diff --git a/_r_e_a_d_m_e_8md.html b/_r_e_a_d_m_e_8md.html index 31aa97ade..e4c4f3bae 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 447336230..2134746ef 100644 --- a/annotated.html +++ b/annotated.html @@ -147,7 +147,7 @@ diff --git a/barray-bones_8hpp.html b/barray-bones_8hpp.html index 9d1d21bf5..9c53b00a0 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 b8931122e..36e87fb60 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 8aa926a8c..de01c72ba 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 c66707358..9a7419688 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 8fb27a4d2..c58c8746f 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 ed4e76971..b831d2e03 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 99540a864..25d553543 100644 --- a/barray-meat_8hpp.html +++ b/barray-meat_8hpp.html @@ -164,7 +164,7 @@

  • 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
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 f115f7f09..350e3fb86 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 779e30e1d..e5e1ce79b 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 e8a12b9be..3adb77dcb 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 3e0437857..1a7e640f4 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 00f5a7f88..2ae535715 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 8c911c839..1c3d7d56e 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 d5c993328..62f4cd79e 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 24607ff33..01f44ea83 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 33cda638f..774e9ca2c 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 c5254d6cc..77d8f262c 100644 --- a/barraydense-meat_8hpp.html +++ b/barraydense-meat_8hpp.html @@ -252,7 +252,7 @@

  • include
  • barry
  • barraydense-meat.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 a098646dd..bedb77e49 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 bb2bb0ec9..5b9708c9f 100644 --- a/barraydensecell-bones_8hpp.html +++ b/barraydensecell-bones_8hpp.html @@ -158,7 +158,7 @@

  • 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
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 8a9df64bd..ea350e7cf 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 6eec6e04e..f729346ca 100644 --- a/barraydensecell-meat_8hpp.html +++ b/barraydensecell-meat_8hpp.html @@ -152,7 +152,7 @@

  • include
  • barry
  • barraydensecell-meat.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 74bbeb95b..44e5f5888 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 949c69c4d..7659799e9 100644 --- a/barraydensecol-bones_8hpp.html +++ b/barraydensecol-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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  • barraydensecol-bones.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 c6907f3c3..4a3cb8973 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 aabb95665..074b4a5c1 100644 --- a/barraydenserow-bones_8hpp.html +++ b/barraydenserow-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
  • barry
  • barraydenserow-bones.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 9c4edb24f..54608ef9b 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 7f3d03c36..c2f28d437 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 fbfdfa37b..65330ae9e 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 54298b400..60984b28b 100644 --- a/barrayrow-meat_8hpp.html +++ b/barrayrow-meat_8hpp.html @@ -350,7 +350,7 @@

  • include
  • barry
  • barrayrow-meat.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 c761d05d6..2217a5ced 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 f032c8999..eb638a53c 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 ec00c8725..fd7fa083a 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 730ea59c6..8d57861a3 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 9e230f235..09d120f49 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 36e79c6e7..65875bf1a 100644 --- a/barry-configuration_8hpp.html +++ b/barry-configuration_8hpp.html @@ -257,7 +257,7 @@

  • include
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  • barry-configuration.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 0f2af03d1..771592ec3 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 804ea8257..8f3a3ddc6 100644 --- a/barry-debug_8hpp.html +++ b/barry-debug_8hpp.html @@ -139,7 +139,7 @@

  • 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
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  • Generated on Fri Nov 3 2023 17:45:00 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry-debug_8hpp_source.html b/barry-debug_8hpp_source.html index 356f199d0..134971669 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 8d19d9be2..e9ab6fe14 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
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  • Generated on Fri Nov 3 2023 17:45:00 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 6d7722ca2..ed5a63865 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 d5d5a774c..4e8d8b7f4 100644 --- a/barry_8hpp.html +++ b/barry_8hpp.html @@ -401,7 +401,7 @@

  • include
  • barry
  • barry.hpp
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:00 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 ed0dd73e3..5be049df1 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 c2c61de50..df77a9917 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 5aad6198d..c0d306541 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 09cc0feef..0439f4d7a 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 de89f1bb2..4adcf1dde 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 ee0e3f407..51a70007b 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 d6c155b60..b27c06230 100644 --- a/class_b_array.html +++ b/class_b_array.html @@ -2141,7 +2141,7 @@

  • BArray
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 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 5143e7314..b65383707 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 2e43d805a..100d51f06 100644 --- a/class_b_array_cell.html +++ b/class_b_array_cell.html @@ -430,7 +430,7 @@

  • BArrayCell
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_cell__const-members.html b/class_b_array_cell__const-members.html index 7e27e0a38..519578ada 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 6909aa105..4f55cb515 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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  • 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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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense-members.html b/class_b_array_dense-members.html index 6efa01876..851a0bb07 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 65bd2641a..dfab770d2 100644 --- a/class_b_array_dense.html +++ b/class_b_array_dense.html @@ -2668,7 +2668,7 @@

  • BArrayDense
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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
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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_cell-members.html b/class_b_array_dense_cell-members.html index dd8bf1bb0..c5ad3e6d9 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 3be953a75..a94208970 100644 --- a/class_b_array_dense_cell.html +++ b/class_b_array_dense_cell.html @@ -550,7 +550,7 @@

  • BArrayDenseCell
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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
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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_cell__const.html b/class_b_array_dense_cell__const.html index 57c0f237d..ee9152523 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 8e7aba9a6..57f083616 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 70bdb5672..ecf3d55f7 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_col__const-members.html b/class_b_array_dense_col__const-members.html index adc0fdd81..a40f6f8f4 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 8f9dd34d4..93c22e00f 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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  • 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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diff --git a/class_b_array_dense_row-members.html b/class_b_array_dense_row-members.html index bcfefbaad..ae09bc08d 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 91252b6ce..704fedc28 100644 --- a/class_b_array_dense_row.html +++ b/class_b_array_dense_row.html @@ -379,7 +379,7 @@

  • BArrayDenseRow
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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
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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_row__const-members.html b/class_b_array_dense_row__const-members.html index d25ccceda..4f0d5e2aa 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 9b67d9851..a90e7557e 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 Nov 1 2023 23:08:23 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 2ed91256d..2d970aef5 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 53fcd7c91..6da2d43c5 100644 --- a/class_b_array_row.html +++ b/class_b_array_row.html @@ -354,7 +354,7 @@

  • BArrayRow
    • -
  • 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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diff --git a/class_b_array_row__const-members.html b/class_b_array_row__const-members.html index 6426d4682..957b63e9d 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 285165550..453b124d9 100644 --- a/class_b_array_row__const.html +++ b/class_b_array_row__const.html @@ -354,7 +354,7 @@

  • BArrayRow_const
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 2d6bfb5b3..adf491060 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 3d6337999..95ae79ffa 100644 --- a/class_b_array_vector.html +++ b/class_b_array_vector.html @@ -585,7 +585,7 @@

  • BArrayVector
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 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 d3f0316de..a649d1d2a 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 1dbd6c839..768a8682c 100644 --- a/class_b_array_vector__const.html +++ b/class_b_array_vector__const.html @@ -567,7 +567,7 @@

  • BArrayVector_const
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 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 3cf2e9de7..55547e0f9 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 7af8e4234..3c405af5c 100644 --- a/class_cell.html +++ b/class_cell.html @@ -695,7 +695,7 @@

  • Cell
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 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 f5b9b485f..dd0e0e799 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 8f3d34967..ec15cb9b8 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 229131594..31f3b8684 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Fri Nov 3 2023 17:45:01 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 927aa1031..cda8b30ea 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 653874651..185fb13ba 100644 --- a/class_counter.html +++ b/class_counter.html @@ -679,7 +679,7 @@

  • Counter
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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
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  • Generated on Fri Nov 3 2023 17:45:01 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 302406210..10494de66 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 747046419..ef847466a 100644 --- a/class_counters.html +++ b/class_counters.html @@ -573,7 +573,7 @@

  • Counters
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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
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  • Generated on Fri Nov 3 2023 17:45:01 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 3b8edf253..af886693d 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 0f8f203ee..bc36d4407 100644 --- a/class_d_e_f_m.html +++ b/class_d_e_f_m.html @@ -811,7 +811,7 @@

  • DEFM
    • -
  • 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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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
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#include <defm-types.hpp>

-
-Inheritance diagram for DEFMRuleData:
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[legend]
@@ -150,7 +141,7 @@ diff --git a/class_d_e_f_m_rule_data__inherit__graph.map b/class_d_e_f_m_rule_data__inherit__graph.map deleted file mode 100644 index b9bdbbea7..000000000 --- a/class_d_e_f_m_rule_data__inherit__graph.map +++ /dev/null @@ -1,4 +0,0 @@ - - - - diff --git a/class_d_e_f_m_rule_data__inherit__graph.md5 b/class_d_e_f_m_rule_data__inherit__graph.md5 deleted file mode 100644 index a67ae7066..000000000 --- a/class_d_e_f_m_rule_data__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -48abdceeac1bf96890581041f7728800 \ No newline at end of file diff --git a/class_d_e_f_m_rule_data__inherit__graph.png b/class_d_e_f_m_rule_data__inherit__graph.png deleted file mode 100644 index 2d5b52b60..000000000 Binary files a/class_d_e_f_m_rule_data__inherit__graph.png and /dev/null differ 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 06f0871e1..6144bdf08 100644 --- a/class_d_e_f_m_rule_dyn_data-members.html +++ b/class_d_e_f_m_rule_dyn_data-members.html @@ -100,24 +100,18 @@

This is the complete list of members for DEFMRuleDynData, including all inherited members.

Public Member Functions

- - - - - - - - - - - + + + + +
countsDEFMRuleDynData
DEFMRuleData()DEFMRuleDatainline
DEFMRuleData(std::vector< double > numbers_, std::vector< size_t > indices_, std::vector< bool > logical_)DEFMRuleDatainline
DEFMRuleData(std::vector< double > numbers_, std::vector< size_t > indices_)DEFMRuleDatainline
DEFMRuleDynData(const std::vector< double > *counts_, std::vector< double > numbers_={}, std::vector< size_t > indices_={}, std::vector< bool > logical_={})DEFMRuleDynDatainline
idx(size_t i) constDEFMRuleDatainline
indicesDEFMRuleData
initDEFMRuleData
is_true(size_t i) constDEFMRuleDatainline
logicalDEFMRuleData
num(size_t i) constDEFMRuleDatainline
numbersDEFMRuleData
DEFMRuleDynData(const std::vector< double > *counts_, size_t pos_, size_t lb_, size_t ub_)DEFMRuleDynDatainline
lbDEFMRuleDynData
operator()() constDEFMRuleDynDatainline
posDEFMRuleDynData
ubDEFMRuleDynData
~DEFMRuleDynData()DEFMRuleDynDatainline
diff --git a/class_d_e_f_m_rule_dyn_data.html b/class_d_e_f_m_rule_dyn_data.html index d18be6f85..e068ff9a7 100644 --- a/class_d_e_f_m_rule_dyn_data.html +++ b/class_d_e_f_m_rule_dyn_data.html @@ -102,58 +102,26 @@

#include <defm-types.hpp>

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-Collaboration diagram for DEFMRuleDynData:
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Public Member Functions

 DEFMRuleDynData (const std::vector< double > *counts_, std::vector< double > numbers_={}, std::vector< size_t > indices_={}, std::vector< bool > logical_={})
 
 DEFMRuleDynData (const std::vector< double > *counts_, size_t pos_, size_t lb_, size_t ub_)
 
 ~DEFMRuleDynData ()
 
- Public Member Functions inherited from DEFMRuleData
double num (size_t i) const
 
size_t idx (size_t i) const
 
bool is_true (size_t i) const
 
 DEFMRuleData ()
 
 DEFMRuleData (std::vector< double > numbers_, std::vector< size_t > indices_, std::vector< bool > logical_)
 
 DEFMRuleData (std::vector< double > numbers_, std::vector< size_t > indices_)
 
const double operator() () const
 
- - - - - - - - - + + + + + +

Public Attributes

const std::vector< double > * counts
 
- Public Attributes inherited from DEFMRuleData
std::vector< double > numbers
 
std::vector< size_t > indices
 
std::vector< bool > logical
 
bool init = false
 
size_t pos
 
size_t lb
 
size_t ub
 

Detailed Description

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  • Entries
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diff --git a/class_flock-members.html b/class_flock-members.html index 771a143f1..5c93d607c 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 747a2c9b1..6be1eb50a 100644 --- a/class_flock.html +++ b/class_flock.html @@ -948,7 +948,7 @@

  • Flock
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  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1

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  • FreqTable
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  • Geese
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diff --git a/class_model-members.html b/class_model-members.html index 9f6754ad8..6c366b43d 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 121951d42..abba4f055 100644 --- a/class_model.html +++ b/class_model.html @@ -3234,7 +3234,7 @@

  • Model
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diff --git a/class_net_counter_data-members.html b/class_net_counter_data-members.html index ba65a0d51..3208dd57d 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 4ff7869ca..34729d736 100644 --- a/class_net_counter_data.html +++ b/class_net_counter_data.html @@ -261,7 +261,7 @@

  • NetCounterData
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diff --git a/class_network_data-members.html b/class_network_data-members.html index 05c65f245..7bd4b6644 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 e4469bfb1..4ee08f908 100644 --- a/class_network_data.html +++ b/class_network_data.html @@ -323,7 +323,7 @@

  • NetworkData
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  • Node
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diff --git a/class_node_data-members.html b/class_node_data-members.html index 8af7b7e75..4c97fa067 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 fb43632b1..79ac9fb9d 100644 --- a/class_node_data.html +++ b/class_node_data.html @@ -260,7 +260,7 @@

  • NodeData
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diff --git a/class_phylo_counter_data-members.html b/class_phylo_counter_data-members.html index 2e2fe6780..56720bb63 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 d4762b774..97a1e6f25 100644 --- a/class_phylo_counter_data.html +++ b/class_phylo_counter_data.html @@ -512,7 +512,7 @@

  • PhyloCounterData
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diff --git a/class_phylo_rule_dyn_data-members.html b/class_phylo_rule_dyn_data-members.html index cae99244d..4d9f858d2 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 03ae24152..3fc8c0d94 100644 --- a/class_phylo_rule_dyn_data.html +++ b/class_phylo_rule_dyn_data.html @@ -330,7 +330,7 @@

  • PhyloRuleDynData
    • -
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  • PowerSet
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  • Progress
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    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 fe764b1f1..87d30d972 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 a4b0d5ff0..ffbcbe20e 100644 --- a/class_rule.html +++ b/class_rule.html @@ -452,7 +452,7 @@

  • Rule
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 f6b961fb3..bb60b671d 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 1e2bb4199..be0669d4c 100644 --- a/class_rules.html +++ b/class_rules.html @@ -617,7 +617,7 @@

  • Rules
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 6a71b7d9f..080b6e82e 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 1a3bf764a..bfa89199f 100644 --- a/class_stats_counter.html +++ b/class_stats_counter.html @@ -519,7 +519,7 @@

  • StatsCounter
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 6e185d097..5ec739f76 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 c59e6a5f5..249b6ef2d 100644 --- a/class_support.html +++ b/class_support.html @@ -1277,7 +1277,7 @@

  • Support
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/classes.html b/classes.html index 8ee250f19..709ea92f7 100644 --- a/classes.html +++ b/classes.html @@ -140,7 +140,7 @@ diff --git a/col-bones_8hpp.html b/col-bones_8hpp.html index b4790f83e..229859002 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 f07a363ee..acb3dd764 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 d08153812..1bbb7ca09 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 7f86d58e5..b9b829852 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 811da304a..a208720cf 100644 --- a/counters-meat_8hpp.html +++ b/counters-meat_8hpp.html @@ -1560,7 +1560,7 @@

  • include
  • barry
  • counters-meat.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 6b6e86206..4492a7dd0 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 cbc02fa8b..88082bfa2 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 9db09dcb7..7f9b53cb2 100644 --- a/defm-bones_8hpp_source.html +++ b/defm-bones_8hpp_source.html @@ -209,14 +209,14 @@
j
size_t size_t j
Definition: counters-meat.hpp:84
i
size_t i
Definition: counters-meat.hpp:83
noexcept
Data_Type &&counter_ noexcept
Definition: counters-meat.hpp:27
-
DEFMModel
barry::Model< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMModel
Definition: defm-types.hpp:175
+
DEFMModel
barry::Model< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMModel
Definition: defm-types.hpp:183
diff --git a/defm-meat_8hpp.html b/defm-meat_8hpp.html index efc6f5eb6..23af23e36 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 b3dcfaf5f..6b648a0bc 100644 --- a/defm-meat_8hpp_source.html +++ b/defm-meat_8hpp_source.html @@ -592,7 +592,7 @@ diff --git a/defm-types_8hpp.html b/defm-types_8hpp.html index bef05d0db..26c9a4ffb 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 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 55164723f..b144f1e1f 100644 --- a/defm-types_8hpp_source.html +++ b/defm-types_8hpp_source.html @@ -216,34 +216,42 @@
143 }
144 
151 
-
152 class DEFMRuleDynData : public DEFMRuleData {
+
152 class DEFMRuleDynData {
153 public:
154  const std::vector< double > * counts;
-
155 
-
156  DEFMRuleDynData(
-
157  const std::vector< double > * counts_,
-
158  std::vector< double > numbers_ = {},
-
159  std::vector< size_t > indices_ = {},
-
160  std::vector< bool > logical_ = {}
-
161  ) : DEFMRuleData(numbers_, indices_, logical_), counts(counts_) {};
-
162 
-
163  ~DEFMRuleDynData() {};
-
164 
-
165 };
-
166 
-
171 typedef barry::Counter<DEFMArray, DEFMCounterData > DEFMCounter;
-
172 typedef barry::Counters<DEFMArray, DEFMCounterData> DEFMCounters;
-
173 typedef barry::Support<DEFMArray, DEFMCounterData, DEFMRuleData,DEFMRuleDynData> DEFMSupport;
-
174 typedef barry::StatsCounter<DEFMArray, DEFMCounterData> DEFMStatsCounter;
-
175 typedef barry::Model<DEFMArray, DEFMCounterData,DEFMRuleData,DEFMRuleDynData> DEFMModel;
-
176 
-
177 
-
178 typedef barry::Rule<DEFMArray, DEFMRuleData> DEFMRule;
-
179 typedef barry::Rules<DEFMArray, DEFMRuleData> DEFMRules;
-
180 typedef barry::Rule<DEFMArray, DEFMRuleDynData> DEFMRuleDyn;
-
181 typedef barry::Rules<DEFMArray, DEFMRuleDynData> DEFMRulesDyn;
-
183 
-
184 #endif
+
155  size_t pos;
+
156  size_t lb;
+
157  size_t ub;
+
158 
+
159  DEFMRuleDynData(
+
160  const std::vector< double > * counts_,
+
161  size_t pos_,
+
162  size_t lb_,
+
163  size_t ub_
+
164  ) : counts(counts_), pos(pos_), lb(lb_), ub(ub_) {};
+
165 
+
166  ~DEFMRuleDynData() {};
+
167 
+
168  const double operator()() const
+
169  {
+
170  return (*counts)[pos];
+
171  }
+
172 
+
173 };
+
174 
+
179 typedef barry::Counter<DEFMArray, DEFMCounterData > DEFMCounter;
+
180 typedef barry::Counters<DEFMArray, DEFMCounterData> DEFMCounters;
+
181 typedef barry::Support<DEFMArray, DEFMCounterData, DEFMRuleData,DEFMRuleDynData> DEFMSupport;
+
182 typedef barry::StatsCounter<DEFMArray, DEFMCounterData> DEFMStatsCounter;
+
183 typedef barry::Model<DEFMArray, DEFMCounterData,DEFMRuleData,DEFMRuleDynData> DEFMModel;
+
184 
+
185 
+
186 typedef barry::Rule<DEFMArray, DEFMRuleData> DEFMRule;
+
187 typedef barry::Rules<DEFMArray, DEFMRuleData> DEFMRules;
+
188 typedef barry::Rule<DEFMArray, DEFMRuleDynData> DEFMRuleDyn;
+
189 typedef barry::Rules<DEFMArray, DEFMRuleDynData> DEFMRulesDyn;
+
191 
+
192 #endif
printf_barry
#define printf_barry
Definition: barry-configuration.hpp:51
DEFMCounterData
Data class used to store arbitrary size_t or double vectors.
Definition: defm-types.hpp:64
DEFMData
Data class for DEFM arrays.
Definition: defm-types.hpp:16
@@ -256,18 +264,18 @@
DEFMData::X_ncol
size_t X_ncol
Number of columns in the array of covariates.
Definition: defm-types.hpp:22
DEFMData::array
DEFMArray * array
Definition: defm-types.hpp:19
DEFMCounterData::indices
std::vector< size_t > indices
Definition: defm-types.hpp:67
-
DEFMStatsCounter
barry::StatsCounter< DEFMArray, DEFMCounterData > DEFMStatsCounter
Definition: defm-types.hpp:174
+
DEFMStatsCounter
barry::StatsCounter< DEFMArray, DEFMCounterData > DEFMStatsCounter
Definition: defm-types.hpp:182
DEFMRuleData::indices
std::vector< size_t > indices
Definition: defm-types.hpp:93
DEFMCounterData::num
double num(size_t i) const
Definition: defm-types.hpp:82
DEFMData::covar_sort
std::vector< size_t > covar_sort
Definition: defm-types.hpp:24
-
DEFMRuleDynData::DEFMRuleDynData
DEFMRuleDynData(const std::vector< double > *counts_, std::vector< double > numbers_={}, std::vector< size_t > indices_={}, std::vector< bool > logical_={})
Definition: defm-types.hpp:156
DEFMCounterData::is_motif
bool is_motif
If false, then is a logit intercept.
Definition: defm-types.hpp:70
-
DEFMRulesDyn
barry::Rules< DEFMArray, DEFMRuleDynData > DEFMRulesDyn
Definition: defm-types.hpp:181
+
DEFMRulesDyn
barry::Rules< DEFMArray, DEFMRuleDynData > DEFMRulesDyn
Definition: defm-types.hpp:189
DEFMData::covar_used
std::vector< size_t > covar_used
Value where the sorting of the covariates is stored.
Definition: defm-types.hpp:25
DEFMCounterData::numbers
std::vector< double > numbers
Definition: defm-types.hpp:68
DEFMRuleData::num
double num(size_t i) const
Definition: defm-types.hpp:98
+
DEFMRuleDynData::ub
size_t ub
Definition: defm-types.hpp:157
DEFMData::DEFMData
DEFMData(DEFMArray *array_, const double *covariates_, size_t obs_start_, size_t X_ncol_, size_t X_nrow_)
Constructor.
Definition: defm-types.hpp:36
-
DEFMCounters
barry::Counters< DEFMArray, DEFMCounterData > DEFMCounters
Definition: defm-types.hpp:172
+
DEFMCounters
barry::Counters< DEFMArray, DEFMCounterData > DEFMCounters
Definition: defm-types.hpp:180
DEFMCounterData::DEFMCounterData
DEFMCounterData()
Definition: defm-types.hpp:72
DEFMCounterData::is_true
bool is_true(size_t i) const
Definition: defm-types.hpp:83
DEFMData::~DEFMData
~DEFMData()
Definition: defm-types.hpp:58
@@ -280,24 +288,28 @@
DEFMRuleData::init
bool init
Definition: defm-types.hpp:96
DEFMRuleData::logical
std::vector< bool > logical
Definition: defm-types.hpp:94
DEFMData::obs_start
size_t obs_start
Index of the observation in the data.
Definition: defm-types.hpp:21
+
DEFMRuleDynData::DEFMRuleDynData
DEFMRuleDynData(const std::vector< double > *counts_, size_t pos_, size_t lb_, size_t ub_)
Definition: defm-types.hpp:159
DEFMData::nrow
size_t nrow() const
Definition: defm-types.hpp:127
DEFMData::ncol
size_t ncol() const
Definition: defm-types.hpp:123
DEFMData::covariates
const double * covariates
Vector of covariates (complete vector)
Definition: defm-types.hpp:20
-
DEFMModel
barry::Model< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMModel
Definition: defm-types.hpp:175
+
DEFMModel
barry::Model< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMModel
Definition: defm-types.hpp:183
+
DEFMRuleDynData::pos
size_t pos
Definition: defm-types.hpp:155
DEFMRuleData::DEFMRuleData
DEFMRuleData(std::vector< double > numbers_, std::vector< size_t > indices_)
Definition: defm-types.hpp:110
-
DEFMRuleDyn
barry::Rule< DEFMArray, DEFMRuleDynData > DEFMRuleDyn
Definition: defm-types.hpp:180
+
DEFMRuleDyn
barry::Rule< DEFMArray, DEFMRuleDynData > DEFMRuleDyn
Definition: defm-types.hpp:188
DEFMRuleData::DEFMRuleData
DEFMRuleData(std::vector< double > numbers_, std::vector< size_t > indices_, std::vector< bool > logical_)
Definition: defm-types.hpp:104
DEFMData::DEFMData
DEFMData()
Vector indicating which covariates are included in the model.
Definition: defm-types.hpp:27
-
DEFMRules
barry::Rules< DEFMArray, DEFMRuleData > DEFMRules
Definition: defm-types.hpp:179
+
DEFMRules
barry::Rules< DEFMArray, DEFMRuleData > DEFMRules
Definition: defm-types.hpp:187
DEFMData::at
double at(size_t i, size_t j) const
-
DEFMRuleDynData::~DEFMRuleDynData
~DEFMRuleDynData()
Definition: defm-types.hpp:163
+
DEFMRuleDynData::operator()
const double operator()() const
Definition: defm-types.hpp:168
+
DEFMRuleDynData::~DEFMRuleDynData
~DEFMRuleDynData()
Definition: defm-types.hpp:166
DEFMRuleData::idx
size_t idx(size_t i) const
Definition: defm-types.hpp:99
DEFMCounterData::DEFMCounterData
DEFMCounterData(const std::vector< size_t > indices_, const std::vector< double > numbers_, const std::vector< bool > logical_, bool is_motif_=true)
Definition: defm-types.hpp:73
DEFMData::X_nrow
size_t X_nrow
Number of rows in the array of covariates.
Definition: defm-types.hpp:23
DEFMData::print
void print() const
Definition: defm-types.hpp:131
-
DEFMRule
barry::Rule< DEFMArray, DEFMRuleData > DEFMRule
Definition: defm-types.hpp:178
-
DEFMSupport
barry::Support< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMSupport
Definition: defm-types.hpp:173
-
DEFMCounter
barry::Counter< DEFMArray, DEFMCounterData > DEFMCounter
Definition: defm-types.hpp:171
+
DEFMRule
barry::Rule< DEFMArray, DEFMRuleData > DEFMRule
Definition: defm-types.hpp:186
+
DEFMSupport
barry::Support< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMSupport
Definition: defm-types.hpp:181
+
DEFMRuleDynData::lb
size_t lb
Definition: defm-types.hpp:156
+
DEFMCounter
barry::Counter< DEFMArray, DEFMCounterData > DEFMCounter
Definition: defm-types.hpp:179
DEFMRuleData::DEFMRuleData
DEFMRuleData()
Definition: defm-types.hpp:102
@@ -305,7 +317,7 @@ diff --git a/defm_2counters_8hpp.html b/defm_2counters_8hpp.html index 30d41f3a5..b02b7922b 100644 --- a/defm_2counters_8hpp.html +++ b/defm_2counters_8hpp.html @@ -171,6 +171,9 @@ void rules_dont_become_zero (DEFMSupport *support, std::vector< size_t > ids)  Blocks switching a one to zero. More...
  +void rule_constrain_support (DEFMSupport *support, size_t pos, double lb, double ub) + Overall functional gains. More...
+ 

Macro Definition Documentation

@@ -327,7 +330,7 @@

  • include
  • barry
  • models
  • defm
  • counters.hpp
    • -
  • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:00 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm_2counters_8hpp.js b/defm_2counters_8hpp.js index f6cc71d4c..41881dfd2 100644 --- a/defm_2counters_8hpp.js +++ b/defm_2counters_8hpp.js @@ -12,6 +12,7 @@ var defm_2counters_8hpp = [ "counter_ones", "group__counters-network.html#ga5a83cfba69ea83fca5831478055bbc6a", null ], [ "counter_transition", "group__counters-network.html#ga22ed6963a00ae95ec52b89661fa7ca39", null ], [ "counter_transition_formula", "group__counters-network.html#gad8c9e9b4e4a57e96cd604e8e4832a272", null ], + [ "rule_constrain_support", "group__counters-network.html#gaa3845d70400db85c093d2a2acdfe40e7", null ], [ "rules_dont_become_zero", "group__counters-network.html#gad1d106d42f394a9f6272d7bdf043e127", null ], [ "rules_markov_fixed", "group__counters-network.html#ga31452452bf9dad7f6c5767dcabfb4dbe", null ] ]; \ No newline at end of file diff --git a/defm_2counters_8hpp_source.html b/defm_2counters_8hpp_source.html index 2a2a2198c..190992889 100644 --- a/defm_2counters_8hpp_source.html +++ b/defm_2counters_8hpp_source.html @@ -813,11 +813,53 @@
795  return;
796 }
797 
-
799 
-
801 
-
802 #endif
+
807 inline void rule_constrain_support(
+
808  DEFMSupport * support,
+
809  size_t pos,
+
810  double lb,
+
811  double ub
+
812 )
+
813 {
+
814 
+
815  DEFM_RULEDYN_LAMBDA(tmp_rule)
+
816  {
+
817 
+
818  if (data() < data.lb)
+
819  return false;
+
820  else if (data() > data.ub)
+
821  return false;
+
822  else
+
823  return true;
+
824 
+
825  };
+
826 
+
827 
+
828  support->get_rules_dyn()->add_rule(
+
829  tmp_rule,
+
830  DEFMRuleDynData(
+
831  support->get_current_stats(),
+
832  pos, lb, ub
+
833  ),
+
834  support->get_counters()->get_names()[pos] +
+
835  "' within [" + std::to_string(lb) + ", " +
+
836  std::to_string(ub) + std::string("]"),
+
837  std::string("When the support is ennumerated, only states where the statistic '") +
+
838  support->get_counters()->get_names()[pos] +
+
839  std::to_string(pos) + "' falls within [" + std::to_string(lb) + ", " +
+
840  std::to_string(ub) + "] are included."
+
841  );
+
842 
+
843  return;
+
844 
+
845 }
+
846 
+
847 
+
849 
+
851 
+
852 #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))
data
Data_Type &&counter_ data(std::move(counter_.data))
hasher
Data_Type hasher(counter_.hasher)
Definition: counters-meat.hpp:141
@@ -825,6 +867,7 @@
i
size_t i
Definition: counters-meat.hpp:83
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_RULEDYN_LAMBDA
#define DEFM_RULEDYN_LAMBDA(a)
Definition: counters.hpp:71
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:289
@@ -832,13 +875,14 @@
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
+
rule_constrain_support
void rule_constrain_support(DEFMSupport *support, size_t pos, double lb, double ub)
Overall functional gains.
Definition: counters.hpp:807
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
-
DEFMSupport
barry::Support< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMSupport
Definition: defm-types.hpp:173
+
DEFMCounters
barry::Counters< DEFMArray, DEFMCounterData > DEFMCounters
Definition: defm-types.hpp:180
+
DEFMRules
barry::Rules< DEFMArray, DEFMRuleData > DEFMRules
Definition: defm-types.hpp:187
+
DEFMSupport
barry::Support< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData > DEFMSupport
Definition: defm-types.hpp:181
@@ -846,7 +890,7 @@ diff --git a/defm_8hpp.html b/defm_8hpp.html index 7e57d4ae3..7d0302c1c 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 63cb6271a..b5f6f122d 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 b66ad2d32..0fea23a2f 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 15de41f62..3d563927a 100644 --- a/dir_000003_000004.html +++ b/dir_000003_000004.html @@ -98,7 +98,7 @@

models → defm Relation

- - + + + + @@ -213,6 +215,12 @@ + + + + + +
  • include
  • barry
  • models
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 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 d1def2d35..79793f6bd 100644 --- a/dir_000003_000005.html +++ b/dir_000003_000005.html @@ -98,7 +98,7 @@

models → geese Relation

  • include
  • barry
  • models
    • -
  • Generated on Wed Nov 1 2023 23:08:24 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Nov 3 2023 17:45:01 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html index 59c621a6a..dee171045 100644 --- a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html +++ b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html @@ -130,7 +130,7 @@ diff --git a/dir_6e63e3665115632dc5d61b2d6d6c3354.html b/dir_6e63e3665115632dc5d61b2d6d6c3354.html index 941368ed3..cce0aa0ef 100644 --- a/dir_6e63e3665115632dc5d61b2d6d6c3354.html +++ b/dir_6e63e3665115632dc5d61b2d6d6c3354.html @@ -203,7 +203,7 @@ diff --git a/dir_b3150c389b0f5b078392750f1ae70361.html b/dir_b3150c389b0f5b078392750f1ae70361.html index 055098fe7..23a3027c2 100644 --- a/dir_b3150c389b0f5b078392750f1ae70361.html +++ b/dir_b3150c389b0f5b078392750f1ae70361.html @@ -110,7 +110,7 @@ diff --git a/dir_c5954a04c87570f0664da134464d5428.html b/dir_c5954a04c87570f0664da134464d5428.html index 1bd98ef72..d266a6a44 100644 --- a/dir_c5954a04c87570f0664da134464d5428.html +++ b/dir_c5954a04c87570f0664da134464d5428.html @@ -134,7 +134,7 @@ diff --git a/dir_d44c64559bbebec7f509842c48db8b23.html b/dir_d44c64559bbebec7f509842c48db8b23.html index 57a1ed5d1..d9d506980 100644 --- a/dir_d44c64559bbebec7f509842c48db8b23.html +++ b/dir_d44c64559bbebec7f509842c48db8b23.html @@ -117,7 +117,7 @@ diff --git a/dir_d7a554d3e09ed8456d56450fe8436947.html b/dir_d7a554d3e09ed8456d56450fe8436947.html index 1478fa7f5..2006d8a4b 100644 --- a/dir_d7a554d3e09ed8456d56450fe8436947.html +++ b/dir_d7a554d3e09ed8456d56450fe8436947.html @@ -116,7 +116,7 @@ diff --git a/files.html b/files.html index 77ecc5f11..d2021b52d 100644 --- a/files.html +++ b/files.html @@ -173,7 +173,7 @@ diff --git a/flock-bones_8hpp.html b/flock-bones_8hpp.html index d13cd60a1..eba66d6a3 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 3bdd0c8fb..d5cd8f886 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 55ba319ea..feb836c38 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 aacb9040c..68016c1fe 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 44b588282..f0284b8dc 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 76b05cccd..d860adef1 100644 --- a/formula_8hpp_source.html +++ b/formula_8hpp_source.html @@ -316,7 +316,7 @@ diff --git a/freqtable_8hpp.html b/freqtable_8hpp.html index 4f8d34311..96f3bb726 100644 --- a/freqtable_8hpp.html +++ b/freqtable_8hpp.html @@ -122,7 +122,7 @@ diff --git a/freqtable_8hpp_source.html b/freqtable_8hpp_source.html index dd580cc12..e87827a84 100644 --- a/freqtable_8hpp_source.html +++ b/freqtable_8hpp_source.html @@ -356,7 +356,7 @@ diff --git a/functions.html b/functions.html index 24fdd4775..5fd23449a 100644 --- a/functions.html +++ b/functions.html @@ -159,7 +159,7 @@

- a -

    diff --git a/functions_b.html b/functions_b.html index fbf5808be..655b60c34 100644 --- a/functions_b.html +++ b/functions_b.html @@ -192,7 +192,7 @@

    - b -

      diff --git a/functions_c.html b/functions_c.html index 397a2cf34..a23344687 100644 --- a/functions_c.html +++ b/functions_c.html @@ -203,7 +203,7 @@

      - c -

        diff --git a/functions_d.html b/functions_d.html index 4940cde97..7a7f9a2d1 100644 --- a/functions_d.html +++ b/functions_d.html @@ -128,7 +128,7 @@

        - d -

          : DEFMRuleData
        • DEFMRuleDynData() -: DEFMRuleDynData +: DEFMRuleDynData
        • delete_counters : Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type > @@ -166,7 +166,7 @@

          - d -

            diff --git a/functions_e.html b/functions_e.html index f6832e318..e1c981ddc 100644 --- a/functions_e.html +++ b/functions_e.html @@ -137,7 +137,7 @@

            - e -

              diff --git a/functions_f.html b/functions_f.html index d4f312c71..508ac4cd4 100644 --- a/functions_f.html +++ b/functions_f.html @@ -113,7 +113,7 @@

              - f -

                diff --git a/functions_func.html b/functions_func.html index bcf0b3ff2..4420c864c 100644 --- a/functions_func.html +++ b/functions_func.html @@ -140,7 +140,7 @@

                - a -

                  diff --git a/functions_func_b.html b/functions_func_b.html index 135d0c16b..13ba89f10 100644 --- a/functions_func_b.html +++ b/functions_func_b.html @@ -151,7 +151,7 @@

                  - b -

                    diff --git a/functions_func_c.html b/functions_func_c.html index 8be5fe566..aabf2216e 100644 --- a/functions_func_c.html +++ b/functions_func_c.html @@ -155,7 +155,7 @@

                    - c -

                      diff --git a/functions_func_d.html b/functions_func_d.html index ee7b771fd..8f2516270 100644 --- a/functions_func_d.html +++ b/functions_func_d.html @@ -121,7 +121,7 @@

                      - d -

                      @@ -129,7 +129,7 @@

                      - d -

                        diff --git a/functions_func_e.html b/functions_func_e.html index 4e49dcb25..5ff06c037 100644 --- a/functions_func_e.html +++ b/functions_func_e.html @@ -122,7 +122,7 @@

                        - e -

                          diff --git a/functions_func_f.html b/functions_func_f.html index 9cebc49d2..e3631b501 100644 --- a/functions_func_f.html +++ b/functions_func_f.html @@ -110,7 +110,7 @@

                          - f -

                            diff --git a/functions_func_g.html b/functions_func_g.html index f2dd932ba..8a62a2601 100644 --- a/functions_func_g.html +++ b/functions_func_g.html @@ -287,7 +287,7 @@

                            - g -

                              diff --git a/functions_func_i.html b/functions_func_i.html index 5c401ab69..e2cc9d4fe 100644 --- a/functions_func_i.html +++ b/functions_func_i.html @@ -151,7 +151,7 @@

                              - i -

                                diff --git a/functions_func_l.html b/functions_func_l.html index 5248b9ae8..ce57b710a 100644 --- a/functions_func_l.html +++ b/functions_func_l.html @@ -117,7 +117,7 @@

                                - l -

                                  diff --git a/functions_func_m.html b/functions_func_m.html index 65e96fceb..ba336fe05 100644 --- a/functions_func_m.html +++ b/functions_func_m.html @@ -110,7 +110,7 @@

                                  - m -

                                    diff --git a/functions_func_n.html b/functions_func_n.html index 0c65242ba..75a65bcfd 100644 --- a/functions_func_n.html +++ b/functions_func_n.html @@ -166,7 +166,7 @@

                                    - n -

                                      diff --git a/functions_func_o.html b/functions_func_o.html index 978672050..a406eb3cf 100644 --- a/functions_func_o.html +++ b/functions_func_o.html @@ -128,6 +128,7 @@

                                      - o -

                                        , BArrayDenseRow< Cell_Type, Data_Type > , BArrayDenseRow_const< Cell_Type, Data_Type > , DEFMData +, DEFMRuleDynData , Flock , PhyloCounterData , PhyloRuleDynData @@ -146,7 +147,7 @@

                                        - o -

                                        • operator+=() : BArray< Cell_Type, Data_Type > , BArrayCell< Cell_Type, Data_Type > -, BArrayDense< Cell_Type, Data_Type > +, BArrayDense< Cell_Type, Data_Type > , BArrayDenseCell< Cell_Type, Data_Type > , BArrayRow< Cell_Type, Data_Type > , BArrayVector< Cell_Type, Data_Type > @@ -178,7 +179,7 @@

                                          - o -

                                            , BArrayVector_const< Cell_Type, Data_Type >
                                          • operator=() -: BArray< Cell_Type, Data_Type > +: BArray< Cell_Type, Data_Type > , BArrayCell< Cell_Type, Data_Type > , BArrayDense< Cell_Type, Data_Type > , BArrayDenseCell< Cell_Type, Data_Type > @@ -186,7 +187,7 @@

                                            - o -

                                              , BArrayVector< Cell_Type, Data_Type > , Cell< Cell_Type > , Counter< Array_Type, Data_Type > -, Counters< Array_Type, Data_Type > +, Counters< Array_Type, Data_Type > , Geese , Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type > , Rules< Array_Type, Data_Type > @@ -228,7 +229,7 @@

                                              - o -

                                                diff --git a/functions_func_p.html b/functions_func_p.html index 69c1478f2..479cb7059 100644 --- a/functions_func_p.html +++ b/functions_func_p.html @@ -158,7 +158,7 @@

                                                - p -

                                                  diff --git a/functions_func_r.html b/functions_func_r.html index 88da88870..c61ac2ac3 100644 --- a/functions_func_r.html +++ b/functions_func_r.html @@ -136,7 +136,7 @@

                                                  - r -

                                                    diff --git a/functions_func_s.html b/functions_func_s.html index 07bdc0d25..bcff74bee 100644 --- a/functions_func_s.html +++ b/functions_func_s.html @@ -189,7 +189,7 @@

                                                    - s -

                                                      diff --git a/functions_func_t.html b/functions_func_t.html index 3e6f03f2c..f3dc2b755 100644 --- a/functions_func_t.html +++ b/functions_func_t.html @@ -116,7 +116,7 @@

                                                      - t -

                                                        diff --git a/functions_func_u.html b/functions_func_u.html index 41b736066..a8b2ee90c 100644 --- a/functions_func_u.html +++ b/functions_func_u.html @@ -113,7 +113,7 @@

                                                        - u -

                                                          diff --git a/functions_func_z.html b/functions_func_z.html index 9e10d85ba..fab477aa4 100644 --- a/functions_func_z.html +++ b/functions_func_z.html @@ -109,7 +109,7 @@

                                                          - z -

                                                            diff --git a/functions_func_~.html b/functions_func_~.html index 3efda4ebb..13bdc75e1 100644 --- a/functions_func_~.html +++ b/functions_func_~.html @@ -194,7 +194,7 @@

                                                            - ~ -

                                                              diff --git a/functions_g.html b/functions_g.html index f1a492d12..8fe87fa51 100644 --- a/functions_g.html +++ b/functions_g.html @@ -287,7 +287,7 @@

                                                              - g -

                                                                diff --git a/functions_h.html b/functions_h.html index 0f0eb7737..2d8150178 100644 --- a/functions_h.html +++ b/functions_h.html @@ -113,7 +113,7 @@

                                                                - h -

                                                                  diff --git a/functions_i.html b/functions_i.html index fcb073f75..0fe878e83 100644 --- a/functions_i.html +++ b/functions_i.html @@ -171,7 +171,7 @@

                                                                  - i -

                                                                    diff --git a/functions_k.html b/functions_k.html index 94c93eb55..1dfffdc22 100644 --- a/functions_k.html +++ b/functions_k.html @@ -104,7 +104,7 @@

                                                                    - k -

                                                                      diff --git a/functions_l.html b/functions_l.html index 2bd5e6352..e83b92f95 100644 --- a/functions_l.html +++ b/functions_l.html @@ -96,7 +96,8 @@

                                                                      - l -

                                                                      • lb -: PhyloRuleDynData +: DEFMRuleDynData +, PhyloRuleDynData
                                                                      • likelihood() : Geese @@ -124,7 +125,7 @@

                                                                        - l -

                                                                          diff --git a/functions_m.html b/functions_m.html index 48200c1ba..b7964103f 100644 --- a/functions_m.html +++ b/functions_m.html @@ -123,7 +123,7 @@

                                                                          - m -

                                                                            diff --git a/functions_n.html b/functions_n.html index 84b6b85b0..99ed17335 100644 --- a/functions_n.html +++ b/functions_n.html @@ -200,7 +200,7 @@

                                                                            - n -

                                                                              diff --git a/functions_o.html b/functions_o.html index 3fced51de..5580ec285 100644 --- a/functions_o.html +++ b/functions_o.html @@ -127,13 +127,14 @@

                                                                              - o -

                                                                                , Cell< Cell_Type >
                                                                              • operator()() -: BArray< Cell_Type, Data_Type > +: BArray< Cell_Type, Data_Type > , BArrayDense< Cell_Type, Data_Type > , BArrayDenseCol< Cell_Type, Data_Type > , BArrayDenseCol_const< Cell_Type, Data_Type > , BArrayDenseRow< Cell_Type, Data_Type > , BArrayDenseRow_const< Cell_Type, Data_Type > , DEFMData +, DEFMRuleDynData , Flock , PhyloCounterData , PhyloRuleDynData @@ -237,7 +238,7 @@

                                                                                - o -

                                                                                  diff --git a/functions_p.html b/functions_p.html index 33602193e..1f8b6cf79 100644 --- a/functions_p.html +++ b/functions_p.html @@ -112,10 +112,11 @@

                                                                                  - p -

                                                                                    : PhyloRuleDynData
                                                                                  • pos -: PhyloRuleDynData +: DEFMRuleDynData +, PhyloRuleDynData
                                                                                  • PowerSet() -: PowerSet< Array_Type, Data_Rule_Type > +: PowerSet< Array_Type, Data_Rule_Type >
                                                                                  • predict() : Geese @@ -188,7 +189,7 @@

                                                                                    - p -

                                                                                      diff --git a/functions_r.html b/functions_r.html index 23dd24814..6543d9328 100644 --- a/functions_r.html +++ b/functions_r.html @@ -153,7 +153,7 @@

                                                                                      - r -

                                                                                        diff --git a/functions_rela.html b/functions_rela.html index fd5a4a72d..ff89cfe9d 100644 --- a/functions_rela.html +++ b/functions_rela.html @@ -137,7 +137,7 @@ diff --git a/functions_s.html b/functions_s.html index 66ab86c35..7cbccde04 100644 --- a/functions_s.html +++ b/functions_s.html @@ -222,7 +222,7 @@

                                                                                        - s -

                                                                                          diff --git a/functions_t.html b/functions_t.html index 5c34a7cb3..d1b82f182 100644 --- a/functions_t.html +++ b/functions_t.html @@ -125,7 +125,7 @@

                                                                                          - t -

                                                                                            diff --git a/functions_u.html b/functions_u.html index 142c91bbe..3b92dbaee 100644 --- a/functions_u.html +++ b/functions_u.html @@ -96,7 +96,8 @@

                                                                                            - u -

                                                                                            • ub -: PhyloRuleDynData +: DEFMRuleDynData +, PhyloRuleDynData
                                                                                            • update_annotations() : Geese @@ -116,7 +117,7 @@

                                                                                              - u -

                                                                                                diff --git a/functions_v.html b/functions_v.html index 5806732bc..6c5362594 100644 --- a/functions_v.html +++ b/functions_v.html @@ -116,7 +116,7 @@

                                                                                                - v -

                                                                                                  diff --git a/functions_vars.html b/functions_vars.html index 5b24d737c..a280efd7d 100644 --- a/functions_vars.html +++ b/functions_vars.html @@ -296,7 +296,8 @@

                                                                                                  - k -

                                                                                                    - l -

                                                                                                    • lb -: PhyloRuleDynData +: DEFMRuleDynData +, PhyloRuleDynData
                                                                                                    • logical : DEFMCounterData @@ -381,7 +382,8 @@

                                                                                                      - p -

                                                                                                        : Node
                                                                                                      • pos -: PhyloRuleDynData +: DEFMRuleDynData +, PhyloRuleDynData
                                                                                                      • probability : Node @@ -480,7 +482,8 @@

                                                                                                        - t -

                                                                                                          - u -

                                                                                                          @@ -524,7 +527,7 @@

                                                                                                          - x -

                                                                                                            diff --git a/functions_w.html b/functions_w.html index 350ba2806..01c476c49 100644 --- a/functions_w.html +++ b/functions_w.html @@ -104,7 +104,7 @@

                                                                                                            - w -

                                                                                                              diff --git a/functions_x.html b/functions_x.html index 44db1c204..2cf79fcf0 100644 --- a/functions_x.html +++ b/functions_x.html @@ -107,7 +107,7 @@

                                                                                                              - x -

                                                                                                                diff --git a/functions_z.html b/functions_z.html index 9253b3b97..75e00d1f5 100644 --- a/functions_z.html +++ b/functions_z.html @@ -109,7 +109,7 @@

                                                                                                                - z -

                                                                                                                  diff --git a/functions_~.html b/functions_~.html index c5dd94a31..c53dbd967 100644 --- a/functions_~.html +++ b/functions_~.html @@ -194,7 +194,7 @@

                                                                                                                  - ~ -

                                                                                                                    diff --git a/geese-bones_8hpp.html b/geese-bones_8hpp.html index dd874ac64..145cb0776 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 Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                      • +
                                                                                                                    • Generated on Fri Nov 3 2023 17:45:00 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                    diff --git a/geese-bones_8hpp_source.html b/geese-bones_8hpp_source.html index 5f9fad3ea..902095453 100644 --- a/geese-bones_8hpp_source.html +++ b/geese-bones_8hpp_source.html @@ -415,7 +415,7 @@ diff --git a/geese-meat-constructors_8hpp.html b/geese-meat-constructors_8hpp.html index 912246ab5..ad70009e1 100644 --- a/geese-meat-constructors_8hpp.html +++ b/geese-meat-constructors_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-constructors_8hpp_source.html b/geese-meat-constructors_8hpp_source.html index 8d9542fd3..234900b81 100644 --- a/geese-meat-constructors_8hpp_source.html +++ b/geese-meat-constructors_8hpp_source.html @@ -484,7 +484,7 @@ diff --git a/geese-meat-likelihood_8hpp.html b/geese-meat-likelihood_8hpp.html index bbf7745ff..d17be5e50 100644 --- a/geese-meat-likelihood_8hpp.html +++ b/geese-meat-likelihood_8hpp.html @@ -230,7 +230,7 @@

                                                                                                                    diff --git a/geese-meat-likelihood_8hpp_source.html b/geese-meat-likelihood_8hpp_source.html index a930e388a..4d8a2f0d1 100644 --- a/geese-meat-likelihood_8hpp_source.html +++ b/geese-meat-likelihood_8hpp_source.html @@ -346,7 +346,7 @@ diff --git a/geese-meat-likelihood__exhaust_8hpp.html b/geese-meat-likelihood__exhaust_8hpp.html index 08ac9bf49..3f006f4e7 100644 --- a/geese-meat-likelihood__exhaust_8hpp.html +++ b/geese-meat-likelihood__exhaust_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-likelihood__exhaust_8hpp_source.html b/geese-meat-likelihood__exhaust_8hpp_source.html index 9612778f9..e632303ee 100644 --- a/geese-meat-likelihood__exhaust_8hpp_source.html +++ b/geese-meat-likelihood__exhaust_8hpp_source.html @@ -247,7 +247,7 @@ diff --git a/geese-meat-predict_8hpp.html b/geese-meat-predict_8hpp.html index 9854318b4..7dbff09ee 100644 --- a/geese-meat-predict_8hpp.html +++ b/geese-meat-predict_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict_8hpp_source.html b/geese-meat-predict_8hpp_source.html index 45f03c067..e310d89e8 100644 --- a/geese-meat-predict_8hpp_source.html +++ b/geese-meat-predict_8hpp_source.html @@ -499,7 +499,7 @@ diff --git a/geese-meat-predict__exhaust_8hpp.html b/geese-meat-predict__exhaust_8hpp.html index 7f7e79369..5ed281aa1 100644 --- a/geese-meat-predict__exhaust_8hpp.html +++ b/geese-meat-predict__exhaust_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict__exhaust_8hpp_source.html b/geese-meat-predict__exhaust_8hpp_source.html index c2b6cd9c2..05e61b076 100644 --- a/geese-meat-predict__exhaust_8hpp_source.html +++ b/geese-meat-predict__exhaust_8hpp_source.html @@ -294,7 +294,7 @@ diff --git a/geese-meat-predict__sim_8hpp.html b/geese-meat-predict__sim_8hpp.html index 7ed49c1e1..6b41a7584 100644 --- a/geese-meat-predict__sim_8hpp.html +++ b/geese-meat-predict__sim_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict__sim_8hpp_source.html b/geese-meat-predict__sim_8hpp_source.html index 65e621e92..940ab0374 100644 --- a/geese-meat-predict__sim_8hpp_source.html +++ b/geese-meat-predict__sim_8hpp_source.html @@ -218,7 +218,7 @@ diff --git a/geese-meat-simulate_8hpp.html b/geese-meat-simulate_8hpp.html index cc4b120e3..c179484a6 100644 --- a/geese-meat-simulate_8hpp.html +++ b/geese-meat-simulate_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-simulate_8hpp_source.html b/geese-meat-simulate_8hpp_source.html index 42a445fb4..278c0c3c9 100644 --- a/geese-meat-simulate_8hpp_source.html +++ b/geese-meat-simulate_8hpp_source.html @@ -207,7 +207,7 @@ diff --git a/geese-meat_8hpp.html b/geese-meat_8hpp.html index ef9547dba..93734fc9c 100644 --- a/geese-meat_8hpp.html +++ b/geese-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat_8hpp_source.html b/geese-meat_8hpp_source.html index d19a49c40..a39e1cfee 100644 --- a/geese-meat_8hpp_source.html +++ b/geese-meat_8hpp_source.html @@ -989,7 +989,7 @@ diff --git a/geese-node-bones_8hpp.html b/geese-node-bones_8hpp.html index d1c9fcbf6..e74de21db 100644 --- a/geese-node-bones_8hpp.html +++ b/geese-node-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/geese-node-bones_8hpp_source.html b/geese-node-bones_8hpp_source.html index ed30a1e09..7fd400e5e 100644 --- a/geese-node-bones_8hpp_source.html +++ b/geese-node-bones_8hpp_source.html @@ -225,7 +225,7 @@ diff --git a/geese-types_8hpp.html b/geese-types_8hpp.html index 9685c0d88..c56967302 100644 --- a/geese-types_8hpp.html +++ b/geese-types_8hpp.html @@ -384,7 +384,7 @@

                                                                                                                    • include
                                                                                                                    • barry
                                                                                                                    • models
                                                                                                                    • geese
                                                                                                                    • geese-types.hpp
                                                                                                                      • -
                                                                                                                    • Generated on Wed Nov 1 2023 23:08:23 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                      • +
                                                                                                                    • Generated on Fri Nov 3 2023 17:45:00 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                    diff --git a/geese-types_8hpp_source.html b/geese-types_8hpp_source.html index 883c7350b..1c24eafe8 100644 --- a/geese-types_8hpp_source.html +++ b/geese-types_8hpp_source.html @@ -286,7 +286,7 @@ diff --git a/geese_2counters_8hpp.html b/geese_2counters_8hpp.html index 6071a79cb..468573887 100644 --- a/geese_2counters_8hpp.html +++ b/geese_2counters_8hpp.html @@ -219,7 +219,7 @@ diff --git a/geese_2counters_8hpp_source.html b/geese_2counters_8hpp_source.html index c6657aed9..d00748875 100644 --- a/geese_2counters_8hpp_source.html +++ b/geese_2counters_8hpp_source.html @@ -2179,7 +2179,7 @@ diff --git a/geese_8hpp.html b/geese_8hpp.html index c849df9c9..67f449f7f 100644 --- a/geese_8hpp.html +++ b/geese_8hpp.html @@ -148,7 +148,7 @@ diff --git a/geese_8hpp_source.html b/geese_8hpp_source.html index c1606d06c..9ed0c7563 100644 --- a/geese_8hpp_source.html +++ b/geese_8hpp_source.html @@ -146,7 +146,7 @@ diff --git a/globals.html b/globals.html index a680fe035..4ecfcc92c 100644 --- a/globals.html +++ b/globals.html @@ -104,7 +104,7 @@

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                                                                                                                      - b -

                                                                                                                        diff --git a/globals_c.html b/globals_c.html index aaaefc1d5..0e97de796 100644 --- a/globals_c.html +++ b/globals_c.html @@ -390,7 +390,7 @@

                                                                                                                        - c -

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                                                                                                                          - d -

                                                                                                                            diff --git a/globals_defs.html b/globals_defs.html index 4c719f95a..35d9d7791 100644 --- a/globals_defs.html +++ b/globals_defs.html @@ -420,7 +420,7 @@

                                                                                                                            - z -

                                                                                                                              diff --git a/globals_e.html b/globals_e.html index f34aa9c13..9a00ea991 100644 --- a/globals_e.html +++ b/globals_e.html @@ -104,7 +104,7 @@

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                                                                                                                                  diff --git a/globals_func.html b/globals_func.html index c059fbb84..16b6687c4 100644 --- a/globals_func.html +++ b/globals_func.html @@ -418,6 +418,9 @@

                                                                                                                                  - r -

                                                                                                                                  • resize() : statscounter-meat.hpp
                                                                                                                                    • +
                                                                                                                                  • rule_constrain_support() +: counters.hpp +
                                                                                                                                  • rule_dyn_limit_changes() : counters.hpp
                                                                                                                                    • @@ -481,7 +484,7 @@

                                                                                                                                    - v -

                                                                                                                                      diff --git a/globals_g.html b/globals_g.html index 8085e0836..7c6d4be23 100644 --- a/globals_g.html +++ b/globals_g.html @@ -104,7 +104,7 @@

                                                                                                                                      - g -

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                                                                                                                                          - i -

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                                                                                                                                            - j -

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                                                                                                                                                    - n -

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                                                                                                                                                        - p -

                                                                                                                                                          diff --git a/globals_r.html b/globals_r.html index b3f1388f3..727ee9e7f 100644 --- a/globals_r.html +++ b/globals_r.html @@ -117,6 +117,9 @@

                                                                                                                                                          - r -

                                                                                                                                                          • Row_type : typedefs.hpp
                                                                                                                                                            • +
                                                                                                                                                          • rule_constrain_support() +: counters.hpp +
                                                                                                                                                          • rule_dyn_limit_changes() : counters.hpp
                                                                                                                                                            • @@ -151,7 +154,7 @@

                                                                                                                                                            - r -

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                                                                                                                                                                - t -

                                                                                                                                                                  diff --git a/globals_type.html b/globals_type.html index d22dea3ab..fb42eb6d5 100644 --- a/globals_type.html +++ b/globals_type.html @@ -242,7 +242,7 @@

                                                                                                                                                                  - r -

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                                                                                                                                                                      - v -

                                                                                                                                                                        diff --git a/globals_vars.html b/globals_vars.html index e3521b7ce..c006a3244 100644 --- a/globals_vars.html +++ b/globals_vars.html @@ -174,7 +174,7 @@ diff --git a/globals_z.html b/globals_z.html index 7a3cb9947..cd298d6e2 100644 --- a/globals_z.html +++ b/globals_z.html @@ -106,7 +106,7 @@

                                                                                                                                                                        - z -

                                                                                                                                                                          diff --git a/graph_legend.html b/graph_legend.html index d2fb35ea4..8a8cb34fc 100644 --- a/graph_legend.html +++ b/graph_legend.html @@ -161,7 +161,7 @@ diff --git a/group__counters-network.html b/group__counters-network.html index 12f516e3c..c4734ffe8 100644 --- a/group__counters-network.html +++ b/group__counters-network.html @@ -227,6 +227,9 @@

+ + +
void rules_dont_become_zero (DEFMSupport *support, std::vector< size_t > ids)
 Blocks switching a one to zero. More...
 
void rule_constrain_support (DEFMSupport *support, size_t pos, double lb, double ub)
 Overall functional gains. More...
 

Detailed Description

Counters for network models.

@@ -1617,6 +1620,68 @@

Definition at line 997 of file network.hpp.

+ + + +

◆ rule_constrain_support()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
void rule_constrain_support (DEFMSupport * support,
size_t pos,
double lb,
double ub 
)
+ 		+inline
+
+ +

Overall functional gains.

+
Parameters
+ + + + + +
supportSupport of a model.
posPosition of the focal statistic.
lbLower bound
ubUpper bound
+
+
+
Returns
(void) adds a rule limiting the support of the model.
+ +

Definition at line 807 of file counters.hpp.

+
@@ -1711,7 +1776,7 @@

diff --git a/group__counters-network.js b/group__counters-network.js index 7bf0299d1..5d02cfbd1 100644 --- a/group__counters-network.js +++ b/group__counters-network.js @@ -34,6 +34,7 @@ var group__counters_network = [ "counter_ttriads", "group__counters-network.html#gadadede01536081fb8b79e4d14368f946", null ], [ "counter_ttriads", "group__counters-network.html#ga465ebcc2edcdae4ff9cd7625f886681f", null ], [ "NETWORK_COUNTER", "group__counters-network.html#gad6539320de604e7c6e31e9fb152f70bd", null ], + [ "rule_constrain_support", "group__counters-network.html#gaa3845d70400db85c093d2a2acdfe40e7", null ], [ "rules_dont_become_zero", "group__counters-network.html#gad1d106d42f394a9f6272d7bdf043e127", null ], [ "rules_markov_fixed", "group__counters-network.html#ga31452452bf9dad7f6c5767dcabfb4dbe", null ] ]; \ No newline at end of file diff --git a/group__counters-phylo.html b/group__counters-phylo.html index c40a86dcc..0e46064eb 100644 --- a/group__counters-phylo.html +++ b/group__counters-phylo.html @@ -1334,7 +1334,7 @@

diff --git a/group__counting.html b/group__counting.html index c4cb3666d..5ed138146 100644 --- a/group__counting.html +++ b/group__counting.html @@ -1662,7 +1662,7 @@

diff --git a/group__rules-phylo.html b/group__rules-phylo.html index 07f382ec8..faf62ad3a 100644 --- a/group__rules-phylo.html +++ b/group__rules-phylo.html @@ -163,10 +163,12 @@

 
 DEFMRuleData::DEFMRuleData (std::vector< double > numbers_, std::vector< size_t > indices_)
 
 DEFMRuleDynData::DEFMRuleDynData (const std::vector< double > *counts_, std::vector< double > numbers_={}, std::vector< size_t > indices_={}, std::vector< bool > logical_={})
 
 DEFMRuleDynData::DEFMRuleDynData (const std::vector< double > *counts_, size_t pos_, size_t lb_, size_t ub_)
 
 DEFMRuleDynData::~DEFMRuleDynData ()
 
const double DEFMRuleDynData::operator() () const
 
void rule_leafs (PhyloSupport *support)
 
void rule_dyn_limit_changes (PhyloSupport *support, size_t pos, size_t lb, size_t ub, size_t duplication=Geese::etype_default)
 
const std::vector< double > * DEFMRuleDynData::counts
 
size_t DEFMRuleDynData::pos
 
size_t DEFMRuleDynData::lb
 
size_t DEFMRuleDynData::ub
 
@@ -255,7 +263,7 @@

-

Definition at line 171 of file defm-types.hpp.

+

Definition at line 179 of file defm-types.hpp.

@@ -271,7 +279,7 @@

-

Definition at line 172 of file defm-types.hpp.

+

Definition at line 180 of file defm-types.hpp.

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-

Definition at line 175 of file defm-types.hpp.

+

Definition at line 183 of file defm-types.hpp.

@@ -303,7 +311,7 @@

-

Definition at line 178 of file defm-types.hpp.

+

Definition at line 186 of file defm-types.hpp.

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-

Definition at line 180 of file defm-types.hpp.

+

Definition at line 188 of file defm-types.hpp.

@@ -335,7 +343,7 @@

-

Definition at line 179 of file defm-types.hpp.

+

Definition at line 187 of file defm-types.hpp.

@@ -351,7 +359,7 @@

-

Definition at line 181 of file defm-types.hpp.

+

Definition at line 189 of file defm-types.hpp.

@@ -367,7 +375,7 @@

-

Definition at line 174 of file defm-types.hpp.

+

Definition at line 182 of file defm-types.hpp.

@@ -383,7 +391,7 @@

-

Definition at line 173 of file defm-types.hpp.

+

Definition at line 181 of file defm-types.hpp.

@@ -697,8 +705,8 @@

-

◆ DEFMRuleDynData()

+ +

◆ DEFMRuleDynData()

@@ -715,20 +723,20 @@

- - + + - - + + - - + + @@ -743,7 +751,7 @@

-

Definition at line 156 of file defm-types.hpp.

+

Definition at line 159 of file defm-types.hpp.

@@ -967,10 +975,37 @@

Definition at line 98 of file defm-types.hpp.

+ + + +

◆ operator()() [1/2]

+ +
+
+

Convenient typedefs for network objects.

typedef barry::Counter< DEFMArray, DEFMCounterData > DEFMCounter
std::vector< double > numbers_ = {}, size_t pos_,
std::vector< size_t > indices_ = {}, size_t lb_,
std::vector< bool > logical_ = {} size_t ub_ 
+ + + + +
+ + + + + + + +
const double DEFMRuleDynData::operator() () const
+ 		+inline
+
+ +

Definition at line 168 of file defm-types.hpp.

+
-

◆ operator()()

+

◆ operator()() [2/2]

@@ -1217,7 +1252,7 @@

-

Definition at line 163 of file defm-types.hpp.

+

Definition at line 166 of file defm-types.hpp.

@@ -1370,6 +1405,22 @@

Definition at line 70 of file defm-types.hpp.

+ + + +

◆ lb

+ +
+
+ + + + +
size_t DEFMRuleDynData::lb
+
+ +

Definition at line 156 of file defm-types.hpp.

+
@@ -1452,6 +1503,38 @@

Definition at line 21 of file defm-types.hpp.

+ + + +

◆ pos

+ +
+
+ + + + +
size_t DEFMRuleDynData::pos
+
+ +

Definition at line 155 of file defm-types.hpp.

+ +
+
+ +

◆ ub

+ +
+
+ + + + +
size_t DEFMRuleDynData::ub
+
+ +

Definition at line 157 of file defm-types.hpp.

+
@@ -1495,7 +1578,7 @@

diff --git a/group__rules-phylo.js b/group__rules-phylo.js index 0fc279e80..2cbe58a5b 100644 --- a/group__rules-phylo.js +++ b/group__rules-phylo.js @@ -1,9 +1,13 @@ var group__rules_phylo = [ [ "DEFMRuleDynData", "class_d_e_f_m_rule_dyn_data.html", [ - [ "DEFMRuleDynData", "group__rules-phylo.html#ga292bf598632c9832614a9ea2a988cf36", null ], + [ "DEFMRuleDynData", "group__rules-phylo.html#ga89bb43889a6cded44ff8f3541695c8a8", null ], [ "~DEFMRuleDynData", "group__rules-phylo.html#gad64e7379376d678c0d7795be221c5e3e", null ], - [ "counts", "group__rules-phylo.html#ga7b639c0b73814eec9015b82f7e2d8439", null ] + [ "operator()", "group__rules-phylo.html#gabb14cfba9583ef918adadba42aa6dd08", null ], + [ "counts", "group__rules-phylo.html#ga7b639c0b73814eec9015b82f7e2d8439", null ], + [ "lb", "group__rules-phylo.html#gaed4423cebc240480f3054a59c14918c7", null ], + [ "pos", "group__rules-phylo.html#ga9760013d213cfe94d98915158d8de9aa", null ], + [ "ub", "group__rules-phylo.html#ga4b1ec53a12795984ac2dcbbc9e0f4fff", null ] ] ], [ "DEFMCounter", "group__rules-phylo.html#gaf30ebbed148db068e31eaba91b5977a7", null ], [ "DEFMCounters", "group__rules-phylo.html#ga5c89d811265cdc84066476226ea138a8", null ], @@ -22,7 +26,7 @@ var group__rules_phylo = [ "DEFMRuleData", "group__rules-phylo.html#gafb84c6ffe48f80056b15e0ae6bad4b3a", null ], [ "DEFMRuleData", "group__rules-phylo.html#ga97709e387171f34facb5410f1d726f9b", null ], [ "DEFMRuleData", "group__rules-phylo.html#ga9b5f63e38cfd56a22a2c00b1b11904bb", null ], - [ "DEFMRuleDynData", "group__rules-phylo.html#ga292bf598632c9832614a9ea2a988cf36", null ], + [ "DEFMRuleDynData", "group__rules-phylo.html#ga89bb43889a6cded44ff8f3541695c8a8", null ], [ "idx", "group__rules-phylo.html#ga7f779ce019f2eaa30af381500384d393", null ], [ "idx", "group__rules-phylo.html#gad92a95c8a2097d1a4cb0cf766409791c", null ], [ "is_true", "group__rules-phylo.html#ga6366be3b3f9e1d0bfd1455f0eee20429", null ], @@ -31,6 +35,7 @@ var group__rules_phylo = [ "nrow", "group__rules-phylo.html#ga8d35cccda96180f18d4f87f3831e68d9", null ], [ "num", "group__rules-phylo.html#ga2145b3b46a20bf7ea646f0a76e4b74b8", null ], [ "num", "group__rules-phylo.html#ga492f81abc80e4de779c95ec8956b5e38", null ], + [ "operator()", "group__rules-phylo.html#gabb14cfba9583ef918adadba42aa6dd08", null ], [ "operator()", "group__rules-phylo.html#ga66b7a40df357b79514dcbc4accfe679d", null ], [ "print", "group__rules-phylo.html#gae1617d2f94e8595c8fde0c6013e21a2d", null ], [ "rule_dyn_limit_changes", "group__rules-phylo.html#ga0773b2dbf4673181e45c93632a5f9cc3", null ], @@ -47,11 +52,14 @@ var group__rules_phylo = [ "indices", "group__rules-phylo.html#ga1d86306bc0d6299ecae2554e226809c1", null ], [ "init", "group__rules-phylo.html#ga87c654a27ccf0b679f804cb05f63f7e5", null ], [ "is_motif", "group__rules-phylo.html#ga34a1cd60ddd3aba7ff8145678d2827fe", null ], + [ "lb", "group__rules-phylo.html#gaed4423cebc240480f3054a59c14918c7", null ], [ "logical", "group__rules-phylo.html#ga83c21423b25668b2343196f11fdc4630", null ], [ "logical", "group__rules-phylo.html#ga8843c9a811b759251788fbedb2e65dde", null ], [ "numbers", "group__rules-phylo.html#ga42bd6d1deaa0d800a878ba9fe87d8b18", null ], [ "numbers", "group__rules-phylo.html#ga66f4ba8b2047a943a426e555a9b63937", null ], [ "obs_start", "group__rules-phylo.html#ga89a3ee0a0a27f78c47b010d5498e1fd2", null ], + [ "pos", "group__rules-phylo.html#ga9760013d213cfe94d98915158d8de9aa", null ], + [ "ub", "group__rules-phylo.html#ga4b1ec53a12795984ac2dcbbc9e0f4fff", null ], [ "X_ncol", "group__rules-phylo.html#ga13a6688217231167d87c033db3803209", null ], [ "X_nrow", "group__rules-phylo.html#gadf8ebba08c3c2b590494ed738c76482a", null ] ]; \ No newline at end of file diff --git a/group__stat-models.html b/group__stat-models.html index 818db5c2d..521a6d558 100644 --- a/group__stat-models.html +++ b/group__stat-models.html @@ -121,7 +121,7 @@ diff --git a/hierarchy.html b/hierarchy.html index 4d68f17e7..f818754a2 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -130,30 +130,30 @@  CDEFMDataData class for DEFM arrays  ▼CDEFMModel  CDEFM - ▼CDEFMRuleData - CDEFMRuleDynData - CEntries< Cell_Type >A wrapper class to store source, target, val from a BArray object - CFlockA Flock is a group of Geese - CFreqTable< T >Frequency table of vectors - CGeeseAnnotated Phylo Model - CModel< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >General framework for discrete exponential models. This class allows generating discrete exponential models in the form of a linear exponential model: - CNetCounterDataData class used to store arbitrary size_t or double vectors - CNetworkDataData class for Networks - CNodeA single node for the model - CNodeDataData definition for the PhyloArray class - CPhyloCounterData - CPhyloRuleDynData - CPowerSet< Array_Type, Data_Rule_Type >Powerset of a binary array - CProgressA simple progress bar - CRule< Array_Type, Data_Type >Rule for determining if a cell should be included in a sequence - CRules< Array_Type, Data_Type >Vector of objects of class Rule - CRules< BArray< bool, bool >, bool > - CRules< BArray<>, bool > - CStatsCounter< Array_Type, Data_Type >Count stats for a single Array - CStatsCounter< BArray<>, bool > - CSupport< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >Compute the support of sufficient statistics - CSupport< BArray<>, bool, bool, bool > - CvecHasher< T > + CDEFMRuleData + CDEFMRuleDynData + CEntries< Cell_Type >A wrapper class to store source, target, val from a BArray object + CFlockA Flock is a group of Geese + CFreqTable< T >Frequency table of vectors + CGeeseAnnotated Phylo Model + CModel< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >General framework for discrete exponential models. This class allows generating discrete exponential models in the form of a linear exponential model: + CNetCounterDataData class used to store arbitrary size_t or double vectors + CNetworkDataData class for Networks + CNodeA single node for the model + CNodeDataData definition for the PhyloArray class + CPhyloCounterData + CPhyloRuleDynData + CPowerSet< Array_Type, Data_Rule_Type >Powerset of a binary array + CProgressA simple progress bar + CRule< Array_Type, Data_Type >Rule for determining if a cell should be included in a sequence + CRules< Array_Type, Data_Type >Vector of objects of class Rule + CRules< BArray< bool, bool >, bool > + CRules< BArray<>, bool > + CStatsCounter< Array_Type, Data_Type >Count stats for a single Array + CStatsCounter< BArray<>, bool > + CSupport< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >Compute the support of sufficient statistics + CSupport< BArray<>, bool, bool, bool > + CvecHasher< T > @@ -161,7 +161,7 @@ diff --git a/hierarchy.js b/hierarchy.js index 5b961b741..4ea032fca 100644 --- a/hierarchy.js +++ b/hierarchy.js @@ -31,9 +31,8 @@ var hierarchy = [ "DEFMModel", null, [ [ "DEFM", "class_d_e_f_m.html", null ] ] ], - [ "DEFMRuleData", "class_d_e_f_m_rule_data.html", [ - [ "DEFMRuleDynData", "class_d_e_f_m_rule_dyn_data.html", null ] - ] ], + [ "DEFMRuleData", "class_d_e_f_m_rule_data.html", null ], + [ "DEFMRuleDynData", "class_d_e_f_m_rule_dyn_data.html", null ], [ "Entries< Cell_Type >", "class_entries.html", null ], [ "Flock", "class_flock.html", null ], [ "FreqTable< T >", "class_freq_table.html", null ], diff --git a/index.html b/index.html index 74001fb24..1c76d0b7f 100644 --- a/index.html +++ b/index.html @@ -206,7 +206,7 @@

Code of Conduct

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index 14c4680d1..319e4edfb 100644 Binary files a/latex/class_d_e_f_m__inherit__graph.pdf and b/latex/class_d_e_f_m__inherit__graph.pdf differ diff --git a/latex/class_d_e_f_m_rule_data.tex b/latex/class_d_e_f_m_rule_data.tex index d177a943a..23975cf74 100644 --- a/latex/class_d_e_f_m_rule_data.tex +++ b/latex/class_d_e_f_m_rule_data.tex @@ -4,16 +4,6 @@ {\ttfamily \#include $<$defm-\/types.\+hpp$>$} - - -Inheritance diagram for DEFMRule\+Data\+: -\nopagebreak -\begin{figure}[H] -\begin{center} -\leavevmode -\includegraphics[width=180pt]{class_d_e_f_m_rule_data__inherit__graph} -\end{center} -\end{figure} \doxysubsection*{Public Member Functions} \begin{DoxyCompactItemize} \item diff --git a/latex/class_d_e_f_m_rule_data__inherit__graph.md5 b/latex/class_d_e_f_m_rule_data__inherit__graph.md5 deleted file mode 100644 index 1f86c4419..000000000 --- a/latex/class_d_e_f_m_rule_data__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ca71feff77b4d70240649176f808d987 \ No newline at end of file diff --git a/latex/class_d_e_f_m_rule_data__inherit__graph.pdf b/latex/class_d_e_f_m_rule_data__inherit__graph.pdf deleted file mode 100644 index f09a6cfee..000000000 Binary files a/latex/class_d_e_f_m_rule_data__inherit__graph.pdf and /dev/null differ diff --git a/latex/class_d_e_f_m_rule_dyn_data.tex b/latex/class_d_e_f_m_rule_dyn_data.tex index d6e69d9ed..3a3da0b10 100644 --- a/latex/class_d_e_f_m_rule_dyn_data.tex +++ b/latex/class_d_e_f_m_rule_dyn_data.tex @@ -4,37 +4,25 @@ {\ttfamily \#include $<$defm-\/types.\+hpp$>$} - - -Inheritance diagram for DEFMRule\+Dyn\+Data\+: -\nopagebreak -\begin{figure}[H] -\begin{center} -\leavevmode -\includegraphics[width=180pt]{class_d_e_f_m_rule_dyn_data__inherit__graph} -\end{center} -\end{figure} - - -Collaboration diagram for DEFMRule\+Dyn\+Data\+: -\nopagebreak -\begin{figure}[H] -\begin{center} -\leavevmode -\includegraphics[width=180pt]{class_d_e_f_m_rule_dyn_data__coll__graph} -\end{center} -\end{figure} \doxysubsection*{Public Member Functions} \begin{DoxyCompactItemize} \item -\mbox{\hyperlink{group__rules-phylo_ga292bf598632c9832614a9ea2a988cf36}{DEFMRule\+Dyn\+Data}} (const std\+::vector$<$ double $>$ $\ast$counts\+\_\+, std\+::vector$<$ double $>$ numbers\+\_\+=\{\}, std\+::vector$<$ size\+\_\+t $>$ indices\+\_\+=\{\}, std\+::vector$<$ bool $>$ logical\+\_\+=\{\}) +\mbox{\hyperlink{group__rules-phylo_ga89bb43889a6cded44ff8f3541695c8a8}{DEFMRule\+Dyn\+Data}} (const std\+::vector$<$ double $>$ $\ast$counts\+\_\+, size\+\_\+t pos\+\_\+, size\+\_\+t lb\+\_\+, size\+\_\+t ub\+\_\+) \item \mbox{\hyperlink{group__rules-phylo_gad64e7379376d678c0d7795be221c5e3e}{$\sim$\+DEFMRule\+Dyn\+Data}} () +\item +const double \mbox{\hyperlink{group__rules-phylo_gabb14cfba9583ef918adadba42aa6dd08}{operator()}} () const \end{DoxyCompactItemize} \doxysubsection*{Public Attributes} \begin{DoxyCompactItemize} \item const std\+::vector$<$ double $>$ $\ast$ \mbox{\hyperlink{group__rules-phylo_ga7b639c0b73814eec9015b82f7e2d8439}{counts}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_ga9760013d213cfe94d98915158d8de9aa}{pos}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_gaed4423cebc240480f3054a59c14918c7}{lb}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_ga4b1ec53a12795984ac2dcbbc9e0f4fff}{ub}} \end{DoxyCompactItemize} diff --git a/latex/class_d_e_f_m_rule_dyn_data__coll__graph.md5 b/latex/class_d_e_f_m_rule_dyn_data__coll__graph.md5 deleted file mode 100644 index 07b97d8b1..000000000 --- a/latex/class_d_e_f_m_rule_dyn_data__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -35163c16fd409f070e6b31cd931e7786 \ No newline at end of file diff --git a/latex/class_d_e_f_m_rule_dyn_data__coll__graph.pdf b/latex/class_d_e_f_m_rule_dyn_data__coll__graph.pdf deleted file mode 100644 index 8beb68024..000000000 Binary files a/latex/class_d_e_f_m_rule_dyn_data__coll__graph.pdf and /dev/null differ diff --git a/latex/class_d_e_f_m_rule_dyn_data__inherit__graph.md5 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b/latex/defm-meat_8hpp__dep__incl.pdf index b22da90d8..ee5ecfa2b 100644 Binary files a/latex/defm-meat_8hpp__dep__incl.pdf and b/latex/defm-meat_8hpp__dep__incl.pdf differ diff --git a/latex/defm-types_8hpp__dep__incl.pdf b/latex/defm-types_8hpp__dep__incl.pdf index 5dbba9990..a56645840 100644 Binary files a/latex/defm-types_8hpp__dep__incl.pdf and b/latex/defm-types_8hpp__dep__incl.pdf differ diff --git a/latex/defm_2counters_8hpp.tex b/latex/defm_2counters_8hpp.tex index b183a76cd..c5378b956 100644 --- a/latex/defm_2counters_8hpp.tex +++ b/latex/defm_2counters_8hpp.tex @@ -66,7 +66,9 @@ void \mbox{\hyperlink{group__counters-network_ga31452452bf9dad7f6c5767dcabfb4dbe}{rules\+\_\+markov\+\_\+fixed}} (\mbox{\hyperlink{group__rules-phylo_gaae5b274ab680fe97a6da3615ad08b45b}{DEFMRules}} $\ast$rules, size\+\_\+t markov\+\_\+order) \begin{DoxyCompactList}\small\item\em Number of edges. \end{DoxyCompactList}\item void \mbox{\hyperlink{group__counters-network_gad1d106d42f394a9f6272d7bdf043e127}{rules\+\_\+dont\+\_\+become\+\_\+zero}} (\mbox{\hyperlink{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}{DEFMSupport}} $\ast$support, std\+::vector$<$ size\+\_\+t $>$ ids) -\begin{DoxyCompactList}\small\item\em Blocks switching a one to zero. \end{DoxyCompactList}\end{DoxyCompactItemize} +\begin{DoxyCompactList}\small\item\em Blocks switching a one to zero. \end{DoxyCompactList}\item +void \mbox{\hyperlink{group__counters-network_gaa3845d70400db85c093d2a2acdfe40e7}{rule\+\_\+constrain\+\_\+support}} (\mbox{\hyperlink{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}{DEFMSupport}} $\ast$support, size\+\_\+t pos, double lb, double ub) +\begin{DoxyCompactList}\small\item\em Overall functional gains. \end{DoxyCompactList}\end{DoxyCompactItemize} \end{Indent} diff --git a/latex/defm_2counters_8hpp__dep__incl.pdf b/latex/defm_2counters_8hpp__dep__incl.pdf index 444a50dfe..77c794b04 100644 Binary files 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-88,7 +88,9 @@ void \mbox{\hyperlink{group__counters-network_ga31452452bf9dad7f6c5767dcabfb4dbe}{rules\+\_\+markov\+\_\+fixed}} (\mbox{\hyperlink{group__rules-phylo_gaae5b274ab680fe97a6da3615ad08b45b}{DEFMRules}} $\ast$rules, size\+\_\+t markov\+\_\+order) \begin{DoxyCompactList}\small\item\em Number of edges. \end{DoxyCompactList}\item void \mbox{\hyperlink{group__counters-network_gad1d106d42f394a9f6272d7bdf043e127}{rules\+\_\+dont\+\_\+become\+\_\+zero}} (\mbox{\hyperlink{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}{DEFMSupport}} $\ast$support, std\+::vector$<$ size\+\_\+t $>$ ids) -\begin{DoxyCompactList}\small\item\em Blocks switching a one to zero. \end{DoxyCompactList}\end{DoxyCompactItemize} +\begin{DoxyCompactList}\small\item\em Blocks switching a one to zero. \end{DoxyCompactList}\item +void \mbox{\hyperlink{group__counters-network_gaa3845d70400db85c093d2a2acdfe40e7}{rule\+\_\+constrain\+\_\+support}} (\mbox{\hyperlink{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}{DEFMSupport}} $\ast$support, size\+\_\+t pos, double lb, double ub) +\begin{DoxyCompactList}\small\item\em Overall functional gains. \end{DoxyCompactList}\end{DoxyCompactItemize} \doxysubsection{Detailed Description} @@ -567,6 +569,34 @@ Definition at line 997 of file network.\+hpp. +\mbox{\Hypertarget{group__counters-network_gaa3845d70400db85c093d2a2acdfe40e7}\label{group__counters-network_gaa3845d70400db85c093d2a2acdfe40e7}} +\index{Network counters@{Network counters}!rule\_constrain\_support@{rule\_constrain\_support}} +\index{rule\_constrain\_support@{rule\_constrain\_support}!Network counters@{Network counters}} +\doxysubsubsection{\texorpdfstring{rule\_constrain\_support()}{rule\_constrain\_support()}} +{\footnotesize\ttfamily void rule\+\_\+constrain\+\_\+support (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}{DEFMSupport}} $\ast$}]{support, }\item[{size\+\_\+t}]{pos, }\item[{double}]{lb, }\item[{double}]{ub }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} + + + +Overall functional gains. + + +\begin{DoxyParams}{Parameters} +{\em support} & \mbox{\hyperlink{class_support}{Support}} of a model. \\ +\hline +{\em pos} & Position of the focal statistic. \\ +\hline +{\em lb} & Lower bound \\ +\hline +{\em ub} & Upper bound\\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +(void) adds a rule limiting the support of the model. +\end{DoxyReturn} + + +Definition at line 807 of file counters.\+hpp. + \mbox{\Hypertarget{group__counters-network_gad1d106d42f394a9f6272d7bdf043e127}\label{group__counters-network_gad1d106d42f394a9f6272d7bdf043e127}} \index{Network counters@{Network counters}!rules\_dont\_become\_zero@{rules\_dont\_become\_zero}} \index{rules\_dont\_become\_zero@{rules\_dont\_become\_zero}!Network counters@{Network counters}} diff --git a/latex/group__counters-phylo.pdf b/latex/group__counters-phylo.pdf index f207a0dee..32b7c0701 100644 Binary files a/latex/group__counters-phylo.pdf and b/latex/group__counters-phylo.pdf differ diff --git a/latex/group__rules-phylo.pdf b/latex/group__rules-phylo.pdf index cfdd26238..6caea1b23 100644 Binary files a/latex/group__rules-phylo.pdf and b/latex/group__rules-phylo.pdf differ diff --git a/latex/group__rules-phylo.tex b/latex/group__rules-phylo.tex index 93265fd3a..9e367135f 100644 --- a/latex/group__rules-phylo.tex +++ b/latex/group__rules-phylo.tex @@ -61,10 +61,12 @@ \item \mbox{\hyperlink{group__rules-phylo_ga97709e387171f34facb5410f1d726f9b}{DEFMRule\+Data\+::\+DEFMRule\+Data}} (std\+::vector$<$ double $>$ numbers\+\_\+, std\+::vector$<$ size\+\_\+t $>$ indices\+\_\+) \item -\mbox{\hyperlink{group__rules-phylo_ga292bf598632c9832614a9ea2a988cf36}{DEFMRule\+Dyn\+Data\+::\+DEFMRule\+Dyn\+Data}} (const std\+::vector$<$ double $>$ $\ast$counts\+\_\+, std\+::vector$<$ double $>$ numbers\+\_\+=\{\}, std\+::vector$<$ size\+\_\+t $>$ indices\+\_\+=\{\}, std\+::vector$<$ bool $>$ logical\+\_\+=\{\}) +\mbox{\hyperlink{group__rules-phylo_ga89bb43889a6cded44ff8f3541695c8a8}{DEFMRule\+Dyn\+Data\+::\+DEFMRule\+Dyn\+Data}} (const std\+::vector$<$ double $>$ $\ast$counts\+\_\+, size\+\_\+t pos\+\_\+, size\+\_\+t lb\+\_\+, size\+\_\+t ub\+\_\+) \item \mbox{\hyperlink{group__rules-phylo_gad64e7379376d678c0d7795be221c5e3e}{DEFMRule\+Dyn\+Data\+::$\sim$\+DEFMRule\+Dyn\+Data}} () \item +const double \mbox{\hyperlink{group__rules-phylo_gabb14cfba9583ef918adadba42aa6dd08}{DEFMRule\+Dyn\+Data\+::operator()}} () const +\item void \mbox{\hyperlink{group__rules-phylo_ga276c18987041a32224c61990ae4d6ca1}{rule\+\_\+leafs}} (\mbox{\hyperlink{geese-types_8hpp_ae66aa4dbb13f90c073bc0d5c3df58d83}{Phylo\+Support}} $\ast$support) \item void \mbox{\hyperlink{group__rules-phylo_ga0773b2dbf4673181e45c93632a5f9cc3}{rule\+\_\+dyn\+\_\+limit\+\_\+changes}} (\mbox{\hyperlink{geese-types_8hpp_ae66aa4dbb13f90c073bc0d5c3df58d83}{Phylo\+Support}} $\ast$support, size\+\_\+t pos, size\+\_\+t lb, size\+\_\+t ub, size\+\_\+t duplication=\mbox{\hyperlink{class_geese_aff47a7a24431f0ee1ba9b40b3cd93557}{Geese\+::etype\+\_\+default}}) @@ -103,6 +105,12 @@ bool \mbox{\hyperlink{group__rules-phylo_ga87c654a27ccf0b679f804cb05f63f7e5}{DEFMRule\+Data\+::init}} = false \item const std\+::vector$<$ double $>$ $\ast$ \mbox{\hyperlink{group__rules-phylo_ga7b639c0b73814eec9015b82f7e2d8439}{DEFMRule\+Dyn\+Data\+::counts}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_ga9760013d213cfe94d98915158d8de9aa}{DEFMRule\+Dyn\+Data\+::pos}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_gaed4423cebc240480f3054a59c14918c7}{DEFMRule\+Dyn\+Data\+::lb}} +\item +size\+\_\+t \mbox{\hyperlink{group__rules-phylo_ga4b1ec53a12795984ac2dcbbc9e0f4fff}{DEFMRule\+Dyn\+Data\+::ub}} \end{DoxyCompactItemize} \doxysubsection*{Convenient typedefs for network objects.} \begin{DoxyCompactItemize} @@ -146,7 +154,7 @@ -Definition at line 171 of file defm-\/types.\+hpp. +Definition at line 179 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga5c89d811265cdc84066476226ea138a8}\label{group__rules-phylo_ga5c89d811265cdc84066476226ea138a8}} \index{Phylo rules@{Phylo rules}!DEFMCounters@{DEFMCounters}} @@ -156,7 +164,7 @@ -Definition at line 172 of file defm-\/types.\+hpp. +Definition at line 180 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga9716da2197dde4338078d890e7ffcf05}\label{group__rules-phylo_ga9716da2197dde4338078d890e7ffcf05}} \index{Phylo rules@{Phylo rules}!DEFMModel@{DEFMModel}} @@ -166,7 +174,7 @@ -Definition at line 175 of file defm-\/types.\+hpp. +Definition at line 183 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_gae7ef10f17b5ca193abec479ea233212f}\label{group__rules-phylo_gae7ef10f17b5ca193abec479ea233212f}} \index{Phylo rules@{Phylo rules}!DEFMRule@{DEFMRule}} @@ -176,7 +184,7 @@ -Definition at line 178 of file defm-\/types.\+hpp. +Definition at line 186 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga9a767b57f79612eb39de35038ee2d0ea}\label{group__rules-phylo_ga9a767b57f79612eb39de35038ee2d0ea}} \index{Phylo rules@{Phylo rules}!DEFMRuleDyn@{DEFMRuleDyn}} @@ -186,7 +194,7 @@ -Definition at line 180 of file defm-\/types.\+hpp. +Definition at line 188 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_gaae5b274ab680fe97a6da3615ad08b45b}\label{group__rules-phylo_gaae5b274ab680fe97a6da3615ad08b45b}} \index{Phylo rules@{Phylo rules}!DEFMRules@{DEFMRules}} @@ -196,7 +204,7 @@ -Definition at line 179 of file defm-\/types.\+hpp. +Definition at line 187 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga38a5a5b78ba2b492093f0744a1166acb}\label{group__rules-phylo_ga38a5a5b78ba2b492093f0744a1166acb}} \index{Phylo rules@{Phylo rules}!DEFMRulesDyn@{DEFMRulesDyn}} @@ -206,7 +214,7 @@ -Definition at line 181 of file defm-\/types.\+hpp. +Definition at line 189 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga1b4873975ddde98ef40c841c6d3b447e}\label{group__rules-phylo_ga1b4873975ddde98ef40c841c6d3b447e}} \index{Phylo rules@{Phylo rules}!DEFMStatsCounter@{DEFMStatsCounter}} @@ -216,7 +224,7 @@ -Definition at line 174 of file defm-\/types.\+hpp. +Definition at line 182 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}\label{group__rules-phylo_gaec94c2fbe37383fd6695bc2d60863077}} \index{Phylo rules@{Phylo rules}!DEFMSupport@{DEFMSupport}} @@ -226,7 +234,7 @@ -Definition at line 173 of file defm-\/types.\+hpp. +Definition at line 181 of file defm-\/types.\+hpp. @@ -324,15 +332,15 @@ Definition at line 104 of file defm-\/types.\+hpp. -\mbox{\Hypertarget{group__rules-phylo_ga292bf598632c9832614a9ea2a988cf36}\label{group__rules-phylo_ga292bf598632c9832614a9ea2a988cf36}} +\mbox{\Hypertarget{group__rules-phylo_ga89bb43889a6cded44ff8f3541695c8a8}\label{group__rules-phylo_ga89bb43889a6cded44ff8f3541695c8a8}} \index{Phylo rules@{Phylo rules}!DEFMRuleDynData@{DEFMRuleDynData}} \index{DEFMRuleDynData@{DEFMRuleDynData}!Phylo rules@{Phylo rules}} \doxysubsubsection{\texorpdfstring{DEFMRuleDynData()}{DEFMRuleDynData()}} -{\footnotesize\ttfamily DEFMRule\+Dyn\+Data\+::\+DEFMRule\+Dyn\+Data (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ $\ast$}]{counts\+\_\+, }\item[{std\+::vector$<$ double $>$}]{numbers\+\_\+ = {\ttfamily \{\}}, }\item[{std\+::vector$<$ size\+\_\+t $>$}]{indices\+\_\+ = {\ttfamily \{\}}, }\item[{std\+::vector$<$ bool $>$}]{logical\+\_\+ = {\ttfamily \{\}} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} +{\footnotesize\ttfamily DEFMRule\+Dyn\+Data\+::\+DEFMRule\+Dyn\+Data (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ $\ast$}]{counts\+\_\+, }\item[{size\+\_\+t}]{pos\+\_\+, }\item[{size\+\_\+t}]{lb\+\_\+, }\item[{size\+\_\+t}]{ub\+\_\+ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} -Definition at line 156 of file defm-\/types.\+hpp. +Definition at line 159 of file defm-\/types.\+hpp. \mbox{\Hypertarget{group__rules-phylo_ga7f779ce019f2eaa30af381500384d393}\label{group__rules-phylo_ga7f779ce019f2eaa30af381500384d393}} \index{Phylo rules@{Phylo rules}!idx@{idx}} @@ -414,10 +422,20 @@ Definition at line 98 of file defm-\/types.\+hpp. +\mbox{\Hypertarget{group__rules-phylo_gabb14cfba9583ef918adadba42aa6dd08}\label{group__rules-phylo_gabb14cfba9583ef918adadba42aa6dd08}} +\index{Phylo rules@{Phylo rules}!operator()@{operator()}} +\index{operator()@{operator()}!Phylo rules@{Phylo rules}} +\doxysubsubsection{\texorpdfstring{operator()()}{operator()()}\hspace{0.1cm}{\footnotesize\ttfamily [1/2]}} +{\footnotesize\ttfamily const double DEFMRule\+Dyn\+Data\+::operator() (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} + + + +Definition at line 168 of file defm-\/types.\+hpp. + \mbox{\Hypertarget{group__rules-phylo_ga66b7a40df357b79514dcbc4accfe679d}\label{group__rules-phylo_ga66b7a40df357b79514dcbc4accfe679d}} \index{Phylo rules@{Phylo rules}!operator()@{operator()}} \index{operator()@{operator()}!Phylo rules@{Phylo rules}} -\doxysubsubsection{\texorpdfstring{operator()()}{operator()()}} +\doxysubsubsection{\texorpdfstring{operator()()}{operator()()}\hspace{0.1cm}{\footnotesize\ttfamily [2/2]}} {\footnotesize\ttfamily double DEFMData\+::operator() (\begin{DoxyParamCaption}\item[{size\+\_\+t}]{i, }\item[{size\+\_\+t}]{j }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} @@ -514,7 +532,7 @@ -Definition at line 163 of file defm-\/types.\+hpp. +Definition at line 166 of file defm-\/types.\+hpp. @@ -621,6 +639,16 @@ Definition at line 70 of file defm-\/types.\+hpp. +\mbox{\Hypertarget{group__rules-phylo_gaed4423cebc240480f3054a59c14918c7}\label{group__rules-phylo_gaed4423cebc240480f3054a59c14918c7}} +\index{Phylo rules@{Phylo rules}!lb@{lb}} +\index{lb@{lb}!Phylo rules@{Phylo rules}} +\doxysubsubsection{\texorpdfstring{lb}{lb}} +{\footnotesize\ttfamily size\+\_\+t DEFMRule\+Dyn\+Data\+::lb} + + + +Definition at line 156 of file defm-\/types.\+hpp. + \mbox{\Hypertarget{group__rules-phylo_ga83c21423b25668b2343196f11fdc4630}\label{group__rules-phylo_ga83c21423b25668b2343196f11fdc4630}} \index{Phylo rules@{Phylo rules}!logical@{logical}} \index{logical@{logical}!Phylo rules@{Phylo rules}} @@ -675,6 +703,26 @@ Definition at line 21 of file defm-\/types.\+hpp. +\mbox{\Hypertarget{group__rules-phylo_ga9760013d213cfe94d98915158d8de9aa}\label{group__rules-phylo_ga9760013d213cfe94d98915158d8de9aa}} +\index{Phylo rules@{Phylo rules}!pos@{pos}} +\index{pos@{pos}!Phylo rules@{Phylo rules}} +\doxysubsubsection{\texorpdfstring{pos}{pos}} +{\footnotesize\ttfamily size\+\_\+t DEFMRule\+Dyn\+Data\+::pos} + + + +Definition at line 155 of file defm-\/types.\+hpp. + +\mbox{\Hypertarget{group__rules-phylo_ga4b1ec53a12795984ac2dcbbc9e0f4fff}\label{group__rules-phylo_ga4b1ec53a12795984ac2dcbbc9e0f4fff}} +\index{Phylo rules@{Phylo rules}!ub@{ub}} +\index{ub@{ub}!Phylo rules@{Phylo rules}} +\doxysubsubsection{\texorpdfstring{ub}{ub}} +{\footnotesize\ttfamily size\+\_\+t DEFMRule\+Dyn\+Data\+::ub} + + + +Definition at line 157 of file defm-\/types.\+hpp. + \mbox{\Hypertarget{group__rules-phylo_ga13a6688217231167d87c033db3803209}\label{group__rules-phylo_ga13a6688217231167d87c033db3803209}} \index{Phylo rules@{Phylo rules}!X\_ncol@{X\_ncol}} \index{X\_ncol@{X\_ncol}!Phylo rules@{Phylo rules}} diff --git a/latex/hierarchy.tex b/latex/hierarchy.tex index 7ac130206..9b9cb5cc1 100644 --- a/latex/hierarchy.tex +++ b/latex/hierarchy.tex @@ -32,9 +32,7 @@ \item \contentsline{section}{DEFM}{\pageref{class_d_e_f_m}}{} \end{DoxyCompactList} \item \contentsline{section}{DEFMRule\+Data}{\pageref{class_d_e_f_m_rule_data}}{} -\begin{DoxyCompactList} \item 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-\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}{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}{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}{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}{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{Phylo rules@{Phylo rules}!ncol@{ncol}|hyperpage}{43} +\indexentry{ncol@{ncol}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!nrow@{nrow}|hyperpage}{43} +\indexentry{nrow@{nrow}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!num@{num}|hyperpage}{43} +\indexentry{num@{num}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!num@{num}|hyperpage}{43} +\indexentry{num@{num}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!operator()@{operator()}|hyperpage}{43} +\indexentry{operator()@{operator()}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!operator()@{operator()}|hyperpage}{43} +\indexentry{operator()@{operator()}!Phylo rules@{Phylo rules}|hyperpage}{43} +\indexentry{Phylo rules@{Phylo rules}!print@{print}|hyperpage}{44} +\indexentry{print@{print}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}|hyperpage}{44} +\indexentry{rule\_dyn\_limit\_changes@{rule\_dyn\_limit\_changes}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!rule\_leafs@{rule\_leafs}|hyperpage}{44} +\indexentry{rule\_leafs@{rule\_leafs}!Phylo rules@{Phylo rules}|hyperpage}{44} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMCounterData@{$\sim$DEFMCounterData}|hyperpage}{45} +\indexentry{````~DEFMCounterData@{$\sim$DEFMCounterData}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMData@{$\sim$DEFMData}|hyperpage}{45} +\indexentry{````~DEFMData@{$\sim$DEFMData}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}|hyperpage}{45} +\indexentry{````~DEFMRuleDynData@{$\sim$DEFMRuleDynData}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!array@{array}|hyperpage}{45} +\indexentry{array@{array}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!counts@{counts}|hyperpage}{45} +\indexentry{counts@{counts}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!covar\_sort@{covar\_sort}|hyperpage}{45} +\indexentry{covar\_sort@{covar\_sort}!Phylo rules@{Phylo rules}|hyperpage}{45} +\indexentry{Phylo rules@{Phylo rules}!covar\_used@{covar\_used}|hyperpage}{46} +\indexentry{covar\_used@{covar\_used}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!covariates@{covariates}|hyperpage}{46} +\indexentry{covariates@{covariates}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!indices@{indices}|hyperpage}{46} +\indexentry{indices@{indices}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!indices@{indices}|hyperpage}{46} +\indexentry{indices@{indices}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!init@{init}|hyperpage}{46} +\indexentry{init@{init}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!is\_motif@{is\_motif}|hyperpage}{46} +\indexentry{is\_motif@{is\_motif}!Phylo rules@{Phylo rules}|hyperpage}{46} +\indexentry{Phylo rules@{Phylo rules}!lb@{lb}|hyperpage}{47} +\indexentry{lb@{lb}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{47} +\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!logical@{logical}|hyperpage}{47} +\indexentry{logical@{logical}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!numbers@{numbers}|hyperpage}{47} +\indexentry{numbers@{numbers}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!numbers@{numbers}|hyperpage}{47} +\indexentry{numbers@{numbers}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!obs\_start@{obs\_start}|hyperpage}{47} +\indexentry{obs\_start@{obs\_start}!Phylo rules@{Phylo rules}|hyperpage}{47} +\indexentry{Phylo rules@{Phylo rules}!pos@{pos}|hyperpage}{48} +\indexentry{pos@{pos}!Phylo rules@{Phylo rules}|hyperpage}{48} +\indexentry{Phylo rules@{Phylo rules}!ub@{ub}|hyperpage}{48} +\indexentry{ub@{ub}!Phylo rules@{Phylo rules}|hyperpage}{48} +\indexentry{Phylo rules@{Phylo rules}!X\_ncol@{X\_ncol}|hyperpage}{48} +\indexentry{X\_ncol@{X\_ncol}!Phylo rules@{Phylo rules}|hyperpage}{48} +\indexentry{Phylo rules@{Phylo rules}!X\_nrow@{X\_nrow}|hyperpage}{48} +\indexentry{X\_nrow@{X\_nrow}!Phylo rules@{Phylo rules}|hyperpage}{48} +\indexentry{Phylo counters@{Phylo counters}|hyperpage}{49} +\indexentry{Phylo counters@{Phylo counters}!counter\_co\_opt@{counter\_co\_opt}|hyperpage}{50} +\indexentry{counter\_co\_opt@{counter\_co\_opt}!Phylo counters@{Phylo counters}|hyperpage}{50} +\indexentry{Phylo counters@{Phylo counters}!counter\_cogain@{counter\_cogain}|hyperpage}{51} +\indexentry{counter\_cogain@{counter\_cogain}!Phylo counters@{Phylo counters}|hyperpage}{51} +\indexentry{Phylo counters@{Phylo counters}!counter\_gains@{counter\_gains}|hyperpage}{51} +\indexentry{counter\_gains@{counter\_gains}!Phylo counters@{Phylo counters}|hyperpage}{51} +\indexentry{Phylo counters@{Phylo counters}!counter\_gains\_from\_0@{counter\_gains\_from\_0}|hyperpage}{51} +\indexentry{counter\_gains\_from\_0@{counter\_gains\_from\_0}!Phylo counters@{Phylo counters}|hyperpage}{51} +\indexentry{Phylo counters@{Phylo counters}!counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}|hyperpage}{51} +\indexentry{counter\_gains\_k\_offspring@{counter\_gains\_k\_offspring}!Phylo counters@{Phylo counters}|hyperpage}{51} +\indexentry{Phylo counters@{Phylo counters}!counter\_genes\_changing@{counter\_genes\_changing}|hyperpage}{52} +\indexentry{counter\_genes\_changing@{counter\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{52} +\indexentry{Phylo counters@{Phylo counters}!counter\_k\_genes\_changing@{counter\_k\_genes\_changing}|hyperpage}{52} +\indexentry{counter\_k\_genes\_changing@{counter\_k\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{52} +\indexentry{Phylo counters@{Phylo counters}!counter\_less\_than\_p\_prop\_genes\_changing@{counter\_less\_than\_p\_prop\_genes\_changing}|hyperpage}{52} +\indexentry{counter\_less\_than\_p\_prop\_genes\_changing@{counter\_less\_than\_p\_prop\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{52} +\indexentry{Phylo counters@{Phylo counters}!counter\_longest@{counter\_longest}|hyperpage}{52} +\indexentry{counter\_longest@{counter\_longest}!Phylo counters@{Phylo counters}|hyperpage}{52} +\indexentry{Phylo counters@{Phylo counters}!counter\_loss@{counter\_loss}|hyperpage}{53} +\indexentry{counter\_loss@{counter\_loss}!Phylo counters@{Phylo counters}|hyperpage}{53} +\indexentry{Phylo counters@{Phylo counters}!counter\_maxfuns@{counter\_maxfuns}|hyperpage}{53} +\indexentry{counter\_maxfuns@{counter\_maxfuns}!Phylo counters@{Phylo counters}|hyperpage}{53} +\indexentry{Phylo counters@{Phylo counters}!counter\_neofun@{counter\_neofun}|hyperpage}{53} +\indexentry{counter\_neofun@{counter\_neofun}!Phylo counters@{Phylo counters}|hyperpage}{53} +\indexentry{Phylo counters@{Phylo counters}!counter\_neofun\_a2b@{counter\_neofun\_a2b}|hyperpage}{53} +\indexentry{counter\_neofun\_a2b@{counter\_neofun\_a2b}!Phylo counters@{Phylo counters}|hyperpage}{53} +\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_changes@{counter\_overall\_changes}|hyperpage}{54} +\indexentry{counter\_overall\_changes@{counter\_overall\_changes}!Phylo counters@{Phylo counters}|hyperpage}{54} +\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_gains@{counter\_overall\_gains}|hyperpage}{54} +\indexentry{counter\_overall\_gains@{counter\_overall\_gains}!Phylo counters@{Phylo counters}|hyperpage}{54} +\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_gains\_from\_0@{counter\_overall\_gains\_from\_0}|hyperpage}{54} +\indexentry{counter\_overall\_gains\_from\_0@{counter\_overall\_gains\_from\_0}!Phylo counters@{Phylo counters}|hyperpage}{54} +\indexentry{Phylo counters@{Phylo counters}!counter\_overall\_loss@{counter\_overall\_loss}|hyperpage}{54} +\indexentry{counter\_overall\_loss@{counter\_overall\_loss}!Phylo counters@{Phylo counters}|hyperpage}{54} +\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_first\_gain@{counter\_pairwise\_first\_gain}|hyperpage}{55} +\indexentry{counter\_pairwise\_first\_gain@{counter\_pairwise\_first\_gain}!Phylo counters@{Phylo counters}|hyperpage}{55} +\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_neofun\_singlefun@{counter\_pairwise\_neofun\_singlefun}|hyperpage}{55} +\indexentry{counter\_pairwise\_neofun\_singlefun@{counter\_pairwise\_neofun\_singlefun}!Phylo counters@{Phylo counters}|hyperpage}{55} +\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_overall\_change@{counter\_pairwise\_overall\_change}|hyperpage}{55} +\indexentry{counter\_pairwise\_overall\_change@{counter\_pairwise\_overall\_change}!Phylo counters@{Phylo counters}|hyperpage}{55} +\indexentry{Phylo counters@{Phylo counters}!counter\_pairwise\_preserving@{counter\_pairwise\_preserving}|hyperpage}{55} +\indexentry{counter\_pairwise\_preserving@{counter\_pairwise\_preserving}!Phylo counters@{Phylo counters}|hyperpage}{55} +\indexentry{Phylo counters@{Phylo counters}!counter\_preserve\_pseudogene@{counter\_preserve\_pseudogene}|hyperpage}{56} +\indexentry{counter\_preserve\_pseudogene@{counter\_preserve\_pseudogene}!Phylo counters@{Phylo counters}|hyperpage}{56} +\indexentry{Phylo counters@{Phylo counters}!counter\_prop\_genes\_changing@{counter\_prop\_genes\_changing}|hyperpage}{56} +\indexentry{counter\_prop\_genes\_changing@{counter\_prop\_genes\_changing}!Phylo counters@{Phylo counters}|hyperpage}{56} +\indexentry{Phylo counters@{Phylo counters}!counter\_subfun@{counter\_subfun}|hyperpage}{56} +\indexentry{counter\_subfun@{counter\_subfun}!Phylo counters@{Phylo counters}|hyperpage}{56} \indexentry{barry@{barry}|hyperpage}{57} \indexentry{barry::counters@{barry::counters}|hyperpage}{57} \indexentry{barry::counters::network@{barry::counters::network}|hyperpage}{58} @@ -970,1282 +980,1282 @@ \indexentry{simulate@{simulate}!DEFM@{DEFM}|hyperpage}{145} \indexentry{DEFMCounterData@{DEFMCounterData}|hyperpage}{146} \indexentry{DEFMData@{DEFMData}|hyperpage}{146} -\indexentry{DEFMRuleData@{DEFMRuleData}|hyperpage}{148} -\indexentry{DEFMRuleDynData@{DEFMRuleDynData}|hyperpage}{149} -\indexentry{Entries$<$ Cell\_Type $>$@{Entries$<$ Cell\_Type $>$}|hyperpage}{150} -\indexentry{Entries$<$ Cell\_Type $>$@{Entries$<$ Cell\_Type $>$}!Entries@{Entries}|hyperpage}{150} -\indexentry{Entries@{Entries}!Entries$<$ Cell\_Type $>$@{Entries$<$ Cell\_Type $>$}|hyperpage}{150} -\indexentry{Entries$<$ Cell\_Type $>$@{Entries$<$ Cell\_Type 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-\indexentry{nleafs@{nleafs}!Flock@{Flock}|hyperpage}{156} -\indexentry{Flock@{Flock}!nnodes@{nnodes}|hyperpage}{156} -\indexentry{nnodes@{nnodes}!Flock@{Flock}|hyperpage}{156} -\indexentry{Flock@{Flock}!nterms@{nterms}|hyperpage}{156} -\indexentry{nterms@{nterms}!Flock@{Flock}|hyperpage}{156} -\indexentry{Flock@{Flock}!ntrees@{ntrees}|hyperpage}{156} -\indexentry{ntrees@{ntrees}!Flock@{Flock}|hyperpage}{156} -\indexentry{Flock@{Flock}!operator()@{operator()}|hyperpage}{156} -\indexentry{operator()@{operator()}!Flock@{Flock}|hyperpage}{156} -\indexentry{Flock@{Flock}!parse\_polytomies@{parse\_polytomies}|hyperpage}{157} -\indexentry{parse\_polytomies@{parse\_polytomies}!Flock@{Flock}|hyperpage}{157} -\indexentry{Flock@{Flock}!print@{print}|hyperpage}{157} -\indexentry{print@{print}!Flock@{Flock}|hyperpage}{157} -\indexentry{Flock@{Flock}!set\_seed@{set\_seed}|hyperpage}{157} -\indexentry{set\_seed@{set\_seed}!Flock@{Flock}|hyperpage}{157} -\indexentry{Flock@{Flock}!support\_size@{support\_size}|hyperpage}{157} -\indexentry{support\_size@{support\_size}!Flock@{Flock}|hyperpage}{157} -\indexentry{Flock@{Flock}!dat@{dat}|hyperpage}{158} -\indexentry{dat@{dat}!Flock@{Flock}|hyperpage}{158} -\indexentry{Flock@{Flock}!initialized@{initialized}|hyperpage}{158} -\indexentry{initialized@{initialized}!Flock@{Flock}|hyperpage}{158} -\indexentry{Flock@{Flock}!model@{model}|hyperpage}{158} -\indexentry{model@{model}!Flock@{Flock}|hyperpage}{158} -\indexentry{Flock@{Flock}!nfunctions@{nfunctions}|hyperpage}{158} -\indexentry{nfunctions@{nfunctions}!Flock@{Flock}|hyperpage}{158} -\indexentry{Flock@{Flock}!rengine@{rengine}|hyperpage}{158} -\indexentry{rengine@{rengine}!Flock@{Flock}|hyperpage}{158} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}|hyperpage}{159} -\indexentry{FreqTable$<$ T $>$@{FreqTable$<$ T $>$}!FreqTable@{FreqTable}|hyperpage}{160} -\indexentry{FreqTable@{FreqTable}!FreqTable$<$ T $>$@{FreqTable$<$ T 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+\indexentry{set\_seed@{set\_seed}!Geese@{Geese}|hyperpage}{172} +\indexentry{Geese@{Geese}!simulate@{simulate}|hyperpage}{172} +\indexentry{simulate@{simulate}!Geese@{Geese}|hyperpage}{172} +\indexentry{Geese@{Geese}!support\_size@{support\_size}|hyperpage}{172} +\indexentry{support\_size@{support\_size}!Geese@{Geese}|hyperpage}{172} +\indexentry{Geese@{Geese}!update\_annotations@{update\_annotations}|hyperpage}{172} +\indexentry{update\_annotations@{update\_annotations}!Geese@{Geese}|hyperpage}{172} +\indexentry{Geese@{Geese}!delete\_rengine@{delete\_rengine}|hyperpage}{173} +\indexentry{delete\_rengine@{delete\_rengine}!Geese@{Geese}|hyperpage}{173} +\indexentry{Geese@{Geese}!delete\_support@{delete\_support}|hyperpage}{173} +\indexentry{delete\_support@{delete\_support}!Geese@{Geese}|hyperpage}{173} +\indexentry{Geese@{Geese}!etype\_default@{etype\_default}|hyperpage}{173} +\indexentry{etype\_default@{etype\_default}!Geese@{Geese}|hyperpage}{173} +\indexentry{Geese@{Geese}!etype\_duplication@{etype\_duplication}|hyperpage}{173} +\indexentry{etype\_duplication@{etype\_duplication}!Geese@{Geese}|hyperpage}{173} +\indexentry{Geese@{Geese}!etype\_either@{etype\_either}|hyperpage}{173} +\indexentry{etype\_either@{etype\_either}!Geese@{Geese}|hyperpage}{173} +\indexentry{Geese@{Geese}!etype\_speciation@{etype\_speciation}|hyperpage}{174} +\indexentry{etype\_speciation@{etype\_speciation}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!initialized@{initialized}|hyperpage}{174} +\indexentry{initialized@{initialized}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!map\_to\_state\_id@{map\_to\_state\_id}|hyperpage}{174} +\indexentry{map\_to\_state\_id@{map\_to\_state\_id}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!nfunctions@{nfunctions}|hyperpage}{174} +\indexentry{nfunctions@{nfunctions}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!nodes@{nodes}|hyperpage}{174} +\indexentry{nodes@{nodes}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!pset\_loc@{pset\_loc}|hyperpage}{174} +\indexentry{pset\_loc@{pset\_loc}!Geese@{Geese}|hyperpage}{174} +\indexentry{Geese@{Geese}!reduced\_sequence@{reduced\_sequence}|hyperpage}{175} +\indexentry{reduced\_sequence@{reduced\_sequence}!Geese@{Geese}|hyperpage}{175} +\indexentry{Geese@{Geese}!sequence@{sequence}|hyperpage}{175} +\indexentry{sequence@{sequence}!Geese@{Geese}|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 $>$}|hyperpage}{176} +\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}{181} +\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}{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 $>$}!Model@{Model}|hyperpage}{181} \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 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$>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}!````~Model@{$\sim$Model}|hyperpage}{182} -\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}{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\_array@{add\_array}|hyperpage}{182} -\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}{182} -\indexentry{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, 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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}{182} +\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}{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\_counter@{add\_counter}|hyperpage}{182} +\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}{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\_hasher@{add\_hasher}|hyperpage}{182} +\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}{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@{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@{add\_rule}|hyperpage}{183} \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}{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}{184} -\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}{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 $>$}!add\_rule\_dyn@{add\_rule\_dyn}|hyperpage}{184} -\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}{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 $>$}!add\_rule\_dyn@{add\_rule\_dyn}|hyperpage}{184} -\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}{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 $>$}!colnames@{colnames}|hyperpage}{184} -\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}{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 $>$}!conditional\_prob@{conditional\_prob}|hyperpage}{184} -\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}{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 $>$}!gen\_key@{gen\_key}|hyperpage}{185} -\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}{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\_arrays2support@{get\_arrays2support}|hyperpage}{185} -\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}{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\_counters@{get\_counters}|hyperpage}{185} 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-\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 $>$}!add\_rule\_dyn@{add\_rule\_dyn}|hyperpage}{183} +\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}{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\_dyn@{add\_rule\_dyn}|hyperpage}{183} +\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}{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 $>$}!colnames@{colnames}|hyperpage}{183} +\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}{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 $>$}!conditional\_prob@{conditional\_prob}|hyperpage}{183} +\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}{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 $>$}!gen\_key@{gen\_key}|hyperpage}{184} +\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}{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\_arrays2support@{get\_arrays2support}|hyperpage}{184} +\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}{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\_counters@{get\_counters}|hyperpage}{184} +\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}{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\_likelihoods@{get\_likelihoods}|hyperpage}{185} +\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}{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\_normalizing\_constants@{get\_normalizing\_constants}|hyperpage}{185} +\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}{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@{get\_pset}|hyperpage}{185} +\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}{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\_arrays@{get\_pset\_arrays}|hyperpage}{185} +\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}{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\_locations@{get\_pset\_locations}|hyperpage}{185} +\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}{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\_probs@{get\_pset\_probs}|hyperpage}{186} +\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}{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\_sizes@{get\_pset\_sizes}|hyperpage}{186} +\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}{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\_stats@{get\_pset\_stats}|hyperpage}{186} +\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}{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\_stats@{get\_pset\_stats}|hyperpage}{186} +\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}{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\_rengine@{get\_rengine}|hyperpage}{187} +\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}{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\_rules@{get\_rules}|hyperpage}{187} +\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}{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\_rules\_dyn@{get\_rules\_dyn}|hyperpage}{187} +\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}{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\_support@{get\_stats\_support}|hyperpage}{187} +\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}{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\_support\_sizes@{get\_stats\_support\_sizes}|hyperpage}{187} +\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}{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\_support\_sizes\_acc@{get\_stats\_support\_sizes\_acc}|hyperpage}{188} +\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}{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\_target@{get\_stats\_target}|hyperpage}{188} +\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}{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\_support\_fun@{get\_support\_fun}|hyperpage}{188} +\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}{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}{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 $>$}!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}{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\_total@{likelihood\_total}|hyperpage}{190} +\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}{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 $>$}!nrules@{nrules}|hyperpage}{190} +\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}{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 $>$}!nrules\_dyn@{nrules\_dyn}|hyperpage}{190} +\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}{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 $>$}!nterms@{nterms}|hyperpage}{190} +\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}{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 $>$}!operator=@{operator=}|hyperpage}{191} +\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}{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 $>$}!print@{print}|hyperpage}{191} +\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}{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 $>$}!print\_stats@{print\_stats}|hyperpage}{191} +\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}{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 $>$}!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 $>$}!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{Model$<$ Array\_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}{192} +\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}{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\_rengine@{set\_rengine}|hyperpage}{192} +\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}{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\_rules@{set\_rules}|hyperpage}{192} +\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}{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\_rules\_dyn@{set\_rules\_dyn}|hyperpage}{193} +\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}{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\_seed@{set\_seed}|hyperpage}{193} +\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}{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\_transform\_model@{set\_transform\_model}|hyperpage}{193} +\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}{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@{size}|hyperpage}{194} +\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}{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\_unique@{size\_unique}|hyperpage}{194} +\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}{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 $>$}!store\_psets@{store\_psets}|hyperpage}{194} +\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}{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 $>$}!support\_size@{support\_size}|hyperpage}{194} +\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}{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 $>$}!transform\_model@{transform\_model}|hyperpage}{194} +\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}{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\_likelihoods@{update\_likelihoods}|hyperpage}{195} +\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}{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\_normalizing\_constants@{update\_normalizing\_constants}|hyperpage}{195} +\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}{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\_pset\_probs@{update\_pset\_probs}|hyperpage}{195} +\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}{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 $>$}!arrays2support@{arrays2support}|hyperpage}{196} +\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}{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 $>$}!counter\_fun@{counter\_fun}|hyperpage}{196} +\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}{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 $>$}!counters@{counters}|hyperpage}{196} +\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}{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\_counters@{delete\_counters}|hyperpage}{196} +\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}{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\_rengine@{delete\_rengine}|hyperpage}{196} +\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}{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@{delete\_rules}|hyperpage}{197} +\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}{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\_dyn@{delete\_rules\_dyn}|hyperpage}{197} +\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}{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 $>$}!first\_calc\_done@{first\_calc\_done}|hyperpage}{197} +\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}{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 $>$}!keys2support@{keys2support}|hyperpage}{197} +\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}{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 $>$}!normalizing\_constants@{normalizing\_constants}|hyperpage}{197} +\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}{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 $>$}!params\_last@{params\_last}|hyperpage}{198} +\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}{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\_arrays@{pset\_arrays}|hyperpage}{198} +\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}{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\_locations@{pset\_locations}|hyperpage}{198} +\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}{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\_probs@{pset\_probs}|hyperpage}{198} +\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}{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\_sizes@{pset\_sizes}|hyperpage}{199} +\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}{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\_stats@{pset\_stats}|hyperpage}{199} +\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}{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 $>$}!rengine@{rengine}|hyperpage}{199} +\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}{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 $>$}!rules@{rules}|hyperpage}{199} +\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}{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 $>$}!rules\_dyn@{rules\_dyn}|hyperpage}{200} +\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}{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\_likelihood@{stats\_likelihood}|hyperpage}{200} +\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}{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@{stats\_support}|hyperpage}{200} +\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}{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\_n\_arrays@{stats\_support\_n\_arrays}|hyperpage}{200} +\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}{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@{stats\_support\_sizes}|hyperpage}{201} +\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}{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\_acc@{stats\_support\_sizes\_acc}|hyperpage}{201} +\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}{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\_target@{stats\_target}|hyperpage}{201} +\indexentry{stats\_target@{stats\_target}!Model$<$ Array\_Type, 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Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$@{Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}|hyperpage}{202} +\indexentry{NetCounterData@{NetCounterData}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{203} +\indexentry{NetCounterData@{NetCounterData}!````~NetCounterData@{$\sim$NetCounterData}|hyperpage}{204} +\indexentry{````~NetCounterData@{$\sim$NetCounterData}!NetCounterData@{NetCounterData}|hyperpage}{204} +\indexentry{NetCounterData@{NetCounterData}!indices@{indices}|hyperpage}{204} +\indexentry{indices@{indices}!NetCounterData@{NetCounterData}|hyperpage}{204} 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+\indexentry{counter@{counter}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{338} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!counter\_deleted@{counter\_deleted}|hyperpage}{339} +\indexentry{counter\_deleted@{counter\_deleted}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{339} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!counters@{counters}|hyperpage}{339} +\indexentry{counters@{counters}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{339} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!counters\_@{counters\_}|hyperpage}{339} +\indexentry{counters\_@{counters\_}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{339} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!current\_stats@{current\_stats}|hyperpage}{339} +\indexentry{current\_stats@{current\_stats}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{339} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!EmptyArray@{EmptyArray}|hyperpage}{339} +\indexentry{EmptyArray@{EmptyArray}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{339} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!f\_@{f\_}|hyperpage}{340} +\indexentry{f\_@{f\_}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{340} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!j@{j}|hyperpage}{340} +\indexentry{j@{j}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{340} +\indexentry{statscounter-\/meat.hpp@{statscounter-\/meat.hpp}!return@{return}|hyperpage}{340} +\indexentry{return@{return}!statscounter-\/meat.hpp@{statscounter-\/meat.hpp}|hyperpage}{340} +\indexentry{include/barry/support-\/bones.hpp@{include/barry/support-\/bones.hpp}|hyperpage}{340} +\indexentry{include/barry/support-\/meat.hpp@{include/barry/support-\/meat.hpp}|hyperpage}{341} +\indexentry{support-\/meat.hpp@{support-\/meat.hpp}!BARRY\_SUPPORT\_MEAT\_HPP@{BARRY\_SUPPORT\_MEAT\_HPP}|hyperpage}{341} +\indexentry{BARRY\_SUPPORT\_MEAT\_HPP@{BARRY\_SUPPORT\_MEAT\_HPP}!support-\/meat.hpp@{support-\/meat.hpp}|hyperpage}{341} +\indexentry{include/barry/typedefs.hpp@{include/barry/typedefs.hpp}|hyperpage}{342} +\indexentry{typedefs.hpp@{typedefs.hpp}!Col\_type@{Col\_type}|hyperpage}{344} +\indexentry{Col\_type@{Col\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{344} +\indexentry{typedefs.hpp@{typedefs.hpp}!Counter\_fun\_type@{Counter\_fun\_type}|hyperpage}{344} +\indexentry{Counter\_fun\_type@{Counter\_fun\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{344} +\indexentry{typedefs.hpp@{typedefs.hpp}!Counts\_type@{Counts\_type}|hyperpage}{344} +\indexentry{Counts\_type@{Counts\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{344} +\indexentry{typedefs.hpp@{typedefs.hpp}!Hasher\_fun\_type@{Hasher\_fun\_type}|hyperpage}{344} +\indexentry{Hasher\_fun\_type@{Hasher\_fun\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{344} +\indexentry{typedefs.hpp@{typedefs.hpp}!MapVec\_type@{MapVec\_type}|hyperpage}{345} +\indexentry{MapVec\_type@{MapVec\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{345} +\indexentry{typedefs.hpp@{typedefs.hpp}!Row\_type@{Row\_type}|hyperpage}{345} +\indexentry{Row\_type@{Row\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{345} +\indexentry{typedefs.hpp@{typedefs.hpp}!Rule\_fun\_type@{Rule\_fun\_type}|hyperpage}{345} +\indexentry{Rule\_fun\_type@{Rule\_fun\_type}!typedefs.hpp@{typedefs.hpp}|hyperpage}{345} +\indexentry{typedefs.hpp@{typedefs.hpp}!sort\_array@{sort\_array}|hyperpage}{345} +\indexentry{sort\_array@{sort\_array}!typedefs.hpp@{typedefs.hpp}|hyperpage}{345} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_equal@{vec\_equal}|hyperpage}{346} +\indexentry{vec\_equal@{vec\_equal}!typedefs.hpp@{typedefs.hpp}|hyperpage}{346} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_equal\_approx@{vec\_equal\_approx}|hyperpage}{346} +\indexentry{vec\_equal\_approx@{vec\_equal\_approx}!typedefs.hpp@{typedefs.hpp}|hyperpage}{346} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_inner\_prod@{vec\_inner\_prod}|hyperpage}{346} +\indexentry{vec\_inner\_prod@{vec\_inner\_prod}!typedefs.hpp@{typedefs.hpp}|hyperpage}{346} +\indexentry{typedefs.hpp@{typedefs.hpp}!vec\_inner\_prod@{vec\_inner\_prod}|hyperpage}{347} +\indexentry{vec\_inner\_prod@{vec\_inner\_prod}!typedefs.hpp@{typedefs.hpp}|hyperpage}{347} +\indexentry{README.md@{README.md}|hyperpage}{347} diff --git a/latex/refman.ilg b/latex/refman.ilg index 5aed002d9..ad018df46 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 (27767 comparisons). -Generating output file refman.ind......done (2926 lines written, 0 warnings). +Scanning input file refman.idx......done (2261 entries accepted, 0 rejected). +Sorting entries......................done (27285 comparisons). +Generating output file refman.ind......done (2935 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 6427b25f9..a8fa49557 100644 --- a/latex/refman.ind +++ b/latex/refman.ind @@ -34,45 +34,45 @@ \item {$\sim$Counters} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{137} \item {$\sim$DEFMCounterData} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Phylo rules}, \hyperpage{45} \item {$\sim$DEFMData} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Phylo rules}, \hyperpage{45} \item {$\sim$DEFMRuleDynData} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Phylo rules}, \hyperpage{45} \item {$\sim$Entries} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} \item {$\sim$Flock} - \subitem {Flock}, \hyperpage{153} + \subitem {Flock}, \hyperpage{152} \item {$\sim$FreqTable} - \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {FreqTable$<$ T $>$}, \hyperpage{159} \item {$\sim$Geese} - \subitem {Geese}, \hyperpage{166} + \subitem {Geese}, \hyperpage{165} \item {$\sim$Model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{182} + \hyperpage{181} \item {$\sim$NetCounterData} - \subitem {NetCounterData}, \hyperpage{205} + \subitem {NetCounterData}, \hyperpage{204} \item {$\sim$NetworkData} - \subitem {NetworkData}, \hyperpage{207} + \subitem {NetworkData}, \hyperpage{206} \item {$\sim$Node} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{209} \item {$\sim$PhyloRuleDynData} - \subitem {PhyloRuleDynData}, \hyperpage{219} + \subitem {PhyloRuleDynData}, \hyperpage{218} \item {$\sim$PowerSet} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{222} \item {$\sim$Progress} - \subitem {Progress}, \hyperpage{228} + \subitem {Progress}, \hyperpage{227} \item {$\sim$Rule} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} \item {$\sim$Rules} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} \item {$\sim$StatsCounter} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{237} + \hyperpage{236} \item {$\sim$Support} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} + \hyperpage{241} \indexspace @@ -80,63 +80,63 @@ \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {add} \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{125, 126} - \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {FreqTable$<$ T $>$}, \hyperpage{159} \item {add\_array} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{182} + \hyperpage{181} \item {add\_counter} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{137, 138} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{183} + \hyperpage{182} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{237} + \hyperpage{236} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242} + \hyperpage{241} \item {add\_data} - \subitem {Flock}, \hyperpage{153} + \subitem {Flock}, \hyperpage{152} \item {add\_dims} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \item {add\_hash} \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{183} + \hyperpage{182} \item {add\_rule} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{183, 184} + \hyperpage{182, 183} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \hyperpage{222} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{242, 243} + \hyperpage{241, 242} \item {add\_rule\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{183} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{242} \item {annotations} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{210} \item {Array} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{129} \item {array} - \subitem {Node}, \hyperpage{211} - \subitem {Phylo rules}, \hyperpage{44} + \subitem {Node}, \hyperpage{210} + \subitem {Phylo rules}, \hyperpage{45} \item {arrays} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{210} \item {arrays2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{196} \item {AS\_ONE} \subitem {EXISTS}, \hyperpage{59} \item {as\_vector} - \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {FreqTable$<$ T $>$}, \hyperpage{159} \item {AS\_ZERO} \subitem {EXISTS}, \hyperpage{59} \item {at} - \subitem {Phylo rules}, \hyperpage{39} - \subitem {PhyloCounterData}, \hyperpage{216} + \subitem {Phylo rules}, \hyperpage{40} + \subitem {PhyloCounterData}, \hyperpage{215} \indexspace @@ -189,26 +189,26 @@ \subitem {zero\_col}, \hyperpage{74} \subitem {zero\_row}, \hyperpage{74} \item {barray-\/meat-\/operators.hpp} - \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} + \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} \item {barray-\/meat.hpp} - \subitem {COL}, \hyperpage{258} - \subitem {ROW}, \hyperpage{259} + \subitem {COL}, \hyperpage{256} + \subitem {ROW}, \hyperpage{257} \item {BARRAY\_TEMPLATE} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{254--256} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{252--254} \item {BARRAY\_TEMPLATE\_ARGS} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255}, - \hyperpage{257} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253}, + \hyperpage{255} \item {BARRAY\_TYPE} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255}, - \hyperpage{257} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{253}, + \hyperpage{255} \item {BArrayCell} \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} \item {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{76} @@ -295,19 +295,19 @@ \subitem {zero\_col}, \hyperpage{96} \subitem {zero\_row}, \hyperpage{96} \item {barraydense-\/meat-\/operators.hpp} - \subitem {BDENSE\_TEMPLATE}, \hyperpage{261}, \hyperpage{263} - \subitem {BDENSE\_TEMPLATE\_ARGS}, \hyperpage{261}, \hyperpage{263} - \subitem {BDENSE\_TYPE}, \hyperpage{262}, \hyperpage{264} + \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 {COL}, \hyperpage{262} \subitem {POS}, \hyperpage{262} - \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} + \subitem {POS\_N}, \hyperpage{263} + \subitem {ROW}, \hyperpage{263} + \subitem {ZERO\_CELL}, \hyperpage{263} \item {BArrayDenseCell} \subitem {BArrayDenseCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{99} @@ -332,9 +332,9 @@ \subitem {operator=}, \hyperpage{100} \subitem {operator==}, \hyperpage{101} \item {barraydensecell-\/bones.hpp} - \subitem {POS}, \hyperpage{266} + \subitem {POS}, \hyperpage{264} \item {barraydensecell-\/meat.hpp} - \subitem {POS}, \hyperpage{266} + \subitem {POS}, \hyperpage{264} \item {BArrayDenseCell\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{102} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, @@ -361,9 +361,9 @@ \subitem {operator()}, \hyperpage{103} \subitem {size}, \hyperpage{103} \item {barraydensecol-\/bones.hpp} - \subitem {POS}, \hyperpage{267} - \subitem {POS\_N}, \hyperpage{267} - \subitem {ZERO\_CELL}, \hyperpage{268} + \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{105} @@ -396,9 +396,9 @@ \subitem {operator()}, \hyperpage{108} \subitem {size}, \hyperpage{108} \item {barraydenserow-\/bones.hpp} - \subitem {POS}, \hyperpage{269} - \subitem {POS\_N}, \hyperpage{269} - \subitem {ZERO\_CELL}, \hyperpage{269} + \subitem {POS}, \hyperpage{267} + \subitem {POS\_N}, \hyperpage{267} + \subitem {ZERO\_CELL}, \hyperpage{267} \item {BArrayDenseRow\_const} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{109} @@ -429,9 +429,9 @@ \subitem {operator=}, \hyperpage{113} \subitem {operator==}, \hyperpage{113} \item {barrayrow-\/meat.hpp} - \subitem {BROW\_TEMPLATE}, \hyperpage{270, 271} - \subitem {BROW\_TEMPLATE\_ARGS}, \hyperpage{270} - \subitem {BROW\_TYPE}, \hyperpage{270} + \subitem {BROW\_TEMPLATE}, \hyperpage{268, 269} + \subitem {BROW\_TEMPLATE\_ARGS}, \hyperpage{268} + \subitem {BROW\_TYPE}, \hyperpage{268} \item {BArrayRow\_const} \subitem {BArrayRow\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{114} @@ -486,79 +486,79 @@ \subitem {size}, \hyperpage{123} \item {barry}, \hyperpage{57} \item {barry-\/configuration.hpp} - \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} + \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} \item {barry-\/debug.hpp} - \subitem {BARRY\_DEBUG\_LEVEL}, \hyperpage{274} + \subitem {BARRY\_DEBUG\_LEVEL}, \hyperpage{272} \item {barry-\/macros.hpp} - \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} + \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} \item {barry.hpp} - \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} + \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{57} \item {barry::counters::network}, \hyperpage{58} \item {BARRY\_CHECK\_SUPPORT} - \subitem {barry-\/configuration.hpp}, \hyperpage{273} + \subitem {barry-\/configuration.hpp}, \hyperpage{271} \item {BARRY\_DEBUG\_LEVEL} - \subitem {barry-\/debug.hpp}, \hyperpage{274} + \subitem {barry-\/debug.hpp}, \hyperpage{272} \item {BARRY\_HPP} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {BARRY\_ISFINITE} - \subitem {barry-\/configuration.hpp}, \hyperpage{273} + \subitem {barry-\/configuration.hpp}, \hyperpage{271} \item {BARRY\_MAX\_NUM\_ELEMENTS} - \subitem {barry-\/configuration.hpp}, \hyperpage{273} + \subitem {barry-\/configuration.hpp}, \hyperpage{271} \item {BARRY\_NCORES\_ARG} - \subitem {barry-\/macros.hpp}, \hyperpage{275} + \subitem {barry-\/macros.hpp}, \hyperpage{273} \item {BARRY\_ONE} - \subitem {barry-\/macros.hpp}, \hyperpage{275} + \subitem {barry-\/macros.hpp}, \hyperpage{273} \item {BARRY\_ONE\_DENSE} - \subitem {barry-\/macros.hpp}, \hyperpage{275} + \subitem {barry-\/macros.hpp}, \hyperpage{273} \item {BARRY\_PROGRESS\_BAR\_WIDTH} - \subitem {progress.hpp}, \hyperpage{335} + \subitem {progress.hpp}, \hyperpage{333} \item {BARRY\_SAFE\_EXP} - \subitem {barry-\/configuration.hpp}, \hyperpage{273} + \subitem {barry-\/configuration.hpp}, \hyperpage{271} \item {BARRY\_SUPPORT\_MEAT\_HPP} - \subitem {support-\/meat.hpp}, \hyperpage{343} + \subitem {support-\/meat.hpp}, \hyperpage{341} \item {BARRY\_UNUSED} - \subitem {barry-\/macros.hpp}, \hyperpage{276} + \subitem {barry-\/macros.hpp}, \hyperpage{274} \item {BARRY\_VERSION} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {BARRY\_VERSION\_MAYOR} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {BARRY\_VERSION\_MINOR} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {BARRY\_ZERO} - \subitem {barry-\/macros.hpp}, \hyperpage{276} + \subitem {barry-\/macros.hpp}, \hyperpage{274} \item {BARRY\_ZERO\_DENSE} - \subitem {barry-\/macros.hpp}, \hyperpage{276} + \subitem {barry-\/macros.hpp}, \hyperpage{274} \item {BARRY\_ZERO\_NETWORK} - \subitem {network.hpp}, \hyperpage{304} + \subitem {network.hpp}, \hyperpage{302} \item {BARRY\_ZERO\_NETWORK\_DENSE} - \subitem {network.hpp}, \hyperpage{304} + \subitem {network.hpp}, \hyperpage{302} \item {BDENSE\_TEMPLATE} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{261}, - \hyperpage{263} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{259}, + \hyperpage{261} \item {BDENSE\_TEMPLATE\_ARGS} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{261}, - \hyperpage{263} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{259}, + \hyperpage{261} \item {BDENSE\_TYPE} - \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{262}, - \hyperpage{264} + \subitem {barraydense-\/meat-\/operators.hpp}, \hyperpage{260}, + \hyperpage{262} \item {begin} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} @@ -572,33 +572,33 @@ \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{121} - \subitem {PhyloCounterData}, \hyperpage{217} + \subitem {PhyloCounterData}, \hyperpage{216} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \hyperpage{222} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \item {blengths} - \subitem {NodeData}, \hyperpage{214} + \subitem {NodeData}, \hyperpage{213} \item {BOTH} \subitem {CHECK}, \hyperpage{58} \subitem {EXISTS}, \hyperpage{59} \item {BROW\_TEMPLATE} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{270, 271} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{268, 269} \item {BROW\_TEMPLATE\_ARGS} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{270} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{268} \item {BROW\_TYPE} - \subitem {barrayrow-\/meat.hpp}, \hyperpage{270} + \subitem {barrayrow-\/meat.hpp}, \hyperpage{268} \indexspace \item {calc} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{223} + \hyperpage{222} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{243} + \hyperpage{242} \item {calc\_reduced\_sequence} - \subitem {Geese}, \hyperpage{166} + \subitem {Geese}, \hyperpage{165} \item {calc\_sequence} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{166} \item {Cell} \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{124, 125} \item {Cell$<$ Cell\_Type $>$}, \hyperpage{123} @@ -615,7 +615,7 @@ \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{247} + \hyperpage{246} \item {CHECK}, \hyperpage{58} \subitem {BOTH}, \hyperpage{58} \subitem {NONE}, \hyperpage{58} @@ -625,30 +625,30 @@ \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{85} - \subitem {FreqTable$<$ T $>$}, \hyperpage{160} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338} + \subitem {FreqTable$<$ T $>$}, \hyperpage{159} + \subitem {statscounter-\/meat.hpp}, \hyperpage{336} \item {COL} - \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} + \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} \item {col} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{65} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{86} \item {Col\_type} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{344} \item {colnames} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{167} + \subitem {Flock}, \hyperpage{153} + \subitem {Geese}, \hyperpage{166} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{183} \item {colsum} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{86} \item {conditional\_prob} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{184} + \hyperpage{183} \item {ConstBArrayRowIter} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{129} @@ -662,41 +662,41 @@ \subitem {iter}, \hyperpage{130} \item {coordiantes\_n\_free} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{246} \item {coordiantes\_n\_locked} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{247} \item {coordinates\_free} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} + \hyperpage{224} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{247} \item {coordinates\_locked} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} + \hyperpage{224} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{247} \item {count} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} \item {count\_all} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{237} + \hyperpage{236} \item {count\_current} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \item {count\_fun} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} - \subitem {counters-\/meat.hpp}, \hyperpage{284} + \subitem {counters-\/meat.hpp}, \hyperpage{282} \item {count\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \item {count\_init} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \item {Counter} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{132} \item {counter} - \subitem {counters-\/meat.hpp}, \hyperpage{290} - \subitem {statscounter-\/meat.hpp}, \hyperpage{340} + \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {statscounter-\/meat.hpp}, \hyperpage{338} \item {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{130} \subitem {$\sim$Counter}, \hyperpage{132} \subitem {count}, \hyperpage{133} @@ -714,51 +714,51 @@ \subitem {operator=}, \hyperpage{133, 134} \subitem {set\_hasher}, \hyperpage{134} \item {counter\_} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{288} \item {counter\_absdiff} \subitem {Network counters}, \hyperpage{26} \item {counter\_co\_opt} \subitem {Counting}, \hyperpage{18} - \subitem {Phylo counters}, \hyperpage{49} + \subitem {Phylo counters}, \hyperpage{50} \item {counter\_cogain} \subitem {Counting}, \hyperpage{18} - \subitem {Phylo counters}, \hyperpage{49} + \subitem {Phylo counters}, \hyperpage{51} \item {counter\_css\_census01} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {counter\_css\_census02} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {counter\_css\_census03} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {counter\_css\_census04} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {counter\_css\_census05} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {counter\_css\_census06} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {counter\_css\_census07} - \subitem {network-\/css.hpp}, \hyperpage{298} + \subitem {network-\/css.hpp}, \hyperpage{296} \item {counter\_css\_census08} - \subitem {network-\/css.hpp}, \hyperpage{299} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_census09} - \subitem {network-\/css.hpp}, \hyperpage{299} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_census10} - \subitem {network-\/css.hpp}, \hyperpage{299} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_completely\_false\_recip\_comiss} - \subitem {network-\/css.hpp}, \hyperpage{299} + \subitem {network-\/css.hpp}, \hyperpage{297} \item {counter\_css\_completely\_false\_recip\_omiss} - \subitem {network-\/css.hpp}, \hyperpage{300} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_mixed\_recip} - \subitem {network-\/css.hpp}, \hyperpage{300} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_partially\_false\_recip\_commi} - \subitem {network-\/css.hpp}, \hyperpage{300} + \subitem {network-\/css.hpp}, \hyperpage{298} \item {counter\_css\_partially\_false\_recip\_omiss} - \subitem {network-\/css.hpp}, \hyperpage{301} + \subitem {network-\/css.hpp}, \hyperpage{299} \item {counter\_ctriads} \subitem {Network counters}, \hyperpage{27} \item {counter\_degree} \subitem {Network counters}, \hyperpage{27} \item {counter\_deleted} - \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \item {counter\_density} \subitem {Network counters}, \hyperpage{27} \item {counter\_diff} @@ -769,23 +769,23 @@ \subitem {Network counters}, \hyperpage{28} \item {counter\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{196} \item {Counter\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{344} \item {COUNTER\_FUNCTION} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {counter\_gains} \subitem {Counting}, \hyperpage{18} - \subitem {Phylo counters}, \hyperpage{49} + \subitem {Phylo counters}, \hyperpage{51} \item {counter\_gains\_from\_0} \subitem {Counting}, \hyperpage{18} - \subitem {Phylo counters}, \hyperpage{49} + \subitem {Phylo counters}, \hyperpage{51} \item {counter\_gains\_k\_offspring} \subitem {Counting}, \hyperpage{19} - \subitem {Phylo counters}, \hyperpage{50} + \subitem {Phylo counters}, \hyperpage{51} \item {counter\_genes\_changing} \subitem {Counting}, \hyperpage{19} - \subitem {Phylo counters}, \hyperpage{50} + \subitem {Phylo counters}, \hyperpage{52} \item {counter\_idegree} \subitem {Network counters}, \hyperpage{29} \item {counter\_idegree15} @@ -796,31 +796,31 @@ \subitem {Network counters}, \hyperpage{30} \item {counter\_k\_genes\_changing} \subitem {Counting}, \hyperpage{19} - \subitem {Phylo counters}, \hyperpage{50} + \subitem {Phylo counters}, \hyperpage{52} \item {COUNTER\_LAMBDA} - \subitem {barry.hpp}, \hyperpage{278} + \subitem {barry.hpp}, \hyperpage{276} \item {counter\_less\_than\_p\_prop\_genes\_changing} \subitem {Counting}, \hyperpage{19} - \subitem {Phylo counters}, \hyperpage{50} + \subitem {Phylo counters}, \hyperpage{52} \item {counter\_logit\_intercept} \subitem {Network counters}, \hyperpage{30} \item {counter\_longest} \subitem {Counting}, \hyperpage{20} - \subitem {Phylo counters}, \hyperpage{51} + \subitem {Phylo counters}, \hyperpage{52} \item {counter\_loss} \subitem {Counting}, \hyperpage{20} - \subitem {Phylo counters}, \hyperpage{51} + \subitem {Phylo counters}, \hyperpage{53} \item {counter\_maxfuns} \subitem {Counting}, \hyperpage{20} - \subitem {Phylo counters}, \hyperpage{51} + \subitem {Phylo counters}, \hyperpage{53} \item {counter\_mutual} \subitem {Network counters}, \hyperpage{31} \item {counter\_neofun} \subitem {Counting}, \hyperpage{20} - \subitem {Phylo counters}, \hyperpage{51} + \subitem {Phylo counters}, \hyperpage{53} \item {counter\_neofun\_a2b} \subitem {Counting}, \hyperpage{21} - \subitem {Phylo counters}, \hyperpage{52} + \subitem {Phylo counters}, \hyperpage{53} \item {counter\_nodecov} \subitem {Network counters}, \hyperpage{31} \item {counter\_nodeicov} @@ -839,42 +839,42 @@ \subitem {Network counters}, \hyperpage{33} \item {counter\_overall\_changes} \subitem {Counting}, \hyperpage{21} - \subitem {Phylo counters}, \hyperpage{52} + \subitem {Phylo counters}, \hyperpage{54} \item {counter\_overall\_gains} \subitem {Counting}, \hyperpage{21} - \subitem {Phylo counters}, \hyperpage{52} + \subitem {Phylo counters}, \hyperpage{54} \item {counter\_overall\_gains\_from\_0} \subitem {Counting}, \hyperpage{21} - \subitem {Phylo counters}, \hyperpage{52} + \subitem {Phylo counters}, \hyperpage{54} \item {counter\_overall\_loss} \subitem {Counting}, \hyperpage{22} - \subitem {Phylo counters}, \hyperpage{53} + \subitem {Phylo counters}, \hyperpage{54} \item {counter\_pairwise\_first\_gain} \subitem {Counting}, \hyperpage{22} - \subitem {Phylo counters}, \hyperpage{53} + \subitem {Phylo counters}, \hyperpage{55} \item {counter\_pairwise\_neofun\_singlefun} \subitem {Counting}, \hyperpage{22} - \subitem {Phylo counters}, \hyperpage{53} + \subitem {Phylo counters}, \hyperpage{55} \item {counter\_pairwise\_overall\_change} \subitem {Counting}, \hyperpage{22} - \subitem {Phylo counters}, \hyperpage{53} + \subitem {Phylo counters}, \hyperpage{55} \item {counter\_pairwise\_preserving} \subitem {Counting}, \hyperpage{23} - \subitem {Phylo counters}, \hyperpage{54} + \subitem {Phylo counters}, \hyperpage{55} \item {counter\_preserve\_pseudogene} \subitem {Counting}, \hyperpage{23} - \subitem {Phylo counters}, \hyperpage{54} + \subitem {Phylo counters}, \hyperpage{56} \item {counter\_prop\_genes\_changing} \subitem {Counting}, \hyperpage{23} - \subitem {Phylo counters}, \hyperpage{54} + \subitem {Phylo counters}, \hyperpage{56} \item {counter\_subfun} \subitem {Counting}, \hyperpage{23} - \subitem {Phylo counters}, \hyperpage{54} + \subitem {Phylo counters}, \hyperpage{56} \item {COUNTER\_TEMPLATE} - \subitem {counters-\/meat.hpp}, \hyperpage{282}, - \hyperpage{284, 285} + \subitem {counters-\/meat.hpp}, \hyperpage{280}, + \hyperpage{282, 283} \item {COUNTER\_TEMPLATE\_ARGS} - \subitem {counters-\/meat.hpp}, \hyperpage{282} + \subitem {counters-\/meat.hpp}, \hyperpage{280} \item {counter\_transition} \subitem {Network counters}, \hyperpage{33} \item {counter\_transition\_formula} @@ -882,14 +882,14 @@ \item {counter\_ttriads} \subitem {Network counters}, \hyperpage{34, 35} \item {COUNTER\_TYPE} - \subitem {counters-\/meat.hpp}, \hyperpage{283} + \subitem {counters-\/meat.hpp}, \hyperpage{281} \item {Counters} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136, 137} \item {counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} - \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \hyperpage{196} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \item {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{136} \subitem {$\sim$Counters}, \hyperpage{137} \subitem {add\_counter}, \hyperpage{137, 138} @@ -902,55 +902,55 @@ \subitem {operator[]}, \hyperpage{140} \subitem {size}, \hyperpage{140} \item {counters-\/meat.hpp} - \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} + \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} \item {counters.hpp} - \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} + \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} \item {counters\_} - \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \item {COUNTERS\_TEMPLATE} - \subitem {counters-\/meat.hpp}, \hyperpage{283}, - \hyperpage{285--287} + \subitem {counters-\/meat.hpp}, \hyperpage{281}, + \hyperpage{283--285} \item {COUNTERS\_TEMPLATE\_ARGS} - \subitem {counters-\/meat.hpp}, \hyperpage{283} + \subitem {counters-\/meat.hpp}, \hyperpage{281} \item {COUNTERS\_TYPE} - \subitem {counters-\/meat.hpp}, \hyperpage{283} + \subitem {counters-\/meat.hpp}, \hyperpage{281} \item {Counting}, \hyperpage{13} \subitem {counter\_co\_opt}, \hyperpage{18} \subitem {counter\_cogain}, \hyperpage{18} @@ -990,38 +990,38 @@ \subitem {PHYLO\_RULE\_DYN\_LAMBDA}, \hyperpage{17} \subitem {PHYLO\_RULE\_LAMBDA}, \hyperpage{17} \item {counts} - \subitem {Phylo rules}, \hyperpage{44} - \subitem {PhyloRuleDynData}, \hyperpage{220} + \subitem {Phylo rules}, \hyperpage{45} + \subitem {PhyloRuleDynData}, \hyperpage{219} \item {Counts\_type} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{344} \item {covar\_sort} - \subitem {Phylo rules}, \hyperpage{44} - \item {covar\_used} \subitem {Phylo rules}, \hyperpage{45} + \item {covar\_used} + \subitem {Phylo rules}, \hyperpage{46} \item {covariates} - \subitem {Phylo rules}, \hyperpage{45} + \subitem {Phylo rules}, \hyperpage{46} \item {CSS\_APPEND} - \subitem {network-\/css.hpp}, \hyperpage{294} + \subitem {network-\/css.hpp}, \hyperpage{292} \item {CSS\_CASE\_ELSE} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{293} \item {CSS\_CASE\_PERCEIVED} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{293} \item {CSS\_CASE\_TRUTH} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{293} \item {CSS\_CHECK\_SIZE} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{293} \item {CSS\_CHECK\_SIZE\_INIT} - \subitem {network-\/css.hpp}, \hyperpage{295} + \subitem {network-\/css.hpp}, \hyperpage{293} \item {CSS\_MATCH\_TYPE} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{294} \item {CSS\_NET\_COUNTER\_LAMBDA\_INIT} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{294} \item {CSS\_PERCEIVED\_CELLS} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{294} \item {CSS\_SIZE} - \subitem {network-\/css.hpp}, \hyperpage{296} + \subitem {network-\/css.hpp}, \hyperpage{294} \item {CSS\_TRUE\_CELLS} - \subitem {network-\/css.hpp}, \hyperpage{297} + \subitem {network-\/css.hpp}, \hyperpage{295} \item {current\_col} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{130} @@ -1029,9 +1029,9 @@ \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{130} \item {current\_stats} - \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{247} \indexspace @@ -1039,20 +1039,20 @@ \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{86} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} \item {D\_ptr} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{87} \item {dat} - \subitem {Flock}, \hyperpage{158} + \subitem {Flock}, \hyperpage{157} \item {data} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{134} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {counters-\/meat.hpp}, \hyperpage{285} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} + \hyperpage{224} \item {data\_} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{288} \item {default\_val} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -1080,96 +1080,96 @@ \subitem {simulate}, \hyperpage{145} \item {defm}, \hyperpage{59} \item {defm-\/meat.hpp} - \subitem {DEFM\_LOOP\_ARRAYS}, \hyperpage{317} - \subitem {DEFM\_RANGES}, \hyperpage{317} - \subitem {keygen\_defm}, \hyperpage{318} + \subitem {DEFM\_LOOP\_ARRAYS}, \hyperpage{315} + \subitem {DEFM\_RANGES}, \hyperpage{315} + \subitem {keygen\_defm}, \hyperpage{316} \item {defm-\/types.hpp} - \subitem {DEFMArray}, \hyperpage{319} + \subitem {DEFMArray}, \hyperpage{317} \item {DEFM\_COUNTER} - \subitem {counters.hpp}, \hyperpage{312} + \subitem {counters.hpp}, \hyperpage{310} \item {DEFM\_COUNTER\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{313} + \subitem {counters.hpp}, \hyperpage{311} \item {DEFM\_LOOP\_ARRAYS} - \subitem {defm-\/meat.hpp}, \hyperpage{317} + \subitem {defm-\/meat.hpp}, \hyperpage{315} \item {defm\_motif\_parser} - \subitem {formula.hpp}, \hyperpage{319} + \subitem {formula.hpp}, \hyperpage{317} \item {DEFM\_RANGES} - \subitem {defm-\/meat.hpp}, \hyperpage{317} + \subitem {defm-\/meat.hpp}, \hyperpage{315} \item {DEFM\_RULE} - \subitem {counters.hpp}, \hyperpage{313} + \subitem {counters.hpp}, \hyperpage{311} \item {DEFM\_RULE\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{313} + \subitem {counters.hpp}, \hyperpage{311} \item {DEFM\_RULEDYN\_LAMBDA} - \subitem {counters.hpp}, \hyperpage{313} + \subitem {counters.hpp}, \hyperpage{311} \item {DEFMArray} - \subitem {defm-\/types.hpp}, \hyperpage{319} + \subitem {defm-\/types.hpp}, \hyperpage{317} \item {DEFMCounter} \subitem {Phylo rules}, \hyperpage{38} \item {DEFMCounterData}, \hyperpage{146} - \subitem {Phylo rules}, \hyperpage{39} + \subitem {Phylo rules}, \hyperpage{40} \item {DEFMCounters} \subitem {Phylo rules}, \hyperpage{38} \item {DEFMData}, \hyperpage{146} - \subitem {Phylo rules}, \hyperpage{40} + \subitem {Phylo rules}, \hyperpage{40, 41} \item {DEFMModel} - \subitem {Phylo rules}, \hyperpage{38} + \subitem {Phylo rules}, \hyperpage{39} \item {DEFMRule} - \subitem {Phylo rules}, \hyperpage{38} - \item {DEFMRuleData}, \hyperpage{148} - \subitem {Phylo rules}, \hyperpage{40, 41} - \item {DEFMRuleDyn} - \subitem {Phylo rules}, \hyperpage{38} - \item {DEFMRuleDynData}, \hyperpage{149} + \subitem {Phylo rules}, \hyperpage{39} + \item {DEFMRuleData}, \hyperpage{147} \subitem {Phylo rules}, \hyperpage{41} + \item {DEFMRuleDyn} + \subitem {Phylo rules}, \hyperpage{39} + \item {DEFMRuleDynData}, \hyperpage{148} + \subitem {Phylo rules}, \hyperpage{42} \item {DEFMRules} - \subitem {Phylo rules}, \hyperpage{38} + \subitem {Phylo rules}, \hyperpage{39} \item {DEFMRulesDyn} \subitem {Phylo rules}, \hyperpage{39} \item {DEFMStatsCounter} \subitem {Phylo rules}, \hyperpage{39} \item {DEFMSupport} - \subitem {Phylo rules}, \hyperpage{39} + \subitem {Phylo rules}, \hyperpage{40} \item {delete\_counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{196} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{248} + \hyperpage{247} \item {delete\_rengine} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{173} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{197} + \hyperpage{196} \item {delete\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{197} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{249} + \hyperpage{248} \item {delete\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{197} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{249} + \hyperpage{248} \item {delete\_support} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{173} \item {desc} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} - \subitem {counters-\/meat.hpp}, \hyperpage{287} + \subitem {counters-\/meat.hpp}, \hyperpage{285} \item {desc\_} - \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {counters-\/meat.hpp}, \hyperpage{288} \item {directed} - \subitem {NetworkData}, \hyperpage{207} + \subitem {NetworkData}, \hyperpage{206} \item {duplication} - \subitem {Node}, \hyperpage{212} - \subitem {NodeData}, \hyperpage{215} - \subitem {PhyloRuleDynData}, \hyperpage{220} + \subitem {Node}, \hyperpage{211} + \subitem {NodeData}, \hyperpage{214} + \subitem {PhyloRuleDynData}, \hyperpage{219} \indexspace \item {empty} - \subitem {PhyloCounterData}, \hyperpage{217} + \subitem {PhyloCounterData}, \hyperpage{216} \item {EmptyArray} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{226} - \subitem {statscounter-\/meat.hpp}, \hyperpage{341} + \hyperpage{225} + \subitem {statscounter-\/meat.hpp}, \hyperpage{339} \item {end} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} @@ -1183,31 +1183,31 @@ \hyperpage{117} \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{121} - \subitem {PhyloCounterData}, \hyperpage{217} + \subitem {PhyloCounterData}, \hyperpage{216} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} - \subitem {Progress}, \hyperpage{228} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \hyperpage{223} + \subitem {Progress}, \hyperpage{227} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \item {Entries} - \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} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \item {Entries$<$ Cell\_Type $>$}, \hyperpage{149} + \subitem {$\sim$Entries}, \hyperpage{150} + \subitem {Entries}, \hyperpage{149} + \subitem {resize}, \hyperpage{150} + \subitem {source}, \hyperpage{150} + \subitem {target}, \hyperpage{150} + \subitem {val}, \hyperpage{150} \item {etype\_default} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{173} \item {etype\_duplication} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{173} \item {etype\_either} - \subitem {Geese}, \hyperpage{174} + \subitem {Geese}, \hyperpage{173} \item {etype\_speciation} - \subitem {Geese}, \hyperpage{175} + \subitem {Geese}, \hyperpage{174} \item {eval\_rules\_dyn} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{243} \item {EXISTS}, \hyperpage{59} \subitem {AS\_ONE}, \hyperpage{59} \subitem {AS\_ZERO}, \hyperpage{59} @@ -1220,153 +1220,153 @@ \indexspace \item {f\_} - \subitem {statscounter-\/meat.hpp}, \hyperpage{342} + \subitem {statscounter-\/meat.hpp}, \hyperpage{340} \item {first\_calc\_done} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \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} + \hyperpage{197} + \item {Flock}, \hyperpage{151} + \subitem {$\sim$Flock}, \hyperpage{152} + \subitem {add\_data}, \hyperpage{152} + \subitem {colnames}, \hyperpage{153} + \subitem {dat}, \hyperpage{157} + \subitem {Flock}, \hyperpage{152} + \subitem {get\_counters}, \hyperpage{153} + \subitem {get\_model}, \hyperpage{153} + \subitem {get\_stats\_support}, \hyperpage{153} + \subitem {get\_stats\_target}, \hyperpage{153} + \subitem {get\_support\_fun}, \hyperpage{154} + \subitem {init}, \hyperpage{154} + \subitem {initialized}, \hyperpage{157} + \subitem {likelihood\_joint}, \hyperpage{154} + \subitem {model}, \hyperpage{157} + \subitem {nfunctions}, \hyperpage{157} + \subitem {nfuns}, \hyperpage{154} + \subitem {nleafs}, \hyperpage{155} + \subitem {nnodes}, \hyperpage{155} + \subitem {nterms}, \hyperpage{155} + \subitem {ntrees}, \hyperpage{155} + \subitem {operator()}, \hyperpage{155} + \subitem {parse\_polytomies}, \hyperpage{156} + \subitem {print}, \hyperpage{156} + \subitem {rengine}, \hyperpage{157} + \subitem {set\_seed}, \hyperpage{156} + \subitem {support\_size}, \hyperpage{156} \item {flush\_data} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \item {for} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} - \subitem {counters-\/meat.hpp}, \hyperpage{287} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} + \subitem {counters-\/meat.hpp}, \hyperpage{285} + \subitem {statscounter-\/meat.hpp}, \hyperpage{336} \item {formula.hpp} - \subitem {defm\_motif\_parser}, \hyperpage{319} + \subitem {defm\_motif\_parser}, \hyperpage{317} \item {FreqTable} - \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} + \subitem {FreqTable$<$ T $>$}, \hyperpage{159} + \item {FreqTable$<$ T $>$}, \hyperpage{158} + \subitem {$\sim$FreqTable}, \hyperpage{159} + \subitem {add}, \hyperpage{159} + \subitem {as\_vector}, \hyperpage{159} + \subitem {clear}, \hyperpage{159} + \subitem {FreqTable}, \hyperpage{159} + \subitem {get\_data}, \hyperpage{160} + \subitem {get\_index}, \hyperpage{160} + \subitem {make\_hash}, \hyperpage{160} + \subitem {print}, \hyperpage{160} + \subitem {reserve}, \hyperpage{160} + \subitem {size}, \hyperpage{161} \item {fun} - \subitem {counters-\/meat.hpp}, \hyperpage{291} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{291} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \indexspace - \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{161} + \subitem {$\sim$Geese}, \hyperpage{165} + \subitem {calc\_reduced\_sequence}, \hyperpage{165} + \subitem {calc\_sequence}, \hyperpage{166} + \subitem {colnames}, \hyperpage{166} + \subitem {delete\_rengine}, \hyperpage{173} + \subitem {delete\_support}, \hyperpage{173} + \subitem {etype\_default}, \hyperpage{173} + \subitem {etype\_duplication}, \hyperpage{173} + \subitem {etype\_either}, \hyperpage{173} + \subitem {etype\_speciation}, \hyperpage{174} + \subitem {Geese}, \hyperpage{164, 165} + \subitem {get\_annotated\_nodes}, \hyperpage{166} + \subitem {get\_annotations}, \hyperpage{166} + \subitem {get\_counters}, \hyperpage{166} + \subitem {get\_model}, \hyperpage{167} + \subitem {get\_probabilities}, \hyperpage{167} + \subitem {get\_rengine}, \hyperpage{167} + \subitem {get\_states}, \hyperpage{167} + \subitem {get\_support\_fun}, \hyperpage{167} + \subitem {inherit\_support}, \hyperpage{168} + \subitem {init}, \hyperpage{168} + \subitem {init\_node}, \hyperpage{168} + \subitem {initialized}, \hyperpage{174} + \subitem {likelihood}, \hyperpage{168} + \subitem {likelihood\_exhaust}, \hyperpage{168} + \subitem {map\_to\_state\_id}, \hyperpage{174} + \subitem {nannotations}, \hyperpage{169} + \subitem {nfunctions}, \hyperpage{174} + \subitem {nfuns}, \hyperpage{169} + \subitem {nleafs}, \hyperpage{169} + \subitem {nnodes}, \hyperpage{169} + \subitem {nodes}, \hyperpage{174} + \subitem {nterms}, \hyperpage{169} + \subitem {observed\_counts}, \hyperpage{170} + \subitem {operator=}, \hyperpage{170} + \subitem {parse\_polytomies}, \hyperpage{170} + \subitem {predict}, \hyperpage{170} + \subitem {predict\_backend}, \hyperpage{171} + \subitem {predict\_exhaust}, \hyperpage{171} + \subitem {predict\_exhaust\_backend}, \hyperpage{171} + \subitem {predict\_sim}, \hyperpage{171} + \subitem {print}, \hyperpage{171} + \subitem {print\_nodes}, \hyperpage{172} + \subitem {print\_observed\_counts}, \hyperpage{172} + \subitem {pset\_loc}, \hyperpage{174} + \subitem {reduced\_sequence}, \hyperpage{175} + \subitem {sequence}, \hyperpage{175} + \subitem {set\_seed}, \hyperpage{172} + \subitem {simulate}, \hyperpage{172} + \subitem {support\_size}, \hyperpage{172} + \subitem {update\_annotations}, \hyperpage{172} \item {geese}, \hyperpage{60} \item {geese-\/bones.hpp} - \subitem {INITIALIZED}, \hyperpage{323} - \subitem {keygen\_full}, \hyperpage{323} - \subitem {RULE\_FUNCTION}, \hyperpage{323} - \subitem {vec\_diff}, \hyperpage{323} - \subitem {vector\_caster}, \hyperpage{324} + \subitem {INITIALIZED}, \hyperpage{321} + \subitem {keygen\_full}, \hyperpage{321} + \subitem {RULE\_FUNCTION}, \hyperpage{321} + \subitem {vec\_diff}, \hyperpage{321} + \subitem {vector\_caster}, \hyperpage{322} \item {geese-\/meat-\/likelihood.hpp} - \subitem {pset\_loop}, \hyperpage{325} + \subitem {pset\_loop}, \hyperpage{323} \item {geese-\/types.hpp} - \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} + \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} \item {gen\_hash} \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{185} + \hyperpage{184} \item {get\_annotated\_nodes} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{166} \item {get\_annotations} - \subitem {Geese}, \hyperpage{167} + \subitem {Geese}, \hyperpage{166} \item {get\_arrays2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{185} + \hyperpage{184} \item {get\_cell} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{66} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -1378,40 +1378,40 @@ \item {get\_column\_major} \subitem {DEFM}, \hyperpage{142} \item {get\_counters} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{167} + \subitem {Flock}, \hyperpage{153} + \subitem {Geese}, \hyperpage{166} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{185} - \subitem {PhyloCounterData}, \hyperpage{217} + \hyperpage{184} + \subitem {PhyloCounterData}, \hyperpage{216} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{243} \item {get\_counts} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{243} \item {get\_current\_stats} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{244} + \hyperpage{243} \item {get\_data} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{88} - \subitem {FreqTable$<$ T $>$}, \hyperpage{161} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{223} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{244} \item {get\_data\_ptr} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{223} \item {get\_description} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} \item {get\_descriptions} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{138} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \item {get\_entries} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -1421,18 +1421,18 @@ \item {get\_ID} \subitem {DEFM}, \hyperpage{142} \item {get\_index} - \subitem {FreqTable$<$ T $>$}, \hyperpage{161} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \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{186} + \hyperpage{185} \item {get\_m\_order} \subitem {DEFM}, \hyperpage{142} \item {get\_model} \subitem {DEFM}, \hyperpage{143} - \subitem {Flock}, \hyperpage{154} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{153} + \subitem {Geese}, \hyperpage{167} \item {get\_n\_covars} \subitem {DEFM}, \hyperpage{143} \item {get\_n\_obs} @@ -1443,78 +1443,78 @@ \subitem {DEFM}, \hyperpage{143} \item {get\_name} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133} - \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{229} \item {get\_names} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{139} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \item {get\_normalizing\_constants} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{185} \item {get\_parent} - \subitem {Node}, \hyperpage{210} + \subitem {Node}, \hyperpage{209} \item {get\_probabilities} - \subitem {Geese}, \hyperpage{168} + \subitem {Geese}, \hyperpage{167} \item {get\_pset} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{185} \item {get\_pset\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{185} \item {get\_pset\_locations} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{186} + \hyperpage{185} \item {get\_pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{186} \item {get\_pset\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{186} \item {get\_pset\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{187} + \hyperpage{186} \item {get\_rengine} - \subitem {Geese}, \hyperpage{168} + \subitem {Geese}, \hyperpage{167} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{188} + \hyperpage{187} \item {get\_row\_vec} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{67} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{88, 89} \item {get\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{188} + \hyperpage{187} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{244} \item {get\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{188} + \hyperpage{187} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{244} \item {get\_seq} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} \item {get\_states} - \subitem {Geese}, \hyperpage{168} + \subitem {Geese}, \hyperpage{167} \item {get\_stats\_support} - \subitem {Flock}, \hyperpage{154} + \subitem {Flock}, \hyperpage{153} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{188} + \hyperpage{187} \item {get\_stats\_support\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{188} + \hyperpage{187} \item {get\_stats\_support\_sizes\_acc} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{188} \item {get\_stats\_target} - \subitem {Flock}, \hyperpage{154} + \subitem {Flock}, \hyperpage{153} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{188} \item {get\_support\_fun} - \subitem {Flock}, \hyperpage{155} - \subitem {Geese}, \hyperpage{168} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{167} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189} + \hyperpage{188} \item {get\_X} \subitem {DEFM}, \hyperpage{143} \item {get\_X\_names} @@ -1527,136 +1527,136 @@ \indexspace \item {has\_leaf} - \subitem {NodeData}, \hyperpage{215} + \subitem {NodeData}, \hyperpage{214} \item {hasher} - \subitem {counters-\/meat.hpp}, \hyperpage{287, 288} + \subitem {counters-\/meat.hpp}, \hyperpage{285, 286} \item {hasher\_fun} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} - \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {counters-\/meat.hpp}, \hyperpage{286} \item {hasher\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{291} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {Hasher\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{346} + \subitem {typedefs.hpp}, \hyperpage{344} \item {hashes} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{249} + \hyperpage{248} \item {hashes\_initialized} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{249} + \hyperpage{248} \indexspace \item {i} - \subitem {counters-\/meat.hpp}, \hyperpage{291} + \subitem {counters-\/meat.hpp}, \hyperpage{289} \item {id} - \subitem {Node}, \hyperpage{212} + \subitem {Node}, \hyperpage{211} \item {idx} - \subitem {Phylo rules}, \hyperpage{41} + \subitem {Phylo rules}, \hyperpage{42} \item {if} - \subitem {counters-\/meat.hpp}, \hyperpage{288} + \subitem {counters-\/meat.hpp}, \hyperpage{286} \item {IF\_MATCHES} \subitem {Counting}, \hyperpage{15} \item {IF\_NOTMATCHES} \subitem {Counting}, \hyperpage{15} - \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/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/barraydense-\/meat-\/operators.hpp}, - \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} + \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} \item {include/barry/models/geese/geese-\/meat-\/constructors.hpp}, - \hyperpage{324} + \hyperpage{322} \item {include/barry/models/geese/geese-\/meat-\/likelihood.hpp}, - \hyperpage{325} + \hyperpage{323} \item {include/barry/models/geese/geese-\/meat-\/likelihood\_exhaust.hpp}, - \hyperpage{326} + \hyperpage{324} \item {include/barry/models/geese/geese-\/meat-\/predict.hpp}, - \hyperpage{327} + \hyperpage{325} \item {include/barry/models/geese/geese-\/meat-\/predict\_exhaust.hpp}, - \hyperpage{327} + \hyperpage{325} \item {include/barry/models/geese/geese-\/meat-\/predict\_sim.hpp}, - \hyperpage{328} + \hyperpage{326} \item {include/barry/models/geese/geese-\/meat-\/simulate.hpp}, - \hyperpage{328} - \item {include/barry/models/geese/geese-\/meat.hpp}, \hyperpage{329} + \hyperpage{326} + \item {include/barry/models/geese/geese-\/meat.hpp}, \hyperpage{327} \item {include/barry/models/geese/geese-\/node-\/bones.hpp}, - \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} + \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} \item {indices} - \subitem {NetCounterData}, \hyperpage{205} - \subitem {Phylo rules}, \hyperpage{45} + \subitem {NetCounterData}, \hyperpage{204} + \subitem {Phylo rules}, \hyperpage{46} \item {inherit\_support} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{168} \item {init} \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} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{168} + \subitem {Phylo rules}, \hyperpage{46} \item {init\_fun} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \item {init\_fun\_} - \subitem {counters-\/meat.hpp}, \hyperpage{292} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {init\_node} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{168} \item {init\_support} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{223} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{245} + \hyperpage{244} \item {INITIALIZED} - \subitem {geese-\/bones.hpp}, \hyperpage{323} + \subitem {geese-\/bones.hpp}, \hyperpage{321} \item {initialized} - \subitem {Flock}, \hyperpage{158} - \subitem {Geese}, \hyperpage{175} + \subitem {Flock}, \hyperpage{157} + \subitem {Geese}, \hyperpage{174} \item {insert\_cell} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{68} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -1679,10 +1679,10 @@ \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{90} \item {is\_leaf} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{210} \item {is\_motif} \subitem {DEFM}, \hyperpage{144} - \subitem {Phylo rules}, \hyperpage{45} + \subitem {Phylo rules}, \hyperpage{46} \item {is\_row} \subitem {BArrayVector$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{117} @@ -1691,7 +1691,7 @@ \item {IS\_SPECIATION} \subitem {Counting}, \hyperpage{16} \item {is\_true} - \subitem {Phylo rules}, \hyperpage{41, 42} + \subitem {Phylo rules}, \hyperpage{42} \item {iter} \subitem {ConstBArrayRowIter$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{130} @@ -1699,38 +1699,39 @@ \indexspace \item {j} - \subitem {counters-\/meat.hpp}, \hyperpage{292} - \subitem {statscounter-\/meat.hpp}, \hyperpage{342} + \subitem {counters-\/meat.hpp}, \hyperpage{290} + \subitem {statscounter-\/meat.hpp}, \hyperpage{340} \indexspace \item {keygen\_defm} - \subitem {defm-\/meat.hpp}, \hyperpage{318} + \subitem {defm-\/meat.hpp}, \hyperpage{316} \item {keygen\_full} - \subitem {geese-\/bones.hpp}, \hyperpage{323} + \subitem {geese-\/bones.hpp}, \hyperpage{321} \item {keys2support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{198} + \hyperpage{197} \indexspace \item {lb} - \subitem {PhyloRuleDynData}, \hyperpage{220} + \subitem {Phylo rules}, \hyperpage{47} + \subitem {PhyloRuleDynData}, \hyperpage{219} \item {likelihood} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{168} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{189, 190} + \hyperpage{188, 189} \item {likelihood\_} - \subitem {model-\/meat.hpp}, \hyperpage{310} + \subitem {model-\/meat.hpp}, \hyperpage{308} \item {likelihood\_exhaust} - \subitem {Geese}, \hyperpage{169} + \subitem {Geese}, \hyperpage{168} \item {likelihood\_joint} - \subitem {Flock}, \hyperpage{155} + \subitem {Flock}, \hyperpage{154} \item {likelihood\_total} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{190} \item {logical} - \subitem {Phylo rules}, \hyperpage{46} + \subitem {Phylo rules}, \hyperpage{47} \item {logodds} \subitem {DEFM}, \hyperpage{144} @@ -1738,114 +1739,114 @@ \item {M} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{226} + \hyperpage{225} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{249} + \hyperpage{248} \item {MAKE\_DEFM\_HASHER} \subitem {Counting}, \hyperpage{16} \item {MAKE\_DUPL\_VARS} \subitem {Counting}, \hyperpage{16} \item {make\_hash} - \subitem {FreqTable$<$ T $>$}, \hyperpage{161} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} \item {Map} - \subitem {barry-\/configuration.hpp}, \hyperpage{274} + \subitem {barry-\/configuration.hpp}, \hyperpage{272} \item {map\_to\_state\_id} - \subitem {Geese}, \hyperpage{175} + \subitem {Geese}, \hyperpage{174} \item {MapVec\_type} - \subitem {typedefs.hpp}, \hyperpage{347} + \subitem {typedefs.hpp}, \hyperpage{345} \item {max\_num\_elements} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{250} + \hyperpage{249} \item {Model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{181, 182} + \hyperpage{180, 181} \item {model} - \subitem {Flock}, \hyperpage{158} + \subitem {Flock}, \hyperpage{157} \item {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \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} + \hyperpage{176} + \subitem {$\sim$Model}, \hyperpage{181} + \subitem {add\_array}, \hyperpage{181} + \subitem {add\_counter}, \hyperpage{182} + \subitem {add\_hasher}, \hyperpage{182} + \subitem {add\_rule}, \hyperpage{182, 183} + \subitem {add\_rule\_dyn}, \hyperpage{183} + \subitem {arrays2support}, \hyperpage{196} + \subitem {colnames}, \hyperpage{183} + \subitem {conditional\_prob}, \hyperpage{183} + \subitem {counter\_fun}, \hyperpage{196} + \subitem {counters}, \hyperpage{196} + \subitem {delete\_counters}, \hyperpage{196} + \subitem {delete\_rengine}, \hyperpage{196} + \subitem {delete\_rules}, \hyperpage{197} + \subitem {delete\_rules\_dyn}, \hyperpage{197} + \subitem {first\_calc\_done}, \hyperpage{197} + \subitem {gen\_key}, \hyperpage{184} + \subitem {get\_arrays2support}, \hyperpage{184} + \subitem {get\_counters}, \hyperpage{184} + \subitem {get\_likelihoods}, \hyperpage{185} + \subitem {get\_normalizing\_constants}, \hyperpage{185} + \subitem {get\_pset}, \hyperpage{185} + \subitem {get\_pset\_arrays}, \hyperpage{185} + \subitem {get\_pset\_locations}, \hyperpage{185} + \subitem {get\_pset\_probs}, \hyperpage{186} + \subitem {get\_pset\_sizes}, \hyperpage{186} + \subitem {get\_pset\_stats}, \hyperpage{186} + \subitem {get\_rengine}, \hyperpage{187} + \subitem {get\_rules}, \hyperpage{187} + \subitem {get\_rules\_dyn}, \hyperpage{187} + \subitem {get\_stats\_support}, \hyperpage{187} + \subitem {get\_stats\_support\_sizes}, \hyperpage{187} + \subitem {get\_stats\_support\_sizes\_acc}, \hyperpage{188} + \subitem {get\_stats\_target}, \hyperpage{188} + \subitem {get\_support\_fun}, \hyperpage{188} + \subitem {keys2support}, \hyperpage{197} + \subitem {likelihood}, \hyperpage{188, 189} + \subitem {likelihood\_total}, \hyperpage{190} + \subitem {Model}, \hyperpage{180, 181} + \subitem {normalizing\_constants}, \hyperpage{197} + \subitem {nrules}, \hyperpage{190} + \subitem {nrules\_dyn}, \hyperpage{190} + \subitem {nterms}, \hyperpage{190} + \subitem {operator=}, \hyperpage{191} + \subitem {params\_last}, \hyperpage{198} + \subitem {print}, \hyperpage{191} + \subitem {print\_stats}, \hyperpage{191} + \subitem {pset\_arrays}, \hyperpage{198} + \subitem {pset\_locations}, \hyperpage{198} + \subitem {pset\_probs}, \hyperpage{198} + \subitem {pset\_sizes}, \hyperpage{199} + \subitem {pset\_stats}, \hyperpage{199} + \subitem {rengine}, \hyperpage{199} + \subitem {rules}, \hyperpage{199} + \subitem {rules\_dyn}, \hyperpage{200} + \subitem {sample}, \hyperpage{191, 192} + \subitem {set\_counters}, \hyperpage{192} + \subitem {set\_rengine}, \hyperpage{192} + \subitem {set\_rules}, \hyperpage{192} + \subitem {set\_rules\_dyn}, \hyperpage{193} + \subitem {set\_seed}, \hyperpage{193} + \subitem {set\_transform\_model}, \hyperpage{193} + \subitem {size}, \hyperpage{194} + \subitem {size\_unique}, \hyperpage{194} + \subitem {stats\_likelihood}, \hyperpage{200} + \subitem {stats\_support}, \hyperpage{200} + \subitem {stats\_support\_n\_arrays}, \hyperpage{200} + \subitem {stats\_support\_sizes}, \hyperpage{201} + \subitem {stats\_support\_sizes\_acc}, \hyperpage{201} + \subitem {stats\_target}, \hyperpage{201} + \subitem {store\_psets}, \hyperpage{194} + \subitem {support\_fun}, \hyperpage{201} + \subitem {support\_size}, \hyperpage{194} + \subitem {transform\_model}, \hyperpage{194} + \subitem {transform\_model\_fun}, \hyperpage{202} + \subitem {transform\_model\_term\_names}, \hyperpage{202} + \subitem {update\_likelihoods}, \hyperpage{195} + \subitem {update\_normalizing\_constants}, \hyperpage{195} + \subitem {update\_pset\_probs}, \hyperpage{195} + \subitem {with\_pset}, \hyperpage{202} \item {model-\/meat.hpp} - \subitem {likelihood\_}, \hyperpage{310} - \subitem {update\_normalizing\_constant}, \hyperpage{310} + \subitem {likelihood\_}, \hyperpage{308} + \subitem {update\_normalizing\_constant}, \hyperpage{308} \item {motif\_census} \subitem {DEFM}, \hyperpage{145} @@ -1853,57 +1854,57 @@ \item {N} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{226} + \hyperpage{225} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{250} + \hyperpage{249} \item {n\_counters} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{250} + \hyperpage{249} \item {n\_free} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{226} + \hyperpage{225} \item {n\_locked} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{226} + \hyperpage{225} \item {name} \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{135} - \subitem {counters-\/meat.hpp}, \hyperpage{289} + \subitem {counters-\/meat.hpp}, \hyperpage{287} \item {name\_} - \subitem {counters-\/meat.hpp}, \hyperpage{292} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {nannotations} - \subitem {Geese}, \hyperpage{170} + \subitem {Geese}, \hyperpage{169} \item {narray} - \subitem {Node}, \hyperpage{212} + \subitem {Node}, \hyperpage{211} \item {ncol} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{90} - \subitem {Phylo rules}, \hyperpage{42} + \subitem {Phylo rules}, \hyperpage{43} \item {NET\_C\_DATA\_IDX} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{303} \item {NET\_C\_DATA\_NUM} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{303} \item {NetCounter} - \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} + \subitem {network.hpp}, \hyperpage{304} + \item {NetCounterData}, \hyperpage{203} + \subitem {$\sim$NetCounterData}, \hyperpage{204} + \subitem {indices}, \hyperpage{204} + \subitem {NetCounterData}, \hyperpage{203} + \subitem {numbers}, \hyperpage{204} \item {NetCounters} - \subitem {network.hpp}, \hyperpage{306} + \subitem {network.hpp}, \hyperpage{304} \item {NetModel} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {NetRule} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {NetRules} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {NetStatsCounter} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {NetSupport} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {Network} - \subitem {network.hpp}, \hyperpage{307} + \subitem {network.hpp}, \hyperpage{305} \item {Network counters}, \hyperpage{24} \subitem {counter\_absdiff}, \hyperpage{26} \subitem {counter\_ctriads}, \hyperpage{27} @@ -1930,163 +1931,164 @@ \subitem {counter\_transition\_formula}, \hyperpage{34} \subitem {counter\_ttriads}, \hyperpage{34, 35} \subitem {NETWORK\_COUNTER}, \hyperpage{35} + \subitem {rule\_constrain\_support}, \hyperpage{35} \subitem {rules\_dont\_become\_zero}, \hyperpage{35} - \subitem {rules\_markov\_fixed}, \hyperpage{35} + \subitem {rules\_markov\_fixed}, \hyperpage{36} \item {network-\/css.hpp} - \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\_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\_completely\_false\_recip\_comiss}, - \hyperpage{299} + \hyperpage{297} \subitem {counter\_css\_completely\_false\_recip\_omiss}, - \hyperpage{300} - \subitem {counter\_css\_mixed\_recip}, \hyperpage{300} + \hyperpage{298} + \subitem {counter\_css\_mixed\_recip}, \hyperpage{298} \subitem {counter\_css\_partially\_false\_recip\_commi}, - \hyperpage{300} + \hyperpage{298} \subitem {counter\_css\_partially\_false\_recip\_omiss}, - \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} + \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} \item {network.hpp} - \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} + \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} \item {NETWORK\_COUNTER} \subitem {Network counters}, \hyperpage{35} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{303} \item {NETWORK\_COUNTER\_LAMBDA} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{303} \item {NETWORK\_RULE} - \subitem {network.hpp}, \hyperpage{305} + \subitem {network.hpp}, \hyperpage{303} \item {NETWORK\_RULE\_LAMBDA} - \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} + \subitem {network.hpp}, \hyperpage{304} + \item {NetworkData}, \hyperpage{204} + \subitem {$\sim$NetworkData}, \hyperpage{206} + \subitem {directed}, \hyperpage{206} + \subitem {NetworkData}, \hyperpage{205, 206} + \subitem {vertex\_attr}, \hyperpage{206} \item {NetworkDense} - \subitem {network.hpp}, \hyperpage{308} - \item {NETWORKDENSE\_COUNTER\_LAMBDA} \subitem {network.hpp}, \hyperpage{306} + \item {NETWORKDENSE\_COUNTER\_LAMBDA} + \subitem {network.hpp}, \hyperpage{304} \item {next} - \subitem {Progress}, \hyperpage{228} + \subitem {Progress}, \hyperpage{227} \item {nfunctions} - \subitem {Flock}, \hyperpage{158} - \subitem {Geese}, \hyperpage{175} - \item {nfuns} - \subitem {Flock}, \hyperpage{155} - \subitem {Geese}, \hyperpage{170} + \subitem {Flock}, \hyperpage{157} + \subitem {Geese}, \hyperpage{174} + \item {nfuns} + \subitem {Flock}, \hyperpage{154} + \subitem {Geese}, \hyperpage{169} \item {nleafs} - \subitem {Flock}, \hyperpage{156} - \subitem {Geese}, \hyperpage{170} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{169} \item {nnodes} - \subitem {Flock}, \hyperpage{156} - \subitem {Geese}, \hyperpage{170} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{169} \item {nnozero} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \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 {Node}, \hyperpage{207} + \subitem {$\sim$Node}, \hyperpage{209} + \subitem {annotations}, \hyperpage{210} + \subitem {array}, \hyperpage{210} + \subitem {arrays}, \hyperpage{210} + \subitem {duplication}, \hyperpage{211} + \subitem {get\_parent}, \hyperpage{209} + \subitem {id}, \hyperpage{211} + \subitem {is\_leaf}, \hyperpage{210} + \subitem {narray}, \hyperpage{211} + \subitem {Node}, \hyperpage{208, 209} + \subitem {noffspring}, \hyperpage{210} + \subitem {offspring}, \hyperpage{211} + \subitem {ord}, \hyperpage{211} + \subitem {parent}, \hyperpage{212} + \subitem {probability}, \hyperpage{212} + \subitem {subtree\_prob}, \hyperpage{212} + \subitem {visited}, \hyperpage{212} + \item {NodeData}, \hyperpage{213} + \subitem {blengths}, \hyperpage{213} + \subitem {duplication}, \hyperpage{214} + \subitem {has\_leaf}, \hyperpage{214} + \subitem {NodeData}, \hyperpage{213} + \subitem {states}, \hyperpage{214} \item {nodes} - \subitem {Geese}, \hyperpage{175} + \subitem {Geese}, \hyperpage{174} \item {noexcept} - \subitem {counters-\/meat.hpp}, \hyperpage{292} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {noffspring} - \subitem {Node}, \hyperpage{211} + \subitem {Node}, \hyperpage{210} \item {NONE} \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{198} + \hyperpage{197} \item {nrow} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{90} - \subitem {Phylo rules}, \hyperpage{42} + \subitem {Phylo rules}, \hyperpage{43} \item {nrules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{190} \item {nrules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{190} \item {nterms} - \subitem {Flock}, \hyperpage{156} - \subitem {Geese}, \hyperpage{170} + \subitem {Flock}, \hyperpage{155} + \subitem {Geese}, \hyperpage{169} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{191} + \hyperpage{190} \item {ntrees} - \subitem {Flock}, \hyperpage{156} + \subitem {Flock}, \hyperpage{155} \item {num} - \subitem {Phylo rules}, \hyperpage{42} + \subitem {Phylo rules}, \hyperpage{43} \item {numbers} - \subitem {NetCounterData}, \hyperpage{205} - \subitem {Phylo rules}, \hyperpage{46} + \subitem {NetCounterData}, \hyperpage{204} + \subitem {Phylo rules}, \hyperpage{47} \indexspace \item {obs\_start} - \subitem {Phylo rules}, \hyperpage{46} + \subitem {Phylo rules}, \hyperpage{47} \item {observed\_counts} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{170} \item {offspring} - \subitem {Node}, \hyperpage{212} + \subitem {Node}, \hyperpage{211} \item {ONE} \subitem {CHECK}, \hyperpage{58} \subitem {EXISTS}, \hyperpage{60} @@ -2155,7 +2157,7 @@ \hyperpage{118} \item {operator()} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{69} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{90, 91} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, @@ -2166,13 +2168,13 @@ \hyperpage{108} \subitem {BArrayDenseRow\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{110} - \subitem {Flock}, \hyperpage{156} - \subitem {Phylo rules}, \hyperpage{42} - \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} + \subitem {Flock}, \hyperpage{155} + \subitem {Phylo rules}, \hyperpage{43} + \subitem {PhyloCounterData}, \hyperpage{216} + \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{233} + \subitem {vecHasher$<$ T $>$}, \hyperpage{250} \item {operator+=} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{70} \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{77} @@ -2217,10 +2219,10 @@ \subitem {Counter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{133, 134} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{139} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{170} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{235} + \hyperpage{191} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} \item {operator==} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} \subitem {BArrayCell$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{78} @@ -2240,11 +2242,11 @@ \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {operator[]} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{140} - \subitem {PhyloCounterData}, \hyperpage{217} + \subitem {PhyloCounterData}, \hyperpage{216} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{224} + \hyperpage{223} \item {ord} - \subitem {Node}, \hyperpage{212} + \subitem {Node}, \hyperpage{211} \item {out\_of\_range} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -2254,78 +2256,81 @@ \item {params\_last} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{198} \item {parent} - \subitem {Node}, \hyperpage{213} + \subitem {Node}, \hyperpage{212} \item {parse\_polytomies} - \subitem {Flock}, \hyperpage{157} - \subitem {Geese}, \hyperpage{171} - \item {Phylo counters}, \hyperpage{47} - \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{50} - \subitem {counter\_genes\_changing}, \hyperpage{50} - \subitem {counter\_k\_genes\_changing}, \hyperpage{50} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{170} + \item {Phylo counters}, \hyperpage{49} + \subitem {counter\_co\_opt}, \hyperpage{50} + \subitem {counter\_cogain}, \hyperpage{51} + \subitem {counter\_gains}, \hyperpage{51} + \subitem {counter\_gains\_from\_0}, \hyperpage{51} + \subitem {counter\_gains\_k\_offspring}, \hyperpage{51} + \subitem {counter\_genes\_changing}, \hyperpage{52} + \subitem {counter\_k\_genes\_changing}, \hyperpage{52} \subitem {counter\_less\_than\_p\_prop\_genes\_changing}, - \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{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{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{54} - \subitem {counter\_preserve\_pseudogene}, \hyperpage{54} - \subitem {counter\_prop\_genes\_changing}, \hyperpage{54} - \subitem {counter\_subfun}, \hyperpage{54} + \hyperpage{52} + \subitem {counter\_longest}, \hyperpage{52} + \subitem {counter\_loss}, \hyperpage{53} + \subitem {counter\_maxfuns}, \hyperpage{53} + \subitem {counter\_neofun}, \hyperpage{53} + \subitem {counter\_neofun\_a2b}, \hyperpage{53} + \subitem {counter\_overall\_changes}, \hyperpage{54} + \subitem {counter\_overall\_gains}, \hyperpage{54} + \subitem {counter\_overall\_gains\_from\_0}, \hyperpage{54} + \subitem {counter\_overall\_loss}, \hyperpage{54} + \subitem {counter\_pairwise\_first\_gain}, \hyperpage{55} + \subitem {counter\_pairwise\_neofun\_singlefun}, \hyperpage{55} + \subitem {counter\_pairwise\_overall\_change}, \hyperpage{55} + \subitem {counter\_pairwise\_preserving}, \hyperpage{55} + \subitem {counter\_preserve\_pseudogene}, \hyperpage{56} + \subitem {counter\_prop\_genes\_changing}, \hyperpage{56} + \subitem {counter\_subfun}, \hyperpage{56} \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{45} - \subitem {covariates}, \hyperpage{45} + \subitem {$\sim$DEFMCounterData}, \hyperpage{45} + \subitem {$\sim$DEFMData}, \hyperpage{45} + \subitem {$\sim$DEFMRuleDynData}, \hyperpage{45} + \subitem {array}, \hyperpage{45} + \subitem {at}, \hyperpage{40} + \subitem {counts}, \hyperpage{45} + \subitem {covar\_sort}, \hyperpage{45} + \subitem {covar\_used}, \hyperpage{46} + \subitem {covariates}, \hyperpage{46} \subitem {DEFMCounter}, \hyperpage{38} - \subitem {DEFMCounterData}, \hyperpage{39} + \subitem {DEFMCounterData}, \hyperpage{40} \subitem {DEFMCounters}, \hyperpage{38} - \subitem {DEFMData}, \hyperpage{40} - \subitem {DEFMModel}, \hyperpage{38} - \subitem {DEFMRule}, \hyperpage{38} - \subitem {DEFMRuleData}, \hyperpage{40, 41} - \subitem {DEFMRuleDyn}, \hyperpage{38} - \subitem {DEFMRuleDynData}, \hyperpage{41} - \subitem {DEFMRules}, \hyperpage{38} + \subitem {DEFMData}, \hyperpage{40, 41} + \subitem {DEFMModel}, \hyperpage{39} + \subitem {DEFMRule}, \hyperpage{39} + \subitem {DEFMRuleData}, \hyperpage{41} + \subitem {DEFMRuleDyn}, \hyperpage{39} + \subitem {DEFMRuleDynData}, \hyperpage{42} + \subitem {DEFMRules}, \hyperpage{39} \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, 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{43} - \subitem {rule\_dyn\_limit\_changes}, \hyperpage{43} - \subitem {rule\_leafs}, \hyperpage{43} - \subitem {X\_ncol}, \hyperpage{46} - \subitem {X\_nrow}, \hyperpage{47} + \subitem {DEFMSupport}, \hyperpage{40} + \subitem {idx}, \hyperpage{42} + \subitem {indices}, \hyperpage{46} + \subitem {init}, \hyperpage{46} + \subitem {is\_motif}, \hyperpage{46} + \subitem {is\_true}, \hyperpage{42} + \subitem {lb}, \hyperpage{47} + \subitem {logical}, \hyperpage{47} + \subitem {ncol}, \hyperpage{43} + \subitem {nrow}, \hyperpage{43} + \subitem {num}, \hyperpage{43} + \subitem {numbers}, \hyperpage{47} + \subitem {obs\_start}, \hyperpage{47} + \subitem {operator()}, \hyperpage{43} + \subitem {pos}, \hyperpage{48} + \subitem {print}, \hyperpage{44} + \subitem {rule\_dyn\_limit\_changes}, \hyperpage{44} + \subitem {rule\_leafs}, \hyperpage{44} + \subitem {ub}, \hyperpage{48} + \subitem {X\_ncol}, \hyperpage{48} + \subitem {X\_nrow}, \hyperpage{48} \item {PHYLO\_CHECK\_MISSING} \subitem {Counting}, \hyperpage{16} \item {PHYLO\_COUNTER\_LAMBDA} @@ -2335,282 +2340,285 @@ \item {PHYLO\_RULE\_LAMBDA} \subitem {Counting}, \hyperpage{17} \item {PhyloArray} - \subitem {geese-\/types.hpp}, \hyperpage{331} + \subitem {geese-\/types.hpp}, \hyperpage{329} \item {PhyloCounter} - \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} + \subitem {geese-\/types.hpp}, \hyperpage{329} + \item {PhyloCounterData}, \hyperpage{214} + \subitem {at}, \hyperpage{215} + \subitem {begin}, \hyperpage{216} + \subitem {empty}, \hyperpage{216} + \subitem {end}, \hyperpage{216} + \subitem {get\_counters}, \hyperpage{216} + \subitem {operator()}, \hyperpage{216} + \subitem {operator[]}, \hyperpage{216} + \subitem {PhyloCounterData}, \hyperpage{215} + \subitem {push\_back}, \hyperpage{217} + \subitem {reserve}, \hyperpage{217} + \subitem {shrink\_to\_fit}, \hyperpage{217} + \subitem {size}, \hyperpage{217} \item {PhyloCounters} - \subitem {geese-\/types.hpp}, \hyperpage{331} + \subitem {geese-\/types.hpp}, \hyperpage{329} \item {PhyloModel} - \subitem {geese-\/types.hpp}, \hyperpage{331} + \subitem {geese-\/types.hpp}, \hyperpage{329} \item {PhyloPowerSet} - \subitem {geese-\/types.hpp}, \hyperpage{331} + \subitem {geese-\/types.hpp}, \hyperpage{329} \item {PhyloRule} - \subitem {geese-\/types.hpp}, \hyperpage{332} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {PhyloRuleData} - \subitem {geese-\/types.hpp}, \hyperpage{332} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {PhyloRuleDyn} - \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} + \subitem {geese-\/types.hpp}, \hyperpage{330} + \item {PhyloRuleDynData}, \hyperpage{217} + \subitem {$\sim$PhyloRuleDynData}, \hyperpage{218} + \subitem {counts}, \hyperpage{219} + \subitem {duplication}, \hyperpage{219} + \subitem {lb}, \hyperpage{219} + \subitem {operator()}, \hyperpage{218} + \subitem {PhyloRuleDynData}, \hyperpage{218} + \subitem {pos}, \hyperpage{219} + \subitem {ub}, \hyperpage{219} \item {PhyloRules} - \subitem {geese-\/types.hpp}, \hyperpage{332} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {PhyloRulesDyn} - \subitem {geese-\/types.hpp}, \hyperpage{332} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {PhyloStatsCounter} - \subitem {geese-\/types.hpp}, \hyperpage{332} + \subitem {geese-\/types.hpp}, \hyperpage{330} \item {PhyloSupport} - \subitem {geese-\/types.hpp}, \hyperpage{333} + \subitem {geese-\/types.hpp}, \hyperpage{331} \item {POS} - \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} + \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} \item {pos} - \subitem {PhyloRuleDynData}, \hyperpage{220} + \subitem {Phylo rules}, \hyperpage{48} + \subitem {PhyloRuleDynData}, \hyperpage{219} \item {POS\_N} - \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} + \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} \item {PowerSet} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{222} - \item {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, \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 {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, + \hyperpage{220} + \subitem {$\sim$PowerSet}, \hyperpage{222} + \subitem {add\_rule}, \hyperpage{222} + \subitem {begin}, \hyperpage{222} + \subitem {calc}, \hyperpage{222} + \subitem {coordinates\_free}, \hyperpage{224} + \subitem {coordinates\_locked}, \hyperpage{224} + \subitem {data}, \hyperpage{224} + \subitem {EmptyArray}, \hyperpage{225} + \subitem {end}, \hyperpage{223} + \subitem {get\_data}, \hyperpage{223} + \subitem {get\_data\_ptr}, \hyperpage{223} + \subitem {init\_support}, \hyperpage{223} + \subitem {M}, \hyperpage{225} + \subitem {N}, \hyperpage{225} + \subitem {n\_free}, \hyperpage{225} + \subitem {n\_locked}, \hyperpage{225} + \subitem {operator[]}, \hyperpage{223} + \subitem {PowerSet}, \hyperpage{221} + \subitem {reset}, \hyperpage{224} + \subitem {rules}, \hyperpage{225} + \subitem {rules\_deleted}, \hyperpage{226} + \subitem {size}, \hyperpage{224} \item {predict} - \subitem {Geese}, \hyperpage{171} + \subitem {Geese}, \hyperpage{170} \item {predict\_backend} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{171} \item {predict\_exhaust} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{171} \item {predict\_exhaust\_backend} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{171} \item {predict\_sim} - \subitem {Geese}, \hyperpage{172} + \subitem {Geese}, \hyperpage{171} \item {print} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{71} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{93} \subitem {DEFM}, \hyperpage{145} - \subitem {Flock}, \hyperpage{157} - \subitem {FreqTable$<$ T $>$}, \hyperpage{161} - \subitem {Geese}, \hyperpage{172} + \subitem {Flock}, \hyperpage{156} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {Geese}, \hyperpage{171} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} - \subitem {Phylo rules}, \hyperpage{43} + \hyperpage{191} + \subitem {Phylo rules}, \hyperpage{44} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{245} \item {print\_n} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \item {print\_nodes} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{172} \item {print\_observed\_counts} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{172} \item {print\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192} + \hyperpage{191} \item {printf\_barry} - \subitem {barry-\/configuration.hpp}, \hyperpage{273} + \subitem {barry-\/configuration.hpp}, \hyperpage{271} \item {probability} - \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} + \subitem {Node}, \hyperpage{212} + \item {Progress}, \hyperpage{226} + \subitem {$\sim$Progress}, \hyperpage{227} + \subitem {end}, \hyperpage{227} + \subitem {next}, \hyperpage{227} + \subitem {Progress}, \hyperpage{226} \item {progress.hpp} - \subitem {BARRY\_PROGRESS\_BAR\_WIDTH}, \hyperpage{335} + \subitem {BARRY\_PROGRESS\_BAR\_WIDTH}, \hyperpage{333} \item {pset\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{198} \item {pset\_loc} - \subitem {Geese}, \hyperpage{175} + \subitem {Geese}, \hyperpage{174} \item {pset\_locations} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{198} \item {pset\_loop} - \subitem {geese-\/meat-\/likelihood.hpp}, \hyperpage{325} + \subitem {geese-\/meat-\/likelihood.hpp}, \hyperpage{323} \item {pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{199} + \hyperpage{198} \item {pset\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{199} \item {pset\_stats} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{199} \item {push\_back} - \subitem {PhyloCounterData}, \hyperpage{218} + \subitem {PhyloCounterData}, \hyperpage{217} \indexspace - \item {README.md}, \hyperpage{349} + \item {README.md}, \hyperpage{347} \item {reduced\_sequence} - \subitem {Geese}, \hyperpage{176} + \subitem {Geese}, \hyperpage{175} \item {rengine} - \subitem {Flock}, \hyperpage{158} + \subitem {Flock}, \hyperpage{157} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{199} \item {res} - \subitem {counters-\/meat.hpp}, \hyperpage{292} + \subitem {counters-\/meat.hpp}, \hyperpage{290} \item {reserve} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{93} - \subitem {FreqTable$<$ T $>$}, \hyperpage{161} - \subitem {PhyloCounterData}, \hyperpage{218} + \subitem {FreqTable$<$ T $>$}, \hyperpage{160} + \subitem {PhyloCounterData}, \hyperpage{217} \item {reset} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} + \hyperpage{224} \item {reset\_array} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{238} + \hyperpage{237} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{245} \item {resize} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{94} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} - \subitem {statscounter-\/meat.hpp}, \hyperpage{339} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} + \subitem {statscounter-\/meat.hpp}, \hyperpage{337} \item {return} - \subitem {counters-\/meat.hpp}, \hyperpage{293} - \subitem {statscounter-\/meat.hpp}, \hyperpage{342} + \subitem {counters-\/meat.hpp}, \hyperpage{291} + \subitem {statscounter-\/meat.hpp}, \hyperpage{340} \item {rhs} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{257} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{255} \item {rm\_cell} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{94} \item {ROW} - \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} + \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} \item {row} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{72} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{94} \item {Row\_type} - \subitem {typedefs.hpp}, \hyperpage{347} + \subitem {typedefs.hpp}, \hyperpage{345} \item {rowsum} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{94} \item {Rule} - \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} + \subitem {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{228} + \item {Rule$<$ Array\_Type, Data\_Type $>$}, \hyperpage{227} + \subitem {$\sim$Rule}, \hyperpage{228} + \subitem {D}, \hyperpage{229} + \subitem {get\_description}, \hyperpage{229} + \subitem {get\_name}, \hyperpage{229} + \subitem {operator()}, \hyperpage{230} + \subitem {Rule}, \hyperpage{228} + \item {rule\_constrain\_support} + \subitem {Network counters}, \hyperpage{35} \item {rule\_dyn\_limit\_changes} - \subitem {Phylo rules}, \hyperpage{43} + \subitem {Phylo rules}, \hyperpage{44} \item {rule\_fun\_default} - \subitem {rules-\/bones.hpp}, \hyperpage{335} + \subitem {rules-\/bones.hpp}, \hyperpage{333} \item {Rule\_fun\_type} - \subitem {typedefs.hpp}, \hyperpage{347} + \subitem {typedefs.hpp}, \hyperpage{345} \item {RULE\_FUNCTION} - \subitem {barry.hpp}, \hyperpage{279} - \subitem {geese-\/bones.hpp}, \hyperpage{323} + \subitem {barry.hpp}, \hyperpage{277} + \subitem {geese-\/bones.hpp}, \hyperpage{321} \item {RULE\_LAMBDA} - \subitem {barry.hpp}, \hyperpage{279} + \subitem {barry.hpp}, \hyperpage{277} \item {rule\_leafs} - \subitem {Phylo rules}, \hyperpage{43} + \subitem {Phylo rules}, \hyperpage{44} \item {Rules} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{232} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{231} \item {rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{200} + \hyperpage{199} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \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} + \hyperpage{225} + \item {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{230} + \subitem {$\sim$Rules}, \hyperpage{231} + \subitem {add\_rule}, \hyperpage{232} + \subitem {begin}, \hyperpage{232} + \subitem {end}, \hyperpage{232} + \subitem {get\_descriptions}, \hyperpage{232} + \subitem {get\_names}, \hyperpage{233} + \subitem {get\_seq}, \hyperpage{233} + \subitem {operator()}, \hyperpage{233} + \subitem {operator=}, \hyperpage{234} + \subitem {Rules}, \hyperpage{231} + \subitem {size}, \hyperpage{234} \item {rules-\/bones.hpp} - \subitem {rule\_fun\_default}, \hyperpage{335} + \subitem {rule\_fun\_default}, \hyperpage{333} \item {rules\_deleted} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{227} + \hyperpage{226} \item {rules\_dont\_become\_zero} \subitem {Network counters}, \hyperpage{35} \item {rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{200} \item {rules\_markov\_fixed} - \subitem {Network counters}, \hyperpage{35} + \subitem {Network counters}, \hyperpage{36} \item {rules\_zerodiag} - \subitem {network.hpp}, \hyperpage{308} + \subitem {network.hpp}, \hyperpage{306} \indexspace \item {sample} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{192, 193} + \hyperpage{191, 192} \item {sequence} - \subitem {Geese}, \hyperpage{176} + \subitem {Geese}, \hyperpage{175} \item {set\_counters} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{192} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{239} + \hyperpage{238} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{246} + \hyperpage{245} \item {set\_data} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -2621,30 +2629,30 @@ \subitem {DEFM}, \hyperpage{145} \item {set\_rengine} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{192} \item {set\_rules} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{193} + \hyperpage{192} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{246} \item {set\_rules\_dyn} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{193} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{247} + \hyperpage{246} \item {set\_seed} - \subitem {Flock}, \hyperpage{157} - \subitem {Geese}, \hyperpage{173} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{172} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{193} \item {set\_transform\_model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{194} + \hyperpage{193} \item {shrink\_to\_fit} - \subitem {PhyloCounterData}, \hyperpage{218} + \subitem {PhyloCounterData}, \hyperpage{217} \item {simulate} \subitem {DEFM}, \hyperpage{145} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{172} \item {size} \subitem {BArrayDenseCol$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{103} @@ -2659,135 +2667,135 @@ \subitem {BArrayVector\_const$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{123} \subitem {Counters$<$ Array\_Type, Data\_Type $>$}, \hyperpage{140} - \subitem {FreqTable$<$ T $>$}, \hyperpage{162} + \subitem {FreqTable$<$ T $>$}, \hyperpage{161} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} - \subitem {PhyloCounterData}, \hyperpage{218} + \hyperpage{194} + \subitem {PhyloCounterData}, \hyperpage{217} \subitem {PowerSet$<$ Array\_Type, Data\_Rule\_Type $>$}, - \hyperpage{225} - \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{235} + \hyperpage{224} + \subitem {Rules$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \hyperpage{239} + \hyperpage{238} \item {size\_unique} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{194} \item {sort\_array} - \subitem {typedefs.hpp}, \hyperpage{347} + \subitem {typedefs.hpp}, \hyperpage{345} \item {source} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} \item {states} - \subitem {NodeData}, \hyperpage{215} + \subitem {NodeData}, \hyperpage{214} \item {Statistical Models}, \hyperpage{24} \item {stats\_likelihood} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{200} \item {stats\_support} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{200} \item {stats\_support\_n\_arrays} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{201} + \hyperpage{200} \item {stats\_support\_sizes} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{202} + \hyperpage{201} \item {stats\_support\_sizes\_acc} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{202} + \hyperpage{201} \item {stats\_target} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{202} + \hyperpage{201} \item {StatsCounter} \subitem {StatsCounter$<$ Array\_Type, Data\_Type $>$}, - \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} + \hyperpage{235, 236} + \item {StatsCounter$<$ Array\_Type, Data\_Type $>$}, \hyperpage{234} + \subitem {$\sim$StatsCounter}, \hyperpage{236} + \subitem {add\_counter}, \hyperpage{236} + \subitem {count\_all}, \hyperpage{236} + \subitem {count\_current}, \hyperpage{237} + \subitem {count\_init}, \hyperpage{237} + \subitem {get\_counters}, \hyperpage{237} + \subitem {get\_descriptions}, \hyperpage{237} + \subitem {get\_names}, \hyperpage{237} + \subitem {reset\_array}, \hyperpage{237} + \subitem {set\_counters}, \hyperpage{238} + \subitem {size}, \hyperpage{238} + \subitem {StatsCounter}, \hyperpage{235, 236} \item {statscounter-\/meat.hpp} - \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} + \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} \item {STATSCOUNTER\_TEMPLATE} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338--340} + \subitem {statscounter-\/meat.hpp}, \hyperpage{336--338} \item {STATSCOUNTER\_TEMPLATE\_ARGS} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338} + \subitem {statscounter-\/meat.hpp}, \hyperpage{336} \item {STATSCOUNTER\_TYPE} - \subitem {statscounter-\/meat.hpp}, \hyperpage{338} + \subitem {statscounter-\/meat.hpp}, \hyperpage{336} \item {store\_psets} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{194} \item {subtree\_prob} - \subitem {Node}, \hyperpage{213} + \subitem {Node}, \hyperpage{212} \item {Support} \subitem {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{241, 242} + \hyperpage{240, 241} \item {Support$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \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} + \hyperpage{238} + \subitem {$\sim$Support}, \hyperpage{241} + \subitem {add\_counter}, \hyperpage{241} + \subitem {add\_rule}, \hyperpage{241, 242} + \subitem {add\_rule\_dyn}, \hyperpage{242} + \subitem {calc}, \hyperpage{242} + \subitem {change\_stats}, \hyperpage{246} + \subitem {coordiantes\_n\_free}, \hyperpage{246} + \subitem {coordiantes\_n\_locked}, \hyperpage{247} + \subitem {coordinates\_free}, \hyperpage{247} + \subitem {coordinates\_locked}, \hyperpage{247} + \subitem {current\_stats}, \hyperpage{247} + \subitem {delete\_counters}, \hyperpage{247} + \subitem {delete\_rules}, \hyperpage{248} + \subitem {delete\_rules\_dyn}, \hyperpage{248} + \subitem {eval\_rules\_dyn}, \hyperpage{243} + \subitem {get\_counters}, \hyperpage{243} + \subitem {get\_counts}, \hyperpage{243} + \subitem {get\_current\_stats}, \hyperpage{243} + \subitem {get\_data}, \hyperpage{244} + \subitem {get\_rules}, \hyperpage{244} + \subitem {get\_rules\_dyn}, \hyperpage{244} + \subitem {hashes}, \hyperpage{248} + \subitem {hashes\_initialized}, \hyperpage{248} + \subitem {init\_support}, \hyperpage{244} + \subitem {M}, \hyperpage{248} + \subitem {max\_num\_elements}, \hyperpage{249} + \subitem {N}, \hyperpage{249} + \subitem {n\_counters}, \hyperpage{249} + \subitem {print}, \hyperpage{245} + \subitem {reset\_array}, \hyperpage{245} + \subitem {set\_counters}, \hyperpage{245} + \subitem {set\_rules}, \hyperpage{246} + \subitem {set\_rules\_dyn}, \hyperpage{246} + \subitem {Support}, \hyperpage{240, 241} \item {support-\/meat.hpp} - \subitem {BARRY\_SUPPORT\_MEAT\_HPP}, \hyperpage{343} + \subitem {BARRY\_SUPPORT\_MEAT\_HPP}, \hyperpage{341} \item {support\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{202} + \hyperpage{201} \item {support\_size} - \subitem {Flock}, \hyperpage{157} - \subitem {Geese}, \hyperpage{173} + \subitem {Flock}, \hyperpage{156} + \subitem {Geese}, \hyperpage{172} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{194} \item {swap\_cells} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{73} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -2804,11 +2812,11 @@ \indexspace \item {target} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} \item {this} - \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{258} + \subitem {barray-\/meat-\/operators.hpp}, \hyperpage{256} \item {TMP\_HASHER\_CALL} - \subitem {counters-\/meat.hpp}, \hyperpage{283} + \subitem {counters-\/meat.hpp}, \hyperpage{281} \item {toggle\_cell} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -2819,13 +2827,13 @@ \hyperpage{96} \item {transform\_model} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{195} + \hyperpage{194} \item {transform\_model\_fun} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{203} + \hyperpage{202} \item {transform\_model\_term\_names} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{203} + \hyperpage{202} \item {transpose} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, @@ -2834,86 +2842,87 @@ \subitem {CHECK}, \hyperpage{58} \subitem {EXISTS}, \hyperpage{60} \item {typedefs.hpp} - \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} + \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} \indexspace \item {ub} - \subitem {PhyloRuleDynData}, \hyperpage{220} + \subitem {Phylo rules}, \hyperpage{48} + \subitem {PhyloRuleDynData}, \hyperpage{219} \item {UKNOWN} \subitem {EXISTS}, \hyperpage{60} \item {UNI\_SUB} - \subitem {counters.hpp}, \hyperpage{314} + \subitem {counters.hpp}, \hyperpage{312} \item {update\_annotations} - \subitem {Geese}, \hyperpage{173} + \subitem {Geese}, \hyperpage{172} \item {update\_likelihoods} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{195} \item {update\_normalizing\_constant} - \subitem {model-\/meat.hpp}, \hyperpage{310} + \subitem {model-\/meat.hpp}, \hyperpage{308} \item {update\_normalizing\_constants} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{195} \item {update\_pset\_probs} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{196} + \hyperpage{195} \indexspace \item {val} - \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{151} + \subitem {Entries$<$ Cell\_Type $>$}, \hyperpage{150} \item {value} \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} \item {vec\_diff} - \subitem {geese-\/bones.hpp}, \hyperpage{323} + \subitem {geese-\/bones.hpp}, \hyperpage{321} \item {vec\_equal} - \subitem {typedefs.hpp}, \hyperpage{348} + \subitem {typedefs.hpp}, \hyperpage{346} \item {vec\_equal\_approx} - \subitem {typedefs.hpp}, \hyperpage{348} + \subitem {typedefs.hpp}, \hyperpage{346} \item {vec\_inner\_prod} - \subitem {typedefs.hpp}, \hyperpage{348, 349} - \item {vecHasher$<$ T $>$}, \hyperpage{250} - \subitem {operator()}, \hyperpage{251} + \subitem {typedefs.hpp}, \hyperpage{346, 347} + \item {vecHasher$<$ T $>$}, \hyperpage{249} + \subitem {operator()}, \hyperpage{250} \item {vector\_caster} - \subitem {geese-\/bones.hpp}, \hyperpage{324} + \subitem {geese-\/bones.hpp}, \hyperpage{322} \item {vertex\_attr} - \subitem {NetworkData}, \hyperpage{207} + \subitem {NetworkData}, \hyperpage{206} \item {visited} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{75} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{98} \subitem {Cell$<$ Cell\_Type $>$}, \hyperpage{127} - \subitem {Node}, \hyperpage{213} + \subitem {Node}, \hyperpage{212} \indexspace \item {with\_pset} \subitem {Model$<$ Array\_Type, Data\_Counter\_Type, Data\_Rule\_Type, Data\_Rule\_Dyn\_Type $>$}, - \hyperpage{203} + \hyperpage{202} \indexspace \item {X\_ncol} - \subitem {Phylo rules}, \hyperpage{46} + \subitem {Phylo rules}, \hyperpage{48} \item {X\_nrow} - \subitem {Phylo rules}, \hyperpage{47} + \subitem {Phylo rules}, \hyperpage{48} \indexspace \item {ZERO\_CELL} - \subitem {barraydense-\/meat.hpp}, \hyperpage{265} - \subitem {barraydensecol-\/bones.hpp}, \hyperpage{268} - \subitem {barraydenserow-\/bones.hpp}, \hyperpage{269} + \subitem {barraydense-\/meat.hpp}, \hyperpage{263} + \subitem {barraydensecol-\/bones.hpp}, \hyperpage{266} + \subitem {barraydenserow-\/bones.hpp}, \hyperpage{267} \item {zero\_col} \subitem {BArray$<$ Cell\_Type, Data\_Type $>$}, \hyperpage{74} \subitem {BArrayDense$<$ Cell\_Type, Data\_Type $>$}, diff --git a/latex/refman.log b/latex/refman.log index 6497cbbf9..0357ed144 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 2023.11.1) 1 NOV 2023 23:08 +This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Alpine Linux) (preloaded format=pdflatex 2023.11.3) 3 NOV 2023 17:45 entering extended mode restricted \write18 enabled. %&-line parsing enabled. @@ -1180,66 +1180,70 @@ LaTeX Font Info: Font shape `T1/pcr/m/it' in size <7> not available [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 -(Font) scaled to size 7.19995pt on input line 125. +(Font) scaled to size 7.19995pt on input line 127. [27] Overfull \vbox (5.5016pt too high) has occurred while \output is active [] -[28] [29] [30] [31] [32] [33] [34]) (./group__rules-phylo.tex [35] <./group__ru -les-phylo.pdf +[28] [29] [30] [31] [32] [33] [34] +Underfull \hbox (badness 10000) detected at line 593 +[][][] + [] + +[35]) (./group__rules-phylo.tex <./group__rules-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. - -Underfull \hbox (badness 5147) in paragraph at lines 70--71 + [36] +Underfull \hbox (badness 5147) in paragraph at lines 72--73 []\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[]_[] [] -[36] -Underfull \hbox (badness 6157) in paragraph at lines 114--116 +[37] +Underfull \hbox (badness 6157) in paragraph at lines 122--124 []\T1/phv/m/n/10 typedef barry[]::[]Support$\OML/cmm/m/it/10 <$ []\T1/phv/m/n/1 0 , [], [], [] $\OML/cmm/m/it/10 >$ [] -Underfull \hbox (badness 10000) in paragraph at lines 118--120 +Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/phv/m/n/10 typedef barry[]::[]Model$\OML/cmm/m/it/10 <$ []\T1/phv/m/n/10 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[37] [38] [39] +[38] [39] [40] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 covariates[] [] -[40] [41] [42] -Underfull \hbox (badness 10000) detected at line 434 +[41] [42] [43] +Underfull \hbox (badness 10000) detected at line 452 [][][] [] -Underfull \hbox (badness 10000) detected at line 472 +Underfull \hbox (badness 10000) detected at line 490 [][][] [] -[43] [44] [45] [46]) (./group__counters-phylo.tex <./group__counters-phylo.pdf +[44] [45] [46] [47]) (./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. - + [48] 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 +1263,7 @@ 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 +1299,7 @@ Overfull \hbox (27.65639pt too wide) in paragraph at lines 55--56 t nfunA, size[]_[]t nfunB, size[]_[]t duplication=[]) [] - +[49] 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 +1324,15 @@ Underfull \hbox (badness 7576) in paragraph at lines 69--70 t nfunA, size[]_[]t nfunB, size[]_[] [] -[48]pdfTeX warning (ext4): destination with the same identifier (name{group__co -unting_ga39768a8cbb21e6b775c382568a4f98f9}) has been already used, duplicate ig -nored +pdfTeX warning (ext4): destination with the same identifier (name{group__counti +ng_ga39768a8cbb21e6b775c382568a4f98f9}) has been already used, duplicate ignore +d \relax l.84 ...nting_ga39768a8cbb21e6b775c382568a4f98f9}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_ga9d57bfb85ca8ab5a943e46b4 -61e42aea}) has been already used, duplicate ignored + [50]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_ga9d57bfb85ca8ab5a943 +e46b461e42aea}) has been already used, duplicate ignored \relax l.98 ...nting_ga9d57bfb85ca8ab5a943e46b461e42aea}} @@ -1344,9 +1348,9 @@ d2f99d52}) has been already used, duplicate ignored \relax l.126 ...ting_ga8f28f78a8170fcd27f8888bfd2f99d52}} - [49]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_gac5bf2141645db356fbd -1333d56ce8444}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_gac5bf2141645db356fbd1333d +56ce8444}) has been already used, duplicate ignored \relax l.140 ...ting_gac5bf2141645db356fbd1333d56ce8444}} @@ -1356,9 +1360,9 @@ ation with the same identifier (name{group__counting_ga347aabd9065d9ff8352e58fb \relax l.154 ...ting_ga347aabd9065d9ff8352e58fb282b8fd2}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_ga1f7678ddbb9f9084cb5fe1c7 -9f205558}) has been already used, duplicate ignored + [51]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_ga1f7678ddbb9f9084cb5 +fe1c79f205558}) has been already used, duplicate ignored \relax l.168 ...ting_ga1f7678ddbb9f9084cb5fe1c79f205558}} @@ -1374,15 +1378,15 @@ ation with the same identifier (name{group__counting_gac356c5c159d2f37088b162ed \relax l.196 ...ting_gac356c5c159d2f37088b162ed04c362ad}} - [50]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_ga6de412cdee1ec990e62 -edcb29c118824}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_ga6de412cdee1ec990e62edcb2 +9c118824}) has been already used, duplicate ignored \relax l.210 ...ting_ga6de412cdee1ec990e62edcb29c118824}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_gae0453a90fb7c8668a6845fe8 -50477cc7}) has been already used, duplicate ignored + [52]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_gae0453a90fb7c8668a68 +45fe850477cc7}) has been already used, duplicate ignored \relax l.224 ...ting_gae0453a90fb7c8668a6845fe850477cc7}} @@ -1398,7 +1402,7 @@ ation with the same identifier (name{group__counting_ga1bf540113edfb5f96f213837 \relax l.252 ...ting_ga1bf540113edfb5f96f2138370b6f77f6}} - [51]pdfTeX warning (ext4): d + [53]pdfTeX warning (ext4): d estination with the same identifier (name{group__counting_ga23beb6a43e5da922f7c 364714a95a89e}) has been already used, duplicate ignored @@ -1416,9 +1420,9 @@ acfc656c}) has been already used, duplicate ignored \relax l.294 ...ting_gac2eb4b7941b56f783eff66f5acfc656c}} - [52]pdfTeX warning (ext4): d -estination with the same identifier (name{group__counting_ga8f65b1cc27fb2f27eb5 -525b5b36c19f8}) has been already used, duplicate ignored + pdfTeX warning (ext4): destin +ation with the same identifier (name{group__counting_ga8f65b1cc27fb2f27eb5525b5 +b36c19f8}) has been already used, duplicate ignored \relax l.308 ...ting_ga8f65b1cc27fb2f27eb5525b5b36c19f8}} @@ -1428,9 +1432,9 @@ ation with the same identifier (name{group__counting_gaf3bb2dd1c9db36df1d010cc6 \relax l.322 ...ting_gaf3bb2dd1c9db36df1d010cc691573243}} - pdfTeX warning (ext4): destin -ation with the same identifier (name{group__counting_gaa7de3c183a65a0701cbce035 -45421c7d}) has been already used, duplicate ignored + [54]pdfTeX warning (ext4): d +estination with the same identifier (name{group__counting_gaa7de3c183a65a0701cb +ce03545421c7d}) has been already used, duplicate ignored \relax l.336 ...ting_gaa7de3c183a65a0701cbce03545421c7d}} @@ -1446,7 +1450,7 @@ ation with the same identifier (name{group__counting_gaaa5028dec97170c740ea270f \relax l.364 ...ting_gaaa5028dec97170c740ea270f19be9f77}} - [53]pdfTeX warning (ext4): d + [55]pdfTeX warning (ext4): d estination with the same identifier (name{group__counting_gaa8f376142a4cd889fed e792686654d16}) has been already used, duplicate ignored @@ -1464,13 +1468,13 @@ ation with the same identifier (name{group__counting_ga23c694532337cb12a77a64f3 \relax l.406 ...ting_ga23c694532337cb12a77a64f3202a14cf}} - ) [54] [55] [56 - -] + ) [56] Chapter 7. (./namespacebarry.tex) (./namespacebarry_1_1counters.tex) (./namespacebarry_1_1counters_1_1network.tex) (./namespace_c_h_e_c_k.tex -[57]) (./namespacedefm.tex) (./namespace_e_x_i_s_t_s.tex [58] [59]) +[57 + +]) (./namespacedefm.tex) (./namespace_e_x_i_s_t_s.tex [58] [59]) (./namespacegeese.tex) [60] Chapter 8. (./class_b_array.tex @@ -1865,7 +1869,7 @@ 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) @@ -1956,7 +1960,7 @@ 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 @@ -1967,47 +1971,15 @@ Package pdftex.def Info: class_d_e_f_m__inherit__graph.pdf used on input line 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. [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. - [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. - [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) - -Package pdftex.def Info: class_d_e_f_m_rule_dyn_data__coll__graph.pdf used on -input line 24. -(pdftex.def) Requested size: 180.0pt x 156.00162pt. -) (./class_entries.tex +(./class_d_e_f_m_data.tex [146]) (./class_d_e_f_m_rule_data.tex [147]) +(./class_d_e_f_m_rule_dyn_data.tex) (./class_entries.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -2024,29 +1996,29 @@ 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. -[149] [150]) (./class_flock.tex [151] +[148] [149]) (./class_flock.tex [150] 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[]_[] [] -[152] [153] +[151] [152] Underfull \hbox (badness 10000) detected at line 130 [][][] [] -[154] +[153] Underfull \hbox (badness 10000) detected at line 226 [][][] [] -[155] [156] +[154] [155] Underfull \hbox (badness 10000) detected at line 300 [][][] [] -[157]) (./class_freq_table.tex +[156]) (./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 +2035,7 @@ 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. -[158] [159] [160] [161] +[157] [158] [159] [160] Underfull \hbox (badness 10000) detected at line 187 [][][] [] @@ -2073,7 +2045,7 @@ 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. - [162] [163] + [161] [162] Underfull \hbox (badness 10000) detected at line 127 [][][] [] @@ -2083,17 +2055,17 @@ Underfull \hbox (badness 10000) detected at line 146 [][][] [] -[164] +[163] Underfull \hbox (badness 10000) detected at line 215 [][][] [] -[165] [166] [167] +[164] [165] [166] Underfull \hbox (badness 10000) detected at line 392 [][][] [] -[168] [169] [170] [171] [172] [173] [174] [175]) (./class_model.tex +[167] [168] [169] [170] [171] [172] [173] [174]) (./class_model.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -2115,12 +2087,18 @@ 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. - [176] + [175] [176] +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), + [] + Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 22.16548pt. @@ -2128,24 +2106,17 @@ We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [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), - [] - -[178] Underfull \hbox (badness 10000) detected at line 148 [][][] [] -[179] +[178] 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[]_[] [] -[180] +[179] LaTeX Font Info: Font shape `T1/phv/m/n' will be (Font) scaled to size 4.49997pt on input line 298. @@ -2155,7 +2126,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[181] +[180] 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 +2169,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[182] +[181] Underfull \hbox (badness 10000) detected at line 383 [][][] [] @@ -2238,7 +2209,7 @@ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ ][]Type = bool, typename Data[]_[][] [] -[183] +[182] 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 +2258,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[184] +[183] Underfull \hbox (badness 10000) detected at line 498 [][][] [] @@ -2335,7 +2306,7 @@ 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[] [] -[185] +[184] 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 +2371,7 @@ mm/m/it/8 >$ $\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_ ]Rule[]_[][]Dyn[] [] -[186] +[185] 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 +2444,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 645--647 ]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][]Type [] -[187] +[186] 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 +2503,7 @@ mm/m/it/8 >$ $\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr/m/n/8 Array[]_ ]Rule[]_[][]Dyn[] [] -[188] +[187] 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 +2561,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 749--751 n[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::likelihood [] -[189] +[188] 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 +2610,7 @@ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ ][]Type = bool, typename Data[]_[][] [] -[190] +[189] Underfull \hbox (badness 10000) in paragraph at lines 804--806 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2702,7 +2673,7 @@ ta[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][] Dyn[]_[][]Type $\OML/cmm/m/it/8 >$ [] -[191] +[190] 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 +2715,7 @@ Type, Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rul e[]_[][]Dyn[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::sample [] -[192] +[191] 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 +2757,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::set[]_[]rules[]_[]dyn [] -[193] +[192] 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 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -2804,7 +2775,7 @@ e , typename Overfull \vbox (21.45195pt too high) has occurred while \output is active [] -[194] +[193] Underfull \hbox (badness 10000) in paragraph at lines 979--981 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -2888,7 +2859,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::update[]_[] [] -[195] +[194] Underfull \hbox (badness 10000) in paragraph at lines 1041--1043 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -2930,7 +2901,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[196] +[195] 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 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3000,7 +2971,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::delete[]_[]rules [] -[197] +[196] Underfull \hbox (badness 10000) in paragraph at lines 1136--1138 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3056,7 +3027,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 1173--1175 ata[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[198] +[197] Underfull \hbox (badness 10000) in paragraph at lines 1184--1186 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3127,7 +3098,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[199] +[198] Underfull \hbox (badness 10000) in paragraph at lines 1259--1261 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3177,7 +3148,7 @@ _[][]Type$\OML/cmm/m/it/8 >$$\OMS/cmsy/m/n/8 ^^C$ []$\OML/cmm/m/it/8 <$ \T1/pcr ype, [] -[200] +[199] Underfull \hbox (badness 10000) in paragraph at lines 1307--1309 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e = BArray$\OML/cmm/m/it/8 <$$>$\T1/pcr/m/n/8 , typename Data[]_[][]Counter[]_[ @@ -3233,7 +3204,7 @@ mm/m/it/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Typ e, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[201] +[200] 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 +3261,7 @@ 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, [] -[202] +[201] Underfull \hbox (badness 10000) detected at line 1419 [][][] [] @@ -3323,20 +3294,20 @@ _[][]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 [203] [204]) (./class_network_data.tex [205] -[206]) (./class_node.tex [207] <./class_node__coll__graph.pdf +) (./class_net_counter_data.tex [202] [203]) (./class_network_data.tex [204] +[205]) (./class_node.tex [206] <./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. - [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 + [207] [208] [209] [210] [211]) (./class_node_data.tex [212] [213]) +(./class_phylo_counter_data.tex [214] [215] [216]) +(./class_phylo_rule_dyn_data.tex [217] [218]) (./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 +3329,13 @@ 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. - [220] [221] [222] [223] + [219] [220] [221] [222] 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 +3343,7 @@ 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 ( ) [] -[224] [225] [226]) (./class_progress.tex [227]) (./class_rule.tex +[223] [224] [225]) (./class_progress.tex [226]) (./class_rule.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3389,7 +3360,7 @@ 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. -[228] [229] [230]) (./class_rules.tex +[227] [228] [229]) (./class_rules.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3406,7 +3377,7 @@ 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. -[231] [232] +[230] [231] 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 []$\OML/cm @@ -3422,12 +3393,12 @@ m/m/it/8 <$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Type $\OML/cmm/m/it/8 >$ []\T1/pcr/m/n/8 ::end ( ) [] -[233] +[232] Underfull \hbox (badness 10000) detected at line 194 [][][] [] -[234] +[233] Underfull \hbox (badness 10000) detected at line 221 [][][] [] @@ -3449,17 +3420,17 @@ 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. -[235] +[234] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 Array[] [] -[236] [237] +[235] [236] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/sl/10 Array[] [] -[238]) (./class_support.tex +[237]) (./class_support.tex Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. @@ -3484,7 +3455,7 @@ 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[]_[] [] -[239] +[238] Overfull \hbox (3.9776pt too wide) in paragraph at lines 1--1 []\T1/phv/m/n/10 Array[] [] @@ -3499,7 +3470,7 @@ Overfull \hbox (3.9776pt too wide) in paragraph at lines 3--3 []\T1/phv/m/n/10 counters[] [] -[240] [241] +[239] [240] 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 $\OML/cm @@ -3541,7 +3512,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[242] +[241] Underfull \hbox (badness 10000) in paragraph at lines 240--242 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3576,7 +3547,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[243] +[242] Underfull \hbox (badness 10000) in paragraph at lines 286--288 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3647,7 +3618,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 338--340 ]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][] [] -[244] +[243] Underfull \hbox (badness 10000) in paragraph at lines 349--351 \T1/pcr/m/n/8 template$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 typename Array[]_[][]Typ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ @@ -3703,7 +3674,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::print [] -[245] +[244] 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 +3723,7 @@ e , typename Data[]_[][]Counter[]_[][]Type , typename Data[]_[][]Rule[]_[][]Typ e , typename [] -[246] +[245] 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 +3758,7 @@ Data[]_[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[] []Dyn[]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::coordiantes[] [] -[247] +[246] 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 +3786,7 @@ _[][]Counter[]_[][]Type, Data[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[ ]_[][]Type $\OML/cmm/m/it/8 >$[]\T1/pcr/m/n/8 ::delete[]_[] [] -[248] +[247] 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 +3814,7 @@ t/8 >$ []$<$ \T1/pcr/m/n/8 Array[]_[][]Type, Data[]_[][]Counter[]_[][]Type, Dat a[]_[][]Rule[]_[][]Type, Data[]_[][]Rule[]_[][]Dyn[]_[][] [] -[249] +[248] 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[]_[] @@ -3874,16 +3845,14 @@ 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. -[250]) [251] [252 - -] +[249]) [250] Chapter 9. (./barray-bones_8hpp.tex <./barray-bones_8hpp__dep__incl.pdf 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 +3864,30 @@ 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. - [253] [254] [255] [256]) (./barray-meat_8hpp.tex <./barray-meat_8hpp__dep__inc -l.pdf + [251 + +] [252] [253] [254]) (./barray-meat_8hpp.tex <./barray-meat_8hpp__dep__incl.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. - [257] [258]) (./barraycell-bones_8hpp.tex <./barraycell-bones_8hpp__dep__incl. + [255] [256]) (./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 +3898,14 @@ 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 [259] <./barraydense-bones_8hpp__dep__incl.pdf> - +) (./barraydense-bones_8hpp.tex [257] <./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 +3917,37 @@ 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. - [260] [261] [262]) (./barraydense-meat_8hpp.tex <./barraydense-meat_8hpp__dep_ + [258] [259] [260]) (./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. - [263] [264]) (./barraydensecell-bones_8hpp.tex <./barraydensecell-bones_8hpp__ + [261] [262]) (./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. - [265]) (./barraydensecell-meat_8hpp.tex <./barraydensecell-meat_8hpp__dep__inc + [263]) (./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 +3958,35 @@ 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. - [266] [267]) (./barraydenserow-bones_8hpp.tex <./barraydenserow-bones_8hpp__de + [264] [265]) (./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. - [268]) (./barrayrow-bones_8hpp.tex) (./barrayrow-meat_8hpp.tex -[269] [270]) (./barrayvector-bones_8hpp.tex) (./barrayvector-meat_8hpp.tex) + [266]) (./barrayrow-bones_8hpp.tex) (./barrayrow-meat_8hpp.tex +[267] [268]) (./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. - [271] [272] + [269] [270] 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 +3995,37 @@ 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. - [273]) + [271]) (./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. - [274] [275]) (./barry_8hpp.tex <./barry_8hpp__incl.pdf> - + [272] [273]) (./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. - [276] [277] [278]) + [274] [275] [276]) (./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 +4035,14 @@ 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 [279]) (./counters-bones_8hpp.tex <./counters-bones_8hp +) (./col-bones_8hpp.tex [277]) (./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 +4053,18 @@ 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. - [280] + [278] 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 []()[] [] -[281] [282] [283] [284] [285] [286] [287] [288] [289] +[279] [280] [281] [282] [283] [284] [285] [286] [287] 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 +4078,31 @@ 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[] [] -[290] [291] +[288] [289] 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[] [] -[292]) (./network-css_8hpp.tex <./network-css_8hpp__dep__incl.pdf +[290]) (./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. - [293] [294] [295] [296] [297] [298] [299] [300]) (./network_8hpp.tex <./networ + [291] [292] [293] [294] [295] [296] [297] [298]) (./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 +4112,18 @@ 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. - [301] [302] [303] [304] [305] [306] [307]) (./freqtable_8hpp.tex <./freqtable_ + [299] [300] [301] [302] [303] [304] [305]) (./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 +4133,14 @@ 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. - [308]) (./model-meat_8hpp.tex <./model-meat_8hpp__dep__incl.pdf> - + [306]) (./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 +4152,15 @@ 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 [] -[309]) (./defm_8hpp.tex <./defm_8hpp__incl.pdf> - +[307]) (./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. - [310]) + [308]) (./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 +4170,7 @@ 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 +4182,13 @@ Underfull \hbox (badness 3148) in paragraph at lines 32--34 ]t [], size[]_[]t [], [] -[311] [312] [313]) (./geese_2counters_8hpp.tex <./geese_2counters_8hpp__dep__in +[309] [310] [311]) (./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 +4200,7 @@ Underfull \hbox (badness 5147) in paragraph at lines 16--17 []_[]t pos, size[]_[]t lb, size[]_[]t ub, size[]_[] [] -[314] +[312] 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 +4256,7 @@ Overfull \hbox (27.65639pt too wide) in paragraph at lines 74--75 t nfunA, size[]_[]t nfunB, size[]_[]t duplication=[]) [] -[315] +[313] 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 +4286,7 @@ 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 +4296,13 @@ 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. - [316] [317]) (./defm-types_8hpp.tex <./defm-types_8hpp__dep__incl.pdf> - + [314] [315]) (./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 +4319,25 @@ Underfull \hbox (badness 4531) in paragraph at lines 38--40 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[318]) (./formula_8hpp.tex <./formula_8hpp__dep__incl.pdf> - +[316]) (./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. - [319]) + [317]) (./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. - [320]) (./flock-bones_8hpp.tex <./flock-bones_8hpp__dep__incl.pdf + [318]) (./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 +4348,26 @@ 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 [321] <./geese-bones_8hpp__dep__incl.pdf> - +) (./geese-bones_8hpp.tex [319] <./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. - [322] -[323]) (./geese-meat-constructors_8hpp.tex <./geese-meat-constructors_8hpp__dep + [320] +[321]) (./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 +4379,24 @@ 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. - [324] <./geese-meat-likelihood_8hpp__dep__incl.pdf> - + [322] <./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. - [325]) + [323]) (./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 +4409,15 @@ 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 [326] <./geese-meat-predict__exhaust_ +) (./geese-meat-predict__exhaust_8hpp.tex [324] <./geese-meat-predict__exhaust_ 8hpp__dep__incl.pdf> - File: geese-meat-predict__exhaust_8hpp__dep__incl.pdf Graphic file (type pdf) @@ -4459,16 +4430,16 @@ 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 [327] <./geese-meat-simulate_8hpp__dep__incl. +) (./geese-meat-simulate_8hpp.tex [325] <./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 +4450,13 @@ 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 [328] <./geese-node-bones_8hpp__dep__incl.pdf> - +) (./geese-node-bones_8hpp.tex [326] <./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 +4467,19 @@ 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. - [329] + [327] 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 , [], [], [] $\OML/cmm/m/it/10 >$ [] -[330] [331] +[328] [329] 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 +4490,32 @@ 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. - [332]) (./powerset-meat_8hpp.tex <./powerset-meat_8hpp__dep__incl.pdf + [330]) (./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 [333] <./progress_8hpp__dep__incl.pdf> - +) (./progress_8hpp.tex [331] <./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. (pdftex.def) Requested size: 210.0pt x 212.00543pt. - [334]) + [332]) (./rules-bones_8hpp.tex <./rules-bones_8hpp__dep__incl.pdf> - + File: rules-bones_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: rules-bones_8hpp__dep__incl.pdf used on input line 8. @@ -4556,14 +4527,14 @@ Package pdftex.def Info: rules-bones_8hpp__dep__incl.pdf used on input line 8. pdfTeX warning: pdflatex (file ./rules-meat_8hpp__dep__incl.pdf): PDF inclusion : multiple pdfs with page group included in a single page > - + File: rules-meat_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: rules-meat_8hpp__dep__incl.pdf used on input line 8. (pdftex.def) Requested size: 193.0pt x 167.00172pt. -) (./statscounter-bones_8hpp.tex [335] <./statscounter-bones_8hpp__dep__incl.pd +) (./statscounter-bones_8hpp.tex [333] <./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 +4545,31 @@ 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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(pdftex.def) Requested size: 209.0pt x 155.99922pt. - [344] [345] + [342] [343] Underfull \hbox (badness 10000) in paragraph at lines 117--119 \T1/pcr/m/n/8 using [] = std[]::function$\OML/cmm/m/it/8 <$\T1/pcr/m/n/8 double (const Array[]_[][]Type &, size[]_[]t, size[]_[]t, Data[]_[][]Type @@ -4632,7 +4603,7 @@ Underfull \hbox (badness 10000) detected at line 133 [][][] [] -[346] [347] +[344] [345] Underfull \hbox (badness 10000) detected at line 234 [][][] [] @@ -4642,7 +4613,7 @@ Underfull \hbox (badness 10000) detected at line 257 [][][] [] -[348]) (./_r_e_a_d_m_e_8md.tex) [349] [350 +[346]) (./_r_e_a_d_m_e_8md.tex) [347] [348 ] (./refman.ind Underfull \hbox (badness 2088) in paragraph at lines 25--27 @@ -4740,7 +4711,7 @@ Underfull \hbox (badness 3568) in paragraph at lines 106--108 /n/10 , [] -[351 +[349 ] @@ -4797,7 +4768,7 @@ Underfull \hbox (badness 3568) in paragraph at lines 129--131 /n/10 , [] -[352] +[350] Underfull \hbox (badness 1142) in paragraph at lines 254--256 []| 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100644 --- a/latex/refman.toc +++ b/latex/refman.toc @@ -88,89 +88,94 @@ \contentsline {subsubsection}{\numberline {6.3.2.32}counter\_ttriads()\hspace {0.1cm}{\footnotesize \ttfamily [1/2]}}{34}{subsubsection.6.3.2.32}% \contentsline {subsubsection}{\numberline {6.3.2.33}counter\_ttriads()\hspace {0.1cm}{\footnotesize \ttfamily [2/2]}}{35}{subsubsection.6.3.2.33}% \contentsline {subsubsection}{\numberline {6.3.2.34}NETWORK\_COUNTER()}{35}{subsubsection.6.3.2.34}% -\contentsline {subsubsection}{\numberline {6.3.2.35}rules\_dont\_become\_zero()}{35}{subsubsection.6.3.2.35}% -\contentsline {subsubsection}{\numberline {6.3.2.36}rules\_markov\_fixed()}{35}{subsubsection.6.3.2.36}% +\contentsline {subsubsection}{\numberline {6.3.2.35}rule\_constrain\_support()}{35}{subsubsection.6.3.2.35}% +\contentsline {subsubsection}{\numberline {6.3.2.36}rules\_dont\_become\_zero()}{36}{subsubsection.6.3.2.36}% +\contentsline {subsubsection}{\numberline 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