NCBI C++ ToolKit
Classes | Macros | Functions | Variables
blast_formatter.cpp File Reference

Stand-alone command line formatter for BLAST. More...

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbistre.hpp>
#include <serial/iterator.hpp>
#include <algo/blast/api/version.hpp>
#include <algo/blast/api/remote_blast.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
#include <algo/blast/format/blast_format.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <objtools/data_loaders/blastdb/bdbloader_rmt.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/data_loaders/genbank/id2/reader_id2.hpp>
#include "blast_app_util.hpp"
+ Include dependency graph for blast_formatter.cpp:

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Classes

class  CBlastFormatterApp
 The application class. More...
 

Macros

#define EXIT_CODE__UNKNOWN_RID   1
 
#define EXIT_CODE__SEARCH_PENDING   2
 
#define EXIT_CODE__SEARCH_FAILED   3
 

Functions

 USING_SCOPE (blast)
 
static TSeqLocVector s_ConvertSubjects2TSeqLocVector (CRef< CRemoteBlast > remote_blast)
 Extracts the subject sequence data from remote_blast into a TSeqLocVector. More...
 
bool s_InitializeSubject (CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< blast::CLocalDbAdapter > &db_adapter, CRef< objects::CScope > &scope)
 
int main (int argc, const char *argv[])
 

Variables

 USING_NCBI_SCOPE
 

Detailed Description

Stand-alone command line formatter for BLAST.

Definition in file blast_formatter.cpp.

Macro Definition Documentation

◆ EXIT_CODE__SEARCH_FAILED

#define EXIT_CODE__SEARCH_FAILED   3

Definition at line 497 of file blast_formatter.cpp.

◆ EXIT_CODE__SEARCH_PENDING

#define EXIT_CODE__SEARCH_PENDING   2

Definition at line 496 of file blast_formatter.cpp.

◆ EXIT_CODE__UNKNOWN_RID

#define EXIT_CODE__UNKNOWN_RID   1

Definition at line 495 of file blast_formatter.cpp.

Function Documentation

◆ main()

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

Definition at line 591 of file blast_formatter.cpp.

References CNcbiApplicationAPI::AppMain().

◆ s_ConvertSubjects2TSeqLocVector()

static TSeqLocVector s_ConvertSubjects2TSeqLocVector ( CRef< CRemoteBlast remote_blast)
static

Extracts the subject sequence data from remote_blast into a TSeqLocVector.

All subjects are added to/use the same CScope object

Parameters
remote_blastSource of subject sequences

Definition at line 232 of file blast_formatter.cpp.

References CScope::AddBioseq(), CSeq_id::BestRank(), FindBestChoice(), CObjectManager::GetInstance(), CRemoteBlast::GetSubjectSeqLocs(), CRemoteBlast::GetSubjectSequences(), and ITERATE.

Referenced by CBlastFormatterApp::PrintFormattedOutput().

◆ s_InitializeSubject()

bool s_InitializeSubject ( CRef< blast::CBlastDatabaseArgs >  db_args,
CRef< blast::CBlastOptionsHandle >  opts_hndl,
CRef< blast::CLocalDbAdapter > &  db_adapter,
CRef< objects::CScope > &  scope 
)

◆ USING_SCOPE()

USING_SCOPE ( blast  )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 50 of file blast_formatter.cpp.

Modified on Sun Feb 25 03:06:36 2024 by modify_doxy.py rev. 669887