NCBI C++ ToolKit
Classes | Functions
blast_args.cpp File Reference

convert blast-related command line arguments into blast options More...

#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <algo/blast/api/version.hpp>
#include <algo/blast/blastinput/blast_args.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/core/blast_nalookup.h>
#include <algo/blast/core/hspfilter_besthit.h>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <util/format_guess.hpp>
#include <util/line_reader.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/winmask/seq_masker_istat_factory.hpp>
#include <connect/ncbi_connutil.h>
#include <objtools/align_format/align_format_util.hpp>
#include <algo/blast/api/msa_pssm_input.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <objtools/blast/seqdb_reader/tax4blastsqlite.hpp>
+ Include dependency graph for blast_args.cpp:

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Classes

class  CArgAllowGeneticCodeInteger
 Auxiliary class to validate the genetic code input. More...
 

Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (align_format)
 
static bool s_IsDefaultWordThreshold (EProgram program, double threshold)
 
static void s_SetCompositionBasedStats (CBlastOptions &opt, const string &comp_stat_string, bool smith_waterman_value, bool *ungapped)
 Auxiliary function to set the composition based statistics and smith waterman options. More...
 
static string s_RegisterOMDataLoader (CRef< CSeqDB > db_handle)
 
static void s_GetTaxIDList (const string &in, bool isFile, bool isNegativeList, CRef< CSearchDatabase > &sdb, bool isTargetOnly)
 
static void s_ValidateCustomDelim (string custom_fmt_spec, string customDelim)
 
CArgDescriptionsSetUpCommandLineArguments (TBlastCmdLineArgs &args)
 Create a CArgDescriptions object and invoke SetArgumentDescriptions for each of the TBlastCmdLineArgs in its argument list. More...
 

Detailed Description

convert blast-related command line arguments into blast options

Definition in file blast_args.cpp.

Function Documentation

◆ s_GetTaxIDList()

static void s_GetTaxIDList ( const string in,
bool  isFile,
bool  isNegativeList,
CRef< CSearchDatabase > &  sdb,
bool  isTargetOnly 
)
static

◆ s_IsDefaultWordThreshold()

static bool s_IsDefaultWordThreshold ( EProgram  program,
double  threshold 
)
static

◆ s_RegisterOMDataLoader()

static string s_RegisterOMDataLoader ( CRef< CSeqDB db_handle)
static

◆ s_SetCompositionBasedStats()

static void s_SetCompositionBasedStats ( CBlastOptions opt,
const string comp_stat_string,
bool  smith_waterman_value,
bool ungapped 
)
static

Auxiliary function to set the composition based statistics and smith waterman options.

Parameters
optBLAST options object [in|out]
comp_stat_stringcommand line value for composition based statistics [in]
smith_waterman_valuecommand line value for determining the use of the smith-waterman algorithm [in]
ungappedpointer to the value which determines whether the search should be ungapped or not. It is NULL if ungapped searches are not applicable
is_deltablastis program deltablast [in]

Definition at line 820 of file blast_args.cpp.

References eBlastp, eBlastx, eCompoForceFullMatrixAdjust, eCompositionBasedStats, eCompositionMatrixAdjust, eDeltaBlast, eNoCompositionBasedStats, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, CBlastOptions::GetProgram(), NCBI_THROW, CBlastOptions::SetCompositionBasedStats(), CBlastOptions::SetSmithWatermanMode(), CBlastOptions::SetUnifiedP(), and tolower().

Referenced by CCompositionBasedStatsArgs::ExtractAlgorithmOptions().

◆ s_ValidateCustomDelim()

static void s_ValidateCustomDelim ( string  custom_fmt_spec,
string  customDelim 
)
static

◆ SetUpCommandLineArguments()

CArgDescriptions* SetUpCommandLineArguments ( TBlastCmdLineArgs args)

Create a CArgDescriptions object and invoke SetArgumentDescriptions for each of the TBlastCmdLineArgs in its argument list.

Parameters
argsarguments to configure the return value [in]
Returns
a CArgDescriptions object with the command line options set

Definition at line 3640 of file blast_args.cpp.

References NON_CONST_ITERATE.

Referenced by CBlastAppArgs::SetCommandLine().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( align_format  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )
Modified on Wed Feb 28 07:11:28 2024 by modify_doxy.py rev. 669887