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.