src/algo/cobalt/demo/cobalt_app.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbifile.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.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 <algo/cobalt/cobalt.hpp>
#include <algo/cobalt/version.hpp>

Include dependency graph for cobalt_app.cpp:

Go to the source code of this file.

Classes
class	CMultiApplication
Functions
	USING_SCOPE (objects)
	USING_SCOPE (cobalt)
void	x_GetSeqLocFromStream (CNcbiIstream &instream, CObjectManager &objmgr, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope)
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
static char const	rcsid [] = "$Id: cobalt_app.cpp 168664 2009-08-19 13:51:41Z boratyng $"
	USING_NCBI_SCOPE

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Function Documentation

int main (  int  argc, const char *  argv[] )

Definition at line 485 of file cobalt_app.cpp. References eDS_Default.

USING_SCOPE (  cobalt   )

USING_SCOPE (  objects   )

void x_GetSeqLocFromStream (  CNcbiIstream &  instream, CObjectManager &  objmgr, vector< CRef< objects::CSeq_loc > > &  seqs, CRef< objects::CScope > &  scope )

Definition at line 205 of file cobalt_app.cpp. References CStreamLineReader::AtEOF(), ConstBegin(), eInvalid, CFastaReader::fAssumeProt, CFastaReader::fForceType, CFastaReader::fNoParseID, NCBI_THROW, CFastaReader::ReadOneSeq(), and CRef< C, Locker >::Reset().

static void x_LoadConstraints (  string  constraintfile, vector< CMultiAlignerOptions::SConstraint > &  constr )  [static]

Definition at line 241 of file cobalt_app.cpp. References f(), and NCBI_THROW.

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

Definition at line 274 of file cobalt_app.cpp. References f(), and NCBI_THROW.

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Variable Documentation

char const rcsid[] = "$Id: cobalt_app.cpp 168664 2009-08-19 13:51:41Z boratyng $" [static]

Definition at line 1 of file cobalt_app.cpp.

USING_NCBI_SCOPE

Definition at line 52 of file cobalt_app.cpp.

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