NCBI C++ ToolKit
Classes | Functions | Variables
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)

◆ s_GetTreeMethodAsString()

string s_GetTreeMethodAsString ( CMultiAlignerOptions::ETreeMethod  method)

◆ 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.

Modified on Thu Feb 22 17:12:30 2024 by modify_doxy.py rev. 669887