From 12d2cd8ba40b11ec4c8289703baceb5e9ddbb65b Mon Sep 17 00:00:00 2001 From: Brian Ondov Date: Fri, 18 Jul 2014 17:40:17 -0400 Subject: [PATCH] License file and headers --- LICENSE.txt | 44 +++++++++++++++++++++++++++++++ src/harvest/AnnotationList.cpp | 5 ++++ src/harvest/AnnotationList.h | 6 +++++ src/harvest/HarvestIO.cpp | 6 ++++- src/harvest/HarvestIO.h | 5 ++++ src/harvest/LcbList.cpp | 5 ++++ src/harvest/LcbList.h | 6 +++++ src/harvest/PhylogenyTree.cpp | 5 ++++ src/harvest/PhylogenyTree.h | 6 +++++ src/harvest/PhylogenyTreeNode.cpp | 5 ++++ src/harvest/PhylogenyTreeNode.h | 5 ++++ src/harvest/ReferenceList.cpp | 10 ++++++- src/harvest/ReferenceList.h | 7 +++++ src/harvest/TrackList.cpp | 6 +++++ src/harvest/TrackList.h | 5 ++++ src/harvest/VariantList.cpp | 5 ++++ src/harvest/VariantList.h | 5 ++++ src/harvest/harvest.cpp | 10 +++---- src/harvest/parse.cpp | 5 ++++ src/harvest/parse.h | 6 +++++ src/harvest/pb/harvest.proto | 6 +++++ 21 files changed, 155 insertions(+), 8 deletions(-) create mode 100644 LICENSE.txt diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..ce89783 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,44 @@ +PURPOSE + +Harvest is a file format conversion tool for use with the Harvest tool +suite (github.com/marbl/harvest). Harvest is implemented in C++ and +uses Google Protocol Buffers for serialization. + +COPYRIGHT LICENSE + +Copyright © 2014, Battelle National Biodefense Institute (BNBI); +all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +Adam Phillippy + +This Software was prepared for the Department of Homeland Security +(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +part of contract HSHQDC-07-C-00020 to manage and operate the National +Biodefense Analysis and Countermeasures Center (NBACC), a Federally +Funded Research and Development Center. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + +1. Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/src/harvest/AnnotationList.cpp b/src/harvest/AnnotationList.cpp index a81cacf..3e555a1 100644 --- a/src/harvest/AnnotationList.cpp +++ b/src/harvest/AnnotationList.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "AnnotationList.h" #include diff --git a/src/harvest/AnnotationList.h b/src/harvest/AnnotationList.h index e071c1e..5b111be 100644 --- a/src/harvest/AnnotationList.h +++ b/src/harvest/AnnotationList.h @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #ifndef AnnotationList_h #define AnnotationList_h diff --git a/src/harvest/HarvestIO.cpp b/src/harvest/HarvestIO.cpp index 7bb693e..91607f9 100644 --- a/src/harvest/HarvestIO.cpp +++ b/src/harvest/HarvestIO.cpp @@ -1,4 +1,8 @@ - +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "HarvestIO.h" diff --git a/src/harvest/HarvestIO.h b/src/harvest/HarvestIO.h index 95c9032..84a74de 100644 --- a/src/harvest/HarvestIO.h +++ b/src/harvest/HarvestIO.h @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #ifndef HarvestIO_h #define HarvestIO_h diff --git a/src/harvest/LcbList.cpp b/src/harvest/LcbList.cpp index 52c52b9..0f94065 100644 --- a/src/harvest/LcbList.cpp +++ b/src/harvest/LcbList.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "harvest/LcbList.h" #include diff --git a/src/harvest/LcbList.h b/src/harvest/LcbList.h index bcf7467..2933bf7 100644 --- a/src/harvest/LcbList.h +++ b/src/harvest/LcbList.h @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #ifndef LcbList_h #define LcbList_h diff --git a/src/harvest/PhylogenyTree.cpp b/src/harvest/PhylogenyTree.cpp index 8b38215..830511a 100644 --- a/src/harvest/PhylogenyTree.cpp +++ b/src/harvest/PhylogenyTree.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "PhylogenyTree.h" #include diff --git a/src/harvest/PhylogenyTree.h b/src/harvest/PhylogenyTree.h index cf0d62a..47bda5f 100644 --- a/src/harvest/PhylogenyTree.h +++ b/src/harvest/PhylogenyTree.h @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #ifndef harvest_PhylogenyTree #define harvest_PhylogenyTree diff --git a/src/harvest/PhylogenyTreeNode.cpp b/src/harvest/PhylogenyTreeNode.cpp index eba36f5..b130cf7 100644 --- a/src/harvest/PhylogenyTreeNode.cpp +++ b/src/harvest/PhylogenyTreeNode.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "PhylogenyTreeNode.h" diff --git a/src/harvest/PhylogenyTreeNode.h b/src/harvest/PhylogenyTreeNode.h index da7a1b4..9127447 100644 --- a/src/harvest/PhylogenyTreeNode.h +++ b/src/harvest/PhylogenyTreeNode.h @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #ifndef PhylogenyTreeNode_h #define PhylogenyTreeNode_h diff --git a/src/harvest/ReferenceList.cpp b/src/harvest/ReferenceList.cpp index b6013c6..72e2e13 100644 --- a/src/harvest/ReferenceList.cpp +++ b/src/harvest/ReferenceList.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include #include "ReferenceList.h" @@ -55,7 +60,10 @@ int ReferenceList::getReferenceSequenceFromGi(long int gi) const } } - throw GiNotFoundException(std::to_string(gi)); + char giString[1024]; + sprintf(giString, "%ld", gi); + + throw GiNotFoundException(giString); return undef; } diff --git a/src/harvest/ReferenceList.h b/src/harvest/ReferenceList.h index eeff12e..b3621d3 100644 --- a/src/harvest/ReferenceList.h +++ b/src/harvest/ReferenceList.h @@ -1,9 +1,16 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #ifndef ReferenceList_h #define ReferenceList_h #include #include #include +#include #include "harvest/pb/harvest.pb.h" diff --git a/src/harvest/TrackList.cpp b/src/harvest/TrackList.cpp index 330b7da..7d2bef8 100644 --- a/src/harvest/TrackList.cpp +++ b/src/harvest/TrackList.cpp @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #include "harvest/TrackList.h" using namespace::std; diff --git a/src/harvest/TrackList.h b/src/harvest/TrackList.h index 2524e9f..d9cd9c5 100644 --- a/src/harvest/TrackList.h +++ b/src/harvest/TrackList.h @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #ifndef TrackList_h #define TrackList_h diff --git a/src/harvest/VariantList.cpp b/src/harvest/VariantList.cpp index 5983e47..0c56002 100644 --- a/src/harvest/VariantList.cpp +++ b/src/harvest/VariantList.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "harvest/VariantList.h" #include diff --git a/src/harvest/VariantList.h b/src/harvest/VariantList.h index b08c474..ec17b21 100644 --- a/src/harvest/VariantList.h +++ b/src/harvest/VariantList.h @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #ifndef VariantList_h #define VariantList_h diff --git a/src/harvest/harvest.cpp b/src/harvest/harvest.cpp index 0261b4d..363541c 100644 --- a/src/harvest/harvest.cpp +++ b/src/harvest/harvest.cpp @@ -1,10 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy // -// main.cpp -// harvest -// -// Created by Brian Ondov on 6/19/13. -// -// +// See the LICENSE.txt file included with this software for license information. #include #include diff --git a/src/harvest/parse.cpp b/src/harvest/parse.cpp index b204607..bf74d98 100644 --- a/src/harvest/parse.cpp +++ b/src/harvest/parse.cpp @@ -1,3 +1,8 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. #include "parse.h" #include diff --git a/src/harvest/parse.h b/src/harvest/parse.h index 4b36c4e..d4443e3 100644 --- a/src/harvest/parse.h +++ b/src/harvest/parse.h @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + #ifndef parse_h #define parse_h diff --git a/src/harvest/pb/harvest.proto b/src/harvest/pb/harvest.proto index dc6b7ca..3acbb75 100644 --- a/src/harvest/pb/harvest.proto +++ b/src/harvest/pb/harvest.proto @@ -1,3 +1,9 @@ +// Copyright © 2014, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and +// Adam Phillippy +// +// See the LICENSE.txt file included with this software for license information. + message Harvest { message Reference