src/app/blast/psiblast_app.cpp File Reference

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Detailed Description

PSI-BLAST command line application.

Definition in file psiblast_app.cpp.

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbifile.hpp>
#include <algo/blast/api/blast_options.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/seqsrc_seqdb.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/blastinput/psiblast_args.hpp>
#include <algo/blast/api/remote_blast.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/format/blast_format.hpp>
#include "blast_app_util.hpp"
#include <algo/blast/api/psiblast.hpp>
#include <algo/blast/api/psiblast_iteration.hpp>
#include <objects/scoremat/Pssm.hpp>

Include dependency graph for psiblast_app.cpp:

Go to the source code of this file.

Classes
class	CPsiBlastApp
Functions
	USING_SCOPE (blast)
	USING_SCOPE (objects)
static CConstRef< CBioseq >	s_GetQueryBioseq (CConstRef< CBlastQueryVector > query, CRef< CScope > scope, CRef< CPssmWithParameters > pssm)
	Extract the bioseq which represents the query from either a PSSM or a CBlastQueryVector.
static CRef< CBlastAncillaryData >	s_ExtractAncillaryData (const CPssmWithParameters &pssm)
	Auxiliary function to extract the ancillary data from the PSSM.
int	main (int argc, const char *argv[])
Variables
static char const	rcsid []
	USING_NCBI_SCOPE

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Function Documentation

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

Definition at line 409 of file psiblast_app.cpp. References eDS_Default.

static CRef<CBlastAncillaryData> s_ExtractAncillaryData (  const CPssmWithParameters &  pssm  )  [static]

Auxiliary function to extract the ancillary data from the PSSM. Definition at line 150 of file psiblast_app.cpp. References _ASSERT, CPssmWithParameters_Base::CanGetPssm(), and CPssmWithParameters_Base::GetPssm().

static CConstRef<CBioseq> s_GetQueryBioseq (  CConstRef< CBlastQueryVector >  query, CRef< CScope >  scope, CRef< CPssmWithParameters >  pssm )  [static]

Extract the bioseq which represents the query from either a PSSM or a CBlastQueryVector. Parameters: query  container for query sequence(s) [in] scope  Scope from which to retrieve the query if not in the PSSM [in] pssm  if NON-NULL, the query will be extracted from this object [in] Definition at line 117 of file psiblast_app.cpp. References _ASSERT, query, and CConstRef< C, Locker >::Reset().

USING_SCOPE (  objects   )

USING_SCOPE (  blast   )

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Variable Documentation

char const rcsid[] [static]

Initial value: "$Id: psiblast_app.cpp 167662 2009-08-05 14:04:15Z camacho $" Definition at line 35 of file psiblast_app.cpp.

USING_NCBI_SCOPE

Definition at line 57 of file psiblast_app.cpp.

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