298]) (./network_8hpp.tex <./networ + [293] [294] [295] [296] [297] [298] [299] [300]) (./network_8hpp.tex <./networ k_8hpp__incl.pdf pdfTeX warning: pdflatex (file ./network_8hpp__incl.pdf): PDF inclusion: multip le pdfs with page group included in a single page > - + File: network_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: network_8hpp__incl.pdf used on input line 9. @@ -4141,18 +4141,18 @@ Package pdftex.def Info: network_8hpp__incl.pdf used on input line 9. pdfTeX warning: pdflatex (file ./network_8hpp__dep__incl.pdf): PDF inclusion: m ultiple pdfs with page group included in a single page > - + File: network_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: network_8hpp__dep__incl.pdf used on input line 17. (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [299] [300] [301] [302] [303] [304] [305]) (./freqtable_8hpp.tex <./freqtable_ + [301] [302] [303] [304] [305] [306] [307]) (./freqtable_8hpp.tex <./freqtable_ 8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./freqtable_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: freqtable_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: freqtable_8hpp__dep__incl.pdf used on input line 8. @@ -4162,14 +4162,14 @@ Package pdftex.def Info: freqtable_8hpp__dep__incl.pdf used on input line 8. pdfTeX warning: pdflatex (file ./model-bones_8hpp__dep__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: model-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: model-bones_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. - [306]) (./model-meat_8hpp.tex <./model-meat_8hpp__dep__incl.pdf> - + [308]) (./model-meat_8hpp.tex <./model-meat_8hpp__dep__incl.pdf> + File: model-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: model-meat_8hpp__dep__incl.pdf used on input line 8. @@ -4181,15 +4181,15 @@ stats[]_[]target, const std[]::vector$\OML/cmm/m/it/10 <$ \T1/phv/m/n/10 dou-bl e $\OML/cmm/m/it/10 >$ \T1/phv/m/n/10 ¶ms, const dou-ble [] -[307]) (./defm_8hpp.tex <./defm_8hpp__incl.pdf> - +[309]) (./defm_8hpp.tex <./defm_8hpp__incl.pdf> + File: defm_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm_8hpp__incl.pdf used on input line 14. (pdftex.def) Requested size: 350.0pt x 114.94736pt. - [308]) + [310]) (./defm_2counters_8hpp.tex <./defm_2counters_8hpp__incl.pdf> - + File: defm_2counters_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm_2counters_8hpp__incl.pdf used on input line 9. @@ -4199,7 +4199,7 @@ Package pdftex.def Info: defm_2counters_8hpp__incl.pdf used on input line 9. pdfTeX warning: pdflatex (file ./defm_2counters_8hpp__dep__incl.pdf): PDF inclu sion: multiple pdfs with page group included in a single page > - + File: defm_2counters_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm_2counters_8hpp__dep__incl.pdf used on input line @@ -4211,13 +4211,13 @@ Underfull \hbox (badness 3148) in paragraph at lines 32--34 ]t [], size[]_[]t [], [] -[309] [310] [311]) (./geese_2counters_8hpp.tex <./geese_2counters_8hpp__dep__in +[311] [312] [313]) (./geese_2counters_8hpp.tex <./geese_2counters_8hpp__dep__in cl.pdf pdfTeX warning: pdflatex (file ./geese_2counters_8hpp__dep__incl.pdf): PDF incl usion: multiple pdfs with page group included in a single page > - + File: geese_2counters_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese_2counters_8hpp__dep__incl.pdf used on input lin @@ -4229,7 +4229,7 @@ Underfull \hbox (badness 5147) in paragraph at lines 16--17 []_[]t pos, size[]_[]t lb, size[]_[]t ub, size[]_[] [] -[312] +[314] Overfull \hbox (23.90007pt too wide) in paragraph at lines 44--45 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$[]\T1/phv/m/n/10 , std[]::ve ctor$\OML/cmm/m/it/10 <$ \T1/phv/m/n/10 size[]_[]t $\OML/cmm/m/it/10 >$ \T1/phv @@ -4285,7 +4285,7 @@ Overfull \hbox (27.65639pt too wide) in paragraph at lines 74--75 t nfunA, size[]_[]t nfunB, size[]_[]t duplication=[]) [] -[313] +[315] Overfull \hbox (74.95236pt too wide) in paragraph at lines 78--79 []\T1/phv/m/n/10 void [] ([] $\OMS/cmsy/m/n/10 ^^C$[]\T1/phv/m/n/10 , dou-ble p , size[]_[]t duplication=[]) @@ -4315,7 +4315,7 @@ t nfunA, size[]_[]t nfunB, size[]_[] pdfTeX warning: pdflatex (file ./defm-bones_8hpp__dep__incl.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: defm-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm-bones_8hpp__dep__incl.pdf used on input line 8. @@ -4325,13 +4325,13 @@ Package pdftex.def Info: defm-bones_8hpp__dep__incl.pdf used on input line 8. pdfTeX warning: pdflatex (file ./defm-meat_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: defm-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 189.0pt x 178.00456pt. - [314] [315]) (./defm-types_8hpp.tex <./defm-types_8hpp__dep__incl.pdf> - + [316] [317]) (./defm-types_8hpp.tex <./defm-types_8hpp__dep__incl.pdf> + File: defm-types_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: defm-types_8hpp__dep__incl.pdf used on input line 8. @@ -4348,25 +4348,25 @@ Underfull \hbox (badness 4531) in paragraph at lines 38--40 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[316]) (./formula_8hpp.tex <./formula_8hpp__dep__incl.pdf> - +[318]) (./formula_8hpp.tex <./formula_8hpp__dep__incl.pdf> + File: formula_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: formula_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 186.0pt x 245.01004pt. - [317]) + [319]) (./geese_8hpp.tex <./geese_8hpp__incl.pdf> - + File: geese_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese_8hpp__incl.pdf used on input line 22. (pdftex.def) Requested size: 350.0pt x 39.67776pt. - [318]) (./flock-bones_8hpp.tex <./flock-bones_8hpp__dep__incl.pdf + [320]) (./flock-bones_8hpp.tex <./flock-bones_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./flock-bones_8hpp__dep__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: flock-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: flock-bones_8hpp__dep__incl.pdf used on input line 8. @@ -4377,26 +4377,26 @@ Package pdftex.def Info: flock-bones_8hpp__dep__incl.pdf used on input line 8. pdfTeX warning: pdflatex (file ./flock-meat_8hpp__dep__incl.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: flock-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: flock-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 192.0pt x 177.99911pt. -) (./geese-bones_8hpp.tex [319] <./geese-bones_8hpp__dep__incl.pdf> - +) (./geese-bones_8hpp.tex [321] <./geese-bones_8hpp__dep__incl.pdf> + File: geese-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-bones_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 276.0pt x 245.00253pt. - [320] -[321]) (./geese-meat-constructors_8hpp.tex <./geese-meat-constructors_8hpp__dep + [322] +[323]) (./geese-meat-constructors_8hpp.tex <./geese-meat-constructors_8hpp__dep __incl.pdf pdfTeX warning: pdflatex (file ./geese-meat-constructors_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - File: geese-meat-constructors_8hpp__dep__incl.pdf Graphic file (type pdf) @@ -4408,24 +4408,24 @@ nput line 8. pdfTeX warning: pdflatex (file ./geese-meat-likelihood_8hpp__incl.pdf): PDF inc lusion: multiple pdfs with page group included in a single page > - + File: geese-meat-likelihood_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat-likelihood_8hpp__incl.pdf used on input li ne 9. (pdftex.def) Requested size: 241.0pt x 167.00684pt. - [322] <./geese-meat-likelihood_8hpp__dep__incl.pdf> - + [324] <./geese-meat-likelihood_8hpp__dep__incl.pdf> + File: geese-meat-likelihood_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat-likelihood_8hpp__dep__incl.pdf used on inp ut line 17. (pdftex.def) Requested size: 241.0pt x 178.0073pt. - [323]) + [325]) (./geese-meat-likelihood__exhaust_8hpp.tex <./geese-meat-likelihood__exhaust_8h pp__dep__incl.pdf> - File: geese-meat-likelihood__exhaust_8hpp__dep__incl.pdf Graphic file (type pdf ) @@ -4438,15 +4438,15 @@ ed on input line 8. pdfTeX warning: pdflatex (file ./geese-meat-predict_8hpp__dep__incl.pdf): PDF i nclusion: multiple pdfs with page group included in a single page > - + File: geese-meat-predict_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat-predict_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 230.0pt x 178.00185pt. -) (./geese-meat-predict__exhaust_8hpp.tex [324] <./geese-meat-predict__exhaust_ +) (./geese-meat-predict__exhaust_8hpp.tex [326] <./geese-meat-predict__exhaust_ 8hpp__dep__incl.pdf> - File: geese-meat-predict__exhaust_8hpp__dep__incl.pdf Graphic file (type pdf) @@ -4459,16 +4459,16 @@ l.pdf pdfTeX warning: pdflatex (file ./geese-meat-predict__sim_8hpp__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - File: geese-meat-predict__sim_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat-predict__sim_8hpp__dep__incl.pdf used on i nput line 8. (pdftex.def) Requested size: 212.0pt x 189.01065pt. -) (./geese-meat-simulate_8hpp.tex [325] <./geese-meat-simulate_8hpp__dep__incl. +) (./geese-meat-simulate_8hpp.tex [327] <./geese-meat-simulate_8hpp__dep__incl. pdf> - + File: geese-meat-simulate_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat-simulate_8hpp__dep__incl.pdf used on input @@ -4479,13 +4479,13 @@ Package pdftex.def Info: geese-meat-simulate_8hpp__dep__incl.pdf used on input pdfTeX warning: pdflatex (file ./geese-meat_8hpp__dep__incl.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: geese-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 198.0pt x 178.00456pt. -) (./geese-node-bones_8hpp.tex [326] <./geese-node-bones_8hpp__dep__incl.pdf> - +) (./geese-node-bones_8hpp.tex [328] <./geese-node-bones_8hpp__dep__incl.pdf> + File: geese-node-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-node-bones_8hpp__dep__incl.pdf used on input li @@ -4496,19 +4496,19 @@ ne 8. pdfTeX warning: pdflatex (file ./geese-types_8hpp__dep__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: geese-types_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: geese-types_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 199.0pt x 178.01003pt. - [327] + [329] Underfull \hbox (badness 7030) in paragraph at lines 45--47 []\T1/phv/m/n/10 typedef barry[]::[]Support$\OML/cmm/m/it/10 <$ []\T1/phv/m/n/1 0 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[328] [329] +[330] [331] Overfull \hbox (23.5786pt too wide) in paragraph at lines 184--185 \T1/pcr/m/n/8 typedef barry[]::[]Support$\OML/cmm/m/it/8 <$[]\T1/pcr/m/n/8 , [] , [], [] $\OML/cmm/m/it/8 >$ [] @@ -4519,32 +4519,32 @@ Overfull \hbox (23.5786pt too wide) in paragraph at lines 184--185 pdfTeX warning: pdflatex (file ./powerset-bones_8hpp__dep__incl.pdf): PDF inclu sion: multiple pdfs with page group included in a single page > - + File: powerset-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: powerset-bones_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 194.0pt x 167.00684pt. - [330]) (./powerset-meat_8hpp.tex <./powerset-meat_8hpp__dep__incl.pdf + [332]) (./powerset-meat_8hpp.tex <./powerset-meat_8hpp__dep__incl.pdf pdfTeX warning: pdflatex (file ./powerset-meat_8hpp__dep__incl.pdf): PDF inclus ion: multiple pdfs with page group included in a single page > - + File: powerset-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: powerset-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 194.0pt x 167.00684pt. -) (./progress_8hpp.tex [331] <./progress_8hpp__dep__incl.pdf> - +) (./progress_8hpp.tex [333] <./progress_8hpp__dep__incl.pdf> + File: progress_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: progress_8hpp__dep__incl.pdf used on input line 8. 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(pdftex.def) Requested size: 193.0pt x 167.00172pt. -) (./statscounter-bones_8hpp.tex [333] <./statscounter-bones_8hpp__dep__incl.pd +) (./statscounter-bones_8hpp.tex [335] <./statscounter-bones_8hpp__dep__incl.pd f> - + File: statscounter-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: statscounter-bones_8hpp__dep__incl.pdf used on input @@ -4574,31 +4574,31 @@ line 8. pdfTeX warning: pdflatex (file ./statscounter-meat_8hpp__dep__incl.pdf): PDF in clusion: multiple pdfs with page group included in a single page > - + File: statscounter-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: statscounter-meat_8hpp__dep__incl.pdf used on input l ine 8. 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{\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Type, Data\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Rule\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Type $>$ Class Template Reference}{219}{section.8.36}% -\contentsline {subsection}{\numberline {8.36.1}Detailed Description}{220}{subsection.8.36.1}% -\contentsline {subsection}{\numberline {8.36.2}Constructor \& Destructor Documentation}{220}{subsection.8.36.2}% -\contentsline {subsubsection}{\numberline {8.36.2.1}PowerSet()\hspace {0.1cm}{\footnotesize \ttfamily [1/3]}}{220}{subsubsection.8.36.2.1}% -\contentsline {subsubsection}{\numberline 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-\contentsline {subsubsection}{\numberline {8.37.2.1}Progress()}{226}{subsubsection.8.37.2.1}% -\contentsline {subsubsection}{\numberline {8.37.2.2}$\sim $Progress()}{226}{subsubsection.8.37.2.2}% -\contentsline {subsection}{\numberline {8.37.3}Member Function Documentation}{226}{subsection.8.37.3}% -\contentsline {subsubsection}{\numberline {8.37.3.1}end()}{226}{subsubsection.8.37.3.1}% -\contentsline {subsubsection}{\numberline {8.37.3.2}next()}{226}{subsubsection.8.37.3.2}% -\contentsline {section}{\numberline {8.38}Rule$<$ Array\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Type, Data\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel 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{\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Type $>$ Class Template Reference}{229}{section.8.39}% -\contentsline {subsection}{\numberline {8.39.1}Detailed Description}{230}{subsection.8.39.1}% -\contentsline {subsection}{\numberline {8.39.2}Constructor \& Destructor Documentation}{230}{subsection.8.39.2}% -\contentsline {subsubsection}{\numberline {8.39.2.1}Rules()\hspace {0.1cm}{\footnotesize \ttfamily [1/2]}}{230}{subsubsection.8.39.2.1}% -\contentsline {subsubsection}{\numberline {8.39.2.2}Rules()\hspace {0.1cm}{\footnotesize \ttfamily [2/2]}}{230}{subsubsection.8.39.2.2}% -\contentsline {subsubsection}{\numberline {8.39.2.3}$\sim $Rules()}{231}{subsubsection.8.39.2.3}% -\contentsline {subsection}{\numberline {8.39.3}Member Function Documentation}{231}{subsection.8.39.3}% -\contentsline {subsubsection}{\numberline {8.39.3.1}add\_rule()\hspace {0.1cm}{\footnotesize \ttfamily [1/2]}}{231}{subsubsection.8.39.3.1}% -\contentsline {subsubsection}{\numberline 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{\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Dyn\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}\discretionary {\mbox {\scriptsize $\DOTSB \leftarrow \joinrel \rhook $}}{}{}Type $>$ Class Template Reference}{237}{section.8.41}% -\contentsline {subsection}{\numberline {8.41.1}Detailed Description}{239}{subsection.8.41.1}% -\contentsline {subsection}{\numberline {8.41.2}Constructor \& Destructor Documentation}{239}{subsection.8.41.2}% -\contentsline {subsubsection}{\numberline {8.41.2.1}Support()\hspace {0.1cm}{\footnotesize \ttfamily [1/3]}}{239}{subsubsection.8.41.2.1}% -\contentsline {subsubsection}{\numberline {8.41.2.2}Support()\hspace {0.1cm}{\footnotesize \ttfamily [2/3]}}{240}{subsubsection.8.41.2.2}% -\contentsline {subsubsection}{\numberline {8.41.2.3}Support()\hspace 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  • network-css.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/network-css_8hpp_source.html b/network-css_8hpp_source.html index 7d871978b..1c1e5b41c 100644 --- a/network-css_8hpp_source.html +++ b/network-css_8hpp_source.html @@ -874,7 +874,7 @@ diff --git a/network_8hpp.html b/network_8hpp.html index b68219518..1593cca14 100644 --- a/network_8hpp.html +++ b/network_8hpp.html @@ -682,7 +682,7 @@

  • include
  • barry
  • counters
  • network.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/network_8hpp_source.html b/network_8hpp_source.html index a8d013a77..019e24cef 100644 --- a/network_8hpp_source.html +++ b/network_8hpp_source.html @@ -1496,7 +1496,7 @@ diff --git a/powerset-bones_8hpp.html b/powerset-bones_8hpp.html index 9bf402a4e..f251e264a 100644 --- a/powerset-bones_8hpp.html +++ b/powerset-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/powerset-bones_8hpp_source.html b/powerset-bones_8hpp_source.html index d0b407c9f..ec64ca6c7 100644 --- a/powerset-bones_8hpp_source.html +++ b/powerset-bones_8hpp_source.html @@ -187,7 +187,7 @@ diff --git a/powerset-meat_8hpp.html b/powerset-meat_8hpp.html index 6489aec02..3bd040d58 100644 --- a/powerset-meat_8hpp.html +++ b/powerset-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/powerset-meat_8hpp_source.html b/powerset-meat_8hpp_source.html index 535e7c802..be317f99e 100644 --- a/powerset-meat_8hpp_source.html +++ b/powerset-meat_8hpp_source.html @@ -319,7 +319,7 @@ diff --git a/progress_8hpp.html b/progress_8hpp.html index 53341f1bb..4bc99c31c 100644 --- a/progress_8hpp.html +++ b/progress_8hpp.html @@ -146,7 +146,7 @@

  • include
  • barry
  • progress.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/progress_8hpp_source.html b/progress_8hpp_source.html index 36c243a08..e821f5c7b 100644 --- a/progress_8hpp_source.html +++ b/progress_8hpp_source.html @@ -164,7 +164,7 @@ diff --git a/rules-bones_8hpp.html b/rules-bones_8hpp.html index 45e22c51d..cf2f74a6f 100644 --- a/rules-bones_8hpp.html +++ b/rules-bones_8hpp.html @@ -177,7 +177,7 @@

  • include
  • barry
  • rules-bones.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/rules-bones_8hpp_source.html b/rules-bones_8hpp_source.html index 403ea60a4..a7d31699c 100644 --- a/rules-bones_8hpp_source.html +++ b/rules-bones_8hpp_source.html @@ -226,7 +226,7 @@ diff --git a/rules-meat_8hpp.html b/rules-meat_8hpp.html index 479fc554d..1ac954e9f 100644 --- a/rules-meat_8hpp.html +++ b/rules-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/rules-meat_8hpp_source.html b/rules-meat_8hpp_source.html index cf64aafbd..0edfea445 100644 --- a/rules-meat_8hpp_source.html +++ b/rules-meat_8hpp_source.html @@ -318,7 +318,7 @@ diff --git a/statscounter-bones_8hpp.html b/statscounter-bones_8hpp.html index dbea1a5e7..ccb6ac925 100644 --- a/statscounter-bones_8hpp.html +++ b/statscounter-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/statscounter-bones_8hpp_source.html b/statscounter-bones_8hpp_source.html index edf0db12d..742ecfd62 100644 --- a/statscounter-bones_8hpp_source.html +++ b/statscounter-bones_8hpp_source.html @@ -188,7 +188,7 @@ diff --git a/statscounter-meat_8hpp.html b/statscounter-meat_8hpp.html index f92936367..38992f6ad 100644 --- a/statscounter-meat_8hpp.html +++ b/statscounter-meat_8hpp.html @@ -713,7 +713,7 @@

  • include
  • barry
  • statscounter-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/statscounter-meat_8hpp_source.html b/statscounter-meat_8hpp_source.html index fe1f1cecc..b223b93f0 100644 --- a/statscounter-meat_8hpp_source.html +++ b/statscounter-meat_8hpp_source.html @@ -384,7 +384,7 @@ diff --git a/structvec_hasher-members.html b/structvec_hasher-members.html index dae330b0c..42469d2c9 100644 --- a/structvec_hasher-members.html +++ b/structvec_hasher-members.html @@ -105,7 +105,7 @@ diff --git a/structvec_hasher.html b/structvec_hasher.html index 31dc83426..27e8c7786 100644 --- a/structvec_hasher.html +++ b/structvec_hasher.html @@ -153,7 +153,7 @@

  • vecHasher
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/support-bones_8hpp.html b/support-bones_8hpp.html index 59d78d79d..2142d1e76 100644 --- a/support-bones_8hpp.html +++ b/support-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/support-bones_8hpp_source.html b/support-bones_8hpp_source.html index b67552f63..2ff406bb7 100644 --- a/support-bones_8hpp_source.html +++ b/support-bones_8hpp_source.html @@ -289,7 +289,7 @@ diff --git a/support-meat_8hpp.html b/support-meat_8hpp.html index 685ff636d..91bca216f 100644 --- a/support-meat_8hpp.html +++ b/support-meat_8hpp.html @@ -138,7 +138,7 @@

  • include
  • barry
  • support-meat.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/support-meat_8hpp_source.html b/support-meat_8hpp_source.html index 7d526f197..9f26578d6 100644 --- a/support-meat_8hpp_source.html +++ b/support-meat_8hpp_source.html @@ -746,7 +746,7 @@ diff --git a/typedefs_8hpp.html b/typedefs_8hpp.html index 58e998b49..bad95eb68 100644 --- a/typedefs_8hpp.html +++ b/typedefs_8hpp.html @@ -624,7 +624,7 @@

  • include
  • barry
  • typedefs.hpp
    • -
  • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/typedefs_8hpp_source.html b/typedefs_8hpp_source.html index f4e087530..18315b20b 100644 --- a/typedefs_8hpp_source.html +++ b/typedefs_8hpp_source.html @@ -406,7 +406,7 @@

  • include
  • barry
  • models
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_000003_000005.html b/dir_000003_000005.html index 7615ca38b..d1def2d35 100644 --- a/dir_000003_000005.html +++ b/dir_000003_000005.html @@ -98,7 +98,7 @@

models → geese Relation

  • include
  • barry
  • models
    • -
  • Generated on Wed Oct 25 2023 22:41:29 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html index 7feb632a1..59c621a6a 100644 --- a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html +++ b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html @@ -130,7 +130,7 @@ diff --git a/dir_6e63e3665115632dc5d61b2d6d6c3354.html b/dir_6e63e3665115632dc5d61b2d6d6c3354.html index 98eec5bb7..941368ed3 100644 --- a/dir_6e63e3665115632dc5d61b2d6d6c3354.html +++ b/dir_6e63e3665115632dc5d61b2d6d6c3354.html @@ -203,7 +203,7 @@ diff --git a/dir_b3150c389b0f5b078392750f1ae70361.html b/dir_b3150c389b0f5b078392750f1ae70361.html index 0e7d2a072..055098fe7 100644 --- a/dir_b3150c389b0f5b078392750f1ae70361.html +++ b/dir_b3150c389b0f5b078392750f1ae70361.html @@ -110,7 +110,7 @@ diff --git a/dir_c5954a04c87570f0664da134464d5428.html b/dir_c5954a04c87570f0664da134464d5428.html index 0842b965c..1bd98ef72 100644 --- a/dir_c5954a04c87570f0664da134464d5428.html +++ b/dir_c5954a04c87570f0664da134464d5428.html @@ -134,7 +134,7 @@ diff --git a/dir_d44c64559bbebec7f509842c48db8b23.html b/dir_d44c64559bbebec7f509842c48db8b23.html index 95976323b..57a1ed5d1 100644 --- a/dir_d44c64559bbebec7f509842c48db8b23.html +++ b/dir_d44c64559bbebec7f509842c48db8b23.html @@ -117,7 +117,7 @@ diff --git a/dir_d7a554d3e09ed8456d56450fe8436947.html b/dir_d7a554d3e09ed8456d56450fe8436947.html index 55f974f70..1478fa7f5 100644 --- a/dir_d7a554d3e09ed8456d56450fe8436947.html +++ b/dir_d7a554d3e09ed8456d56450fe8436947.html @@ -116,7 +116,7 @@ diff --git a/files.html b/files.html index bff0810a2..77ecc5f11 100644 --- a/files.html +++ b/files.html @@ -173,7 +173,7 @@ diff --git a/flock-bones_8hpp.html b/flock-bones_8hpp.html index 98cd1a340..d13cd60a1 100644 --- a/flock-bones_8hpp.html +++ b/flock-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/flock-bones_8hpp_source.html b/flock-bones_8hpp_source.html index 2998aef83..3bdd0c8fb 100644 --- a/flock-bones_8hpp_source.html +++ b/flock-bones_8hpp_source.html @@ -197,7 +197,7 @@ diff --git a/flock-meat_8hpp.html b/flock-meat_8hpp.html index c58a4418e..55ba319ea 100644 --- a/flock-meat_8hpp.html +++ b/flock-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/flock-meat_8hpp_source.html b/flock-meat_8hpp_source.html index 3e3c6a10f..aacb9040c 100644 --- a/flock-meat_8hpp_source.html +++ b/flock-meat_8hpp_source.html @@ -470,7 +470,7 @@ diff --git a/formula_8hpp.html b/formula_8hpp.html index 441e3d979..44b588282 100644 --- a/formula_8hpp.html +++ b/formula_8hpp.html @@ -218,7 +218,7 @@

Transition effects

diff --git a/formula_8hpp_source.html b/formula_8hpp_source.html index 589012494..76b05cccd 100644 --- a/formula_8hpp_source.html +++ b/formula_8hpp_source.html @@ -114,12 +114,12 @@
59 
60  std::regex pattern_intercept(
61  std::string("\\{\\s*[01]?y[0-9]+(_[0-9]+)?(\\s*,\\s*[01]?y[0-9]+(_[0-9]+)?)*\\s*\\}") +
-
62  std::string("(\\s*\\|\\s*[^\\s]+([(][^)]+[)])?\\s*)?")
+
62  std::string("(\\s*x\\s*[^\\s]+([(].+[)])?\\s*)?")
63  );
64  std::regex pattern_transition(
65  std::string("\\{\\s*[01]?y[0-9]+(_[0-9]+)?(\\s*,\\s*[01]?y[0-9]+(_[0-9]+)?)*\\}\\s*(>)\\s*") +
66  std::string("\\{\\s*[01]?y[0-9]+(_[0-9]+)?(\\s*,\\s*[01]?y[0-9]+(_[0-9]+)?)*\\s*\\}") +
-
67  std::string("(\\s*\\|\\s*[^\\s]+([(][^)]+[)])?\\s*)?")
+
67  std::string("(\\s*x\\s*[^\\s]+([(].+[)])?\\s*)?")
68  );
69 
70  auto empty = std::sregex_iterator();
@@ -137,179 +137,177 @@
82  throw std::logic_error("Transition effects are only valid when the data is a markov process.");
83 
84  // Matching the pattern '| [no spaces]$'
-
85  std::regex pattern_conditional(".+\\|\\s*([^\\s(]+)([(][^)]+[)])?\\s*$");
-
86 
-
87  std::smatch condmatch;
-
88  std::regex_match(formula, condmatch, pattern_conditional);
-
89  // Extracting the [no_spaces] part of the conditional
-
90  if (!condmatch.empty())
-
91  {
-
92  covar_name = condmatch[1].str();
-
93  vname = condmatch[2].str();
-
94 
-
95  // Removing starting and ending parenthesis
-
96  if (vname != "")
-
97  vname = vname.substr(1, vname.size() - 2);
-
98 
-
99  }
-
100 
-
101 
-
102  // Will indicate where the arrow is located at
-
103  size_t arrow_position = match.position(4u);
-
104 
-
105  // This pattern will match
-
106  std::regex pattern("(0?)y([0-9]+)(_([0-9]+))?");
+
85  std::regex pattern_conditional(".+[}]\\s+x\\s+([^(]+)([(][^)]+[)])?\\s*$");
+
86  std::smatch condmatch;
+
87  std::regex_match(formula, condmatch, pattern_conditional);
+
88  // Extracting the [no_spaces] part of the conditional
+
89  if (!condmatch.empty())
+
90  {
+
91  covar_name = condmatch[1].str();
+
92  vname = condmatch[2].str();
+
93 
+
94  // Removing starting and ending parenthesis
+
95  if (vname != "")
+
96  vname = vname.substr(1, vname.size() - 2);
+
97 
+
98  }
+
99 
+
100  // Will indicate where the arrow is located at
+
101  size_t arrow_position = match.position(4u);
+
102 
+
103  // This pattern will match
+
104  std::regex pattern("(0?)y([0-9]+)(_([0-9]+))?");
+
105 
+
106  auto iter = std::sregex_iterator(formula.begin(), formula.end(), pattern);
107 
-
108  auto iter = std::sregex_iterator(formula.begin(), formula.end(), pattern);
-
109 
-
110  for (auto i = iter; i != empty; ++i)
-
111  {
-
112 
-
113  // Baseline position
-
114  size_t current_location = i->position(0u);
-
115 
-
116  // First value true/false
-
117  bool is_positive = true;
-
118  if (i->operator[](1u).str() == "0")
-
119  is_positive = false;
-
120 
-
121  // Variable position
-
122  size_t y_col = std::stoul(i->operator[](2u).str());
-
123  if (y_col >= y_ncol)
-
124  throw std::logic_error("The proposed column is out of range.");
-
125 
-
126  // Time location
-
127  size_t y_row;
-
128  std::string tmp_str = i->operator[](4u).str();
-
129  if (m_order > 1)
-
130  {
-
131  // If missing, we replace with the location
-
132  if (tmp_str == "")
-
133  {
-
134 
-
135  if (current_location > arrow_position)
-
136  y_row = m_order;
-
137  else
-
138  throw std::logic_error("LHS of transition must specify time when m_order > 1");
-
139 
-
140  } else
-
141  y_row = std::stoul(tmp_str);
-
142 
-
143  if (y_row > m_order)
-
144  throw std::logic_error("The proposed row is out of range.");
-
145 
+
108  for (auto i = iter; i != empty; ++i)
+
109  {
+
110 
+
111  // Baseline position
+
112  size_t current_location = i->position(0u);
+
113 
+
114  // First value true/false
+
115  bool is_positive = true;
+
116  if (i->operator[](1u).str() == "0")
+
117  is_positive = false;
+
118 
+
119  // Variable position
+
120  size_t y_col = std::stoul(i->operator[](2u).str());
+
121  if (y_col >= y_ncol)
+
122  throw std::logic_error("The proposed column is out of range.");
+
123 
+
124  // Time location
+
125  size_t y_row;
+
126  std::string tmp_str = i->operator[](4u).str();
+
127  if (m_order > 1)
+
128  {
+
129  // If missing, we replace with the location
+
130  if (tmp_str == "")
+
131  {
+
132 
+
133  if (current_location > arrow_position)
+
134  y_row = m_order;
+
135  else
+
136  throw std::logic_error("LHS of transition must specify time when m_order > 1");
+
137 
+
138  } else
+
139  y_row = std::stoul(tmp_str);
+
140 
+
141  if (y_row > m_order)
+
142  throw std::logic_error("The proposed row is out of range.");
+
143 
+
144 
+
145  } else {
146 
-
147  } else {
-
148 
-
149  // If missing, we replace with the location
-
150  if (tmp_str != "")
-
151  y_row = std::stoul(tmp_str);
-
152  else
-
153  y_row = (current_location < arrow_position ? 0u: 1u);
+
147  // If missing, we replace with the location
+
148  if (tmp_str != "")
+
149  y_row = std::stoul(tmp_str);
+
150  else
+
151  y_row = (current_location < arrow_position ? 0u: 1u);
+
152 
+
153  }
154 
-
155  }
-
156 
-
157  if (selected[y_col * (m_order + 1) + y_row])
-
158  throw std::logic_error(
-
159  "The term " + i->str() + " shows more than once in the formula.");
-
160 
-
161  // Only the end of the chain can be located at position after the
-
162  // arrow
-
163  if ((current_location > arrow_position) && (y_row != m_order))
-
164  throw std::logic_error(
-
165  "Only the row " + std::to_string(m_order) +
-
166  " can be specified at the RHS of the motif."
-
167  );
+
155  if (selected[y_col * (m_order + 1) + y_row])
+
156  throw std::logic_error(
+
157  "The term " + i->str() + " shows more than once in the formula.");
+
158 
+
159  // Only the end of the chain can be located at position after the
+
160  // arrow
+
161  if ((current_location > arrow_position) && (y_row != m_order))
+
162  throw std::logic_error(
+
163  "Only the row " + std::to_string(m_order) +
+
164  " can be specified at the RHS of the motif."
+
165  );
+
166 
+
167  selected[y_col * (m_order + 1) + y_row] = true;
168 
-
169  selected[y_col * (m_order + 1) + y_row] = true;
-
170 
-
171  locations.push_back(y_col * (m_order + 1) + y_row);
-
172  signs.push_back(is_positive);
-
173 
+
169  locations.push_back(y_col * (m_order + 1) + y_row);
+
170  signs.push_back(is_positive);
+
171 
+
172 
+
173  }
174 
-
175  }
+
175  return;
176 
-
177  return;
-
178 
-
179  }
-
180 
-
181  std::regex_match(formula, match, pattern_intercept);
-
182  if (!match.empty())
-
183  {
-
184 
-
185  // Matching the pattern '| [no spaces]$'
-
186  std::regex pattern_conditional(".+\\|\\s*([^\\s(]+)([(][^)]+[)])?\\s*$");
-
187  std::smatch condmatch;
-
188  std::regex_match(formula, condmatch, pattern_conditional);
-
189  // Extracting the [no_spaces] part of the conditional
-
190  if (!condmatch.empty())
-
191  {
-
192  covar_name = condmatch[1].str();
-
193  vname = condmatch[2].str();
-
194 
-
195  // Removing starting and ending parenthesis
-
196  if (vname != "")
-
197  vname = vname.substr(1, vname.size() - 2);
-
198  }
-
199 
-
200  // This pattern will match
-
201  std::regex pattern("(0?)y([0-9]+)(_([0-9]+))?");
+
177  }
+
178 
+
179  std::regex_match(formula, match, pattern_intercept);
+
180  if (!match.empty())
+
181  {
+
182 
+
183  // Matching the pattern '| [no spaces]$'
+
184  std::regex pattern_conditional(".+[}]\\s+x\\s+([^(]+)([(][^)]+[)])?\\s*$");
+
185  std::smatch condmatch;
+
186  std::regex_match(formula, condmatch, pattern_conditional);
+
187  // Extracting the [no_spaces] part of the conditional
+
188  if (!condmatch.empty())
+
189  {
+
190  covar_name = condmatch[1].str();
+
191  vname = condmatch[2].str();
+
192 
+
193  // Removing starting and ending parenthesis
+
194  if (vname != "")
+
195  vname = vname.substr(1, vname.size() - 2);
+
196  }
+
197 
+
198  // This pattern will match
+
199  std::regex pattern("(0?)y([0-9]+)(_([0-9]+))?");
+
200 
+
201  auto iter = std::sregex_iterator(formula.begin(), formula.end(), pattern);
202 
-
203  auto iter = std::sregex_iterator(formula.begin(), formula.end(), pattern);
-
204 
-
205  for (auto i = iter; i != empty; ++i)
-
206  {
-
207 
-
208  // First value true/false
-
209  bool is_positive = true;
-
210  if (i->operator[](1u).str() == "0")
-
211  is_positive = false;
-
212 
-
213  // Variable position
-
214  size_t y_col = std::stoul(i->operator[](2u).str());
-
215  if (y_col >= y_ncol)
-
216  throw std::logic_error("The proposed column is out of range.");
-
217 
-
218  // Time location
-
219  size_t y_row;
-
220  if (i->operator[](4u).str() == "") // Assume is the last
-
221  y_row = m_order;
-
222  else {
+
203  for (auto i = iter; i != empty; ++i)
+
204  {
+
205 
+
206  // First value true/false
+
207  bool is_positive = true;
+
208  if (i->operator[](1u).str() == "0")
+
209  is_positive = false;
+
210 
+
211  // Variable position
+
212  size_t y_col = std::stoul(i->operator[](2u).str());
+
213  if (y_col >= y_ncol)
+
214  throw std::logic_error("The proposed column is out of range.");
+
215 
+
216  // Time location
+
217  size_t y_row;
+
218  if (i->operator[](4u).str() == "") // Assume is the last
+
219  y_row = m_order;
+
220  else {
+
221 
+
222  y_row = std::stoul(i->operator[](4u).str());
223 
-
224  y_row = std::stoul(i->operator[](4u).str());
-
225 
-
226  if (y_row != m_order)
-
227  throw std::logic_error(
-
228  std::string("Intercept motifs cannot feature past events. ") +
-
229  std::string("Only transition motifs can: {...} > {...}.")
-
230  );
+
224  if (y_row != m_order)
+
225  throw std::logic_error(
+
226  std::string("Intercept motifs cannot feature past events. ") +
+
227  std::string("Only transition motifs can: {...} > {...}.")
+
228  );
+
229 
+
230  }
231 
-
232  }
-
233 
-
234  if (selected[y_col * (m_order + 1) + y_row])
-
235  throw std::logic_error(
-
236  "The term " + i->str() + " shows more than once in the formula.");
+
232  if (selected[y_col * (m_order + 1) + y_row])
+
233  throw std::logic_error(
+
234  "The term " + i->str() + " shows more than once in the formula.");
+
235 
+
236  selected[y_col * (m_order + 1) + y_row] = true;
237 
-
238  selected[y_col * (m_order + 1) + y_row] = true;
-
239 
-
240  locations.push_back(y_col * (m_order + 1) + y_row);
-
241  signs.push_back(is_positive);
-
242 
+
238  locations.push_back(y_col * (m_order + 1) + y_row);
+
239  signs.push_back(is_positive);
+
240 
+
241 
+
242  }
243 
-
244  }
+
244  return;
245 
-
246  return;
-
247 
-
248  }
-
249 
-
250  throw std::logic_error(
-
251  "The motif specified in the formula: " + formula +
-
252  " has the wrong syntax."
-
253  );
-
254 
-
255 }
-
256 #endif
-
257 
+
246  }
+
247 
+
248  throw std::logic_error(
+
249  "The motif specified in the formula: " + formula +
+
250  " has the wrong syntax."
+
251  );
+
252 
+
253 }
+
254 #endif
+
255 
i
size_t i
Definition: counters-meat.hpp:83
defm_motif_parser
void defm_motif_parser(std::string formula, std::vector< size_t > &locations, std::vector< bool > &signs, size_t m_order, size_t y_ncol, std::string &covar_name, std::string &vname)
Parses a motif formula.
Definition: formula.hpp:46
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                                                                                          diff --git a/geese-bones_8hpp.html b/geese-bones_8hpp.html index 94cf72297..dd874ac64 100644 --- a/geese-bones_8hpp.html +++ b/geese-bones_8hpp.html @@ -291,7 +291,7 @@

                                                                                          • include
                                                                                          • barry
                                                                                          • models
                                                                                          • geese
                                                                                          • geese-bones.hpp
                                                                                            • -
                                                                                          • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                            • +
                                                                                          • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
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                                                                                          • include
                                                                                          • barry
                                                                                          • models
                                                                                          • geese
                                                                                          • geese-types.hpp
                                                                                            • -
                                                                                          • Generated on Wed Oct 25 2023 22:41:28 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                            • +
                                                                                          • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
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                                                                                                                                            Definition at line 631 of file counters.hpp.

                                                                                                                                            +

                                                                                                                                            Definition at line 680 of file counters.hpp.

                                                                                                                                            @@ -896,8 +896,21 @@

                                                                                                                                            +

                                                                                                                                            Calculates the logit intercept for the DEFM model.

                                                                                                                                            +
                                                                                                                                            Parameters
                                                                                                                                            +

+ + + + + + + +
countersA pointer to the DEFMCounters object.
n_yThe number of response variables.
whichA vector of indices indicating which response variables to use. If empty, all response variables are used.
covar_indexThe index of the covariate to use as the intercept.
vnameThe name of the variable to use as the intercept. If empty, the intercept is set to zero.
x_namesA pointer to a vector of strings containing the names of the covariates.
y_namesA pointer to a vector of strings containing the names of the response variables.
+ + -

Definition at line 150 of file counters.hpp.

+

Definition at line 170 of file counters.hpp.

@@ -1290,7 +1303,7 @@

Definition at line 81 of file counters.hpp.

+

Definition at line 89 of file counters.hpp.

@@ -1439,7 +1452,7 @@

Definition at line 269 of file counters.hpp.

+

Definition at line 289 of file counters.hpp.

@@ -1522,7 +1535,7 @@

Definition at line 578 of file counters.hpp.

+

Definition at line 598 of file counters.hpp.

@@ -1649,7 +1662,7 @@

Definition at line 699 of file counters.hpp.

+

Definition at line 748 of file counters.hpp.

@@ -1689,7 +1702,7 @@

Definition at line 674 of file counters.hpp.

+

Definition at line 723 of file counters.hpp.

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Macros

#define MAKE_DEFM_HASHER(hasher, a, cov)
 Data for the counters. More...
 
#define MAKE_DUPL_VARS()