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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cobalt__app_8cpp.html below:

NCBI C++ ToolKit: src/algo/cobalt/demo/cobalt_app.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbitime.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/create_defline.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include <serial/iterator.hpp>
#include <objtools/readers/fasta.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objtools/align_format/aln_printer.hpp>
#include <objects/blast/Blast4_archive.hpp>
#include <algo/blast/api/blast_usage_report.hpp>
#include <algo/cobalt/cobalt.hpp>
#include <algo/cobalt/version.hpp>
#include "cobalt_app_util.hpp"

Include dependency graph for cobalt_app.cpp:

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Classes class CMultiApplication Functions USING_SCOPE (objects) USING_SCOPE (align_format) USING_SCOPE (cobalt) string s_GetTreeMethodAsString (CMultiAlignerOptions::ETreeMethod method) string s_GetKmerAlphabetAsString (CMultiAlignerOptions::TKMethods::ECompressedAlphabet alph) static void x_LoadConstraints (string constraintfile, vector< CMultiAlignerOptions::SConstraint > &constr) static void x_LoadPatterns (string patternsfile, vector< CMultiAlignerOptions::CPattern > &patterns) int main (int argc, const char *argv[]) Variables USING_NCBI_SCOPE Function Documentation ◆ main() int main ( int argc, const char * argv[] )

Definition at line 691 of file cobalt_app.cpp.

References CNcbiApplicationAPI::AppMain(), and eDS_Default.

◆ s_GetKmerAlphabetAsString() string s_GetKmerAlphabetAsString ( CMultiAlignerOptions::TKMethods::ECompressedAlphabet alph )

Definition at line 107 of file cobalt_app.cpp.

References TKmerMethods< TKmerCounts >::eRegular, TKmerMethods< TKmerCounts >::eSE_B15, and TKmerMethods< TKmerCounts >::eSE_V10.

Referenced by CMultiApplication::Init().

◆ s_GetTreeMethodAsString() string s_GetTreeMethodAsString ( CMultiAlignerOptions::ETreeMethod method )

Definition at line 95 of file cobalt_app.cpp.

References CMultiAlignerOptions::eClusters, CMultiAlignerOptions::eFastME, and CMultiAlignerOptions::eNJ.

Referenced by CMultiApplication::Init().

◆ USING_SCOPE() [1/3] USING_SCOPE ( align_format ) ◆ USING_SCOPE() [2/3] USING_SCOPE ( cobalt ) ◆ USING_SCOPE() [3/3] USING_SCOPE ( objects ) ◆ x_LoadConstraints() static void x_LoadConstraints ( string constraintfile, vector< CMultiAlignerOptions::SConstraint > & constr ) static

Definition at line 313 of file cobalt_app.cpp.

References f, and NCBI_THROW.

Referenced by CMultiApplication::Run().

◆ x_LoadPatterns() static void x_LoadPatterns ( string patternsfile, vector< CMultiAlignerOptions::CPattern > & patterns ) static

Definition at line 346 of file cobalt_app.cpp.

References f, NCBI_THROW, and patterns.

Referenced by CMultiApplication::Run().

Variable Documentation ◆ USING_NCBI_SCOPE USING_NCBI_SCOPE

Definition at line 57 of file cobalt_app.cpp.

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