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

Command line tool to create RPS,COBALT & DELTA BLAST databases. More...

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbimisc.hpp>
#include <corelib/ncbitime.hpp>
#include <util/math/matrix.hpp>
#include <serial/objistrasn.hpp>
#include <algo/blast/api/version.hpp>
#include <algo/blast/blastinput/cmdline_flags.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/psi_pssm_input.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/scoremat/Pssm.hpp>
#include <objects/scoremat/PssmIntermediateData.hpp>
#include <objects/scoremat/PssmParameters.hpp>
#include <objects/scoremat/FormatRpsDbParameters.hpp>
#include <objects/scoremat/PssmFinalData.hpp>
#include <objects/scoremat/CoreBlock.hpp>
#include <objects/scoremat/CoreDef.hpp>
#include <objects/scoremat/LoopConstraint.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <algo/blast/core/blast_aalookup.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/ncbi_math.h>
#include <objtools/blast/seqdb_writer/writedb.hpp>
#include <objtools/blast/seqdb_writer/build_db.hpp>
#include <objtools/blast/seqdb_writer/taxid_set.hpp>
#include <objtools/blast/seqdb_writer/writedb_files.hpp>
#include <objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp>
#include "../blast/blast_app_util.hpp"
+ Include dependency graph for makeprofiledb.cpp:

Go to the source code of this file.

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Classes

class  CMakeDbPosMatrix
 
class  CMakeProfileDBApp
 
class  CMakeProfileDBApp::CRPS_DbInfo
 

Macros

#define kDefaultWordScoreThreshold   (9.82)
 
#define kDefaultPssmScaleFactor   (100.00)
 
#define kDefaultObsrThreshold   (6.0)
 
#define kDefaultMaxSmpFilesPerVol   (2500)
 
#define kEpsylon   (0.0001)
 
#define DEFAULT_POS_MATRIX_SIZE   2000
 
#define RPS_NUM_LOOKUP_CELLS   32768
 
#define RPS_DATABASE_VERSION   RPS_MAGIC_NUM
 
#define kSingleVol   (-1)
 

Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
static const string kInPssmList ("in")
 
static const string kOutDbName ("out")
 
static const string kOutDbType ("dbtype")
 
static const string kPssmScaleFactor ("scale")
 
static const string kOutIndexFile ("index")
 
static const string kObsrThreshold ("obsr_threshold")
 
static const string kExcludeInvalid ("exclude_invalid")
 
static const string kBinaryScoremat ("binary")
 
static const string kUseCmdlineThreshold ("force")
 
static const string kMaxSmpFilesPerVol ("max_smp_vol")
 
static const string kLogFile ("logfile")
 
static const string kDefaultMatrix (kMatrixBLOSUM62)
 
static const string kDefaultOutDbType (kOutDbRps)
 
static const string kDefaultOutIndexFile ("true")
 
static const string kDefaultExcludeInvalid ("true")
 
static bool s_DeleteMakeprofileDb (const string &name)
 
static bool s_HasDefline (const CBioseq &bio)
 
static CRef< CBlast_def_line_sets_GenerateBlastDefline (const CBioseq &bio)
 
static void s_WriteInt4List (CNcbiOfstream &ostr, const list< Int4 > &l)
 
static void s_WriteUint4List (CNcbiOfstream &ostr, const list< Uint4 > &l)
 
int main (int argc, const char *argv[])
 

Variables

 USING_NCBI_SCOPE
 
static const string kOutDbRps = "rps"
 
static const string kOutDbCobalt = "cobalt"
 
static const string kOutDbDelta = "delta"
 
static const string kMatrixBLOSUM62 = "BLOSUM62"
 
static const string kMatrixBLOSUM80 = "BLOSUM80"
 
static const string kMatrixBLOSUM50 = "BLOSUM50"
 
static const string kMatrixBLOSUM45 = "BLOSUM45"
 
static const string kMatrixBLOSUM90 = "BLOSUM90"
 
static const string kMatrixPAM250 = "PAM250"
 
static const string kMatrixPAM30 = "PAM30"
 
static const string kMatrixPAM70 = "PAM70"
 
static const Uint4 kFixedPointScaleFactor = 1000
 

Detailed Description

Command line tool to create RPS,COBALT & DELTA BLAST databases.

This is the successor to formatrpsdb from the C toolkit

Definition in file makeprofiledb.cpp.

Macro Definition Documentation

◆ DEFAULT_POS_MATRIX_SIZE

#define DEFAULT_POS_MATRIX_SIZE   2000

Definition at line 116 of file makeprofiledb.cpp.

◆ kDefaultMaxSmpFilesPerVol

#define kDefaultMaxSmpFilesPerVol   (2500)

Definition at line 110 of file makeprofiledb.cpp.

◆ kDefaultObsrThreshold

#define kDefaultObsrThreshold   (6.0)

Definition at line 109 of file makeprofiledb.cpp.

◆ kDefaultPssmScaleFactor

#define kDefaultPssmScaleFactor   (100.00)

Definition at line 108 of file makeprofiledb.cpp.

◆ kDefaultWordScoreThreshold

#define kDefaultWordScoreThreshold   (9.82)

Definition at line 107 of file makeprofiledb.cpp.

◆ kEpsylon

#define kEpsylon   (0.0001)

Definition at line 114 of file makeprofiledb.cpp.

◆ kSingleVol

#define kSingleVol   (-1)

Definition at line 124 of file makeprofiledb.cpp.

◆ RPS_DATABASE_VERSION

#define RPS_DATABASE_VERSION   RPS_MAGIC_NUM

Definition at line 121 of file makeprofiledb.cpp.

◆ RPS_NUM_LOOKUP_CELLS

#define RPS_NUM_LOOKUP_CELLS   32768

Definition at line 117 of file makeprofiledb.cpp.

Function Documentation

◆ kBinaryScoremat()

static const string kBinaryScoremat ( "binary"  )
static

◆ kDefaultExcludeInvalid()

static const string kDefaultExcludeInvalid ( "true"  )
static

◆ kDefaultMatrix()

static const string kDefaultMatrix ( kMatrixBLOSUM62  )
static

◆ kDefaultOutDbType()

static const string kDefaultOutDbType ( kOutDbRps  )
static

◆ kDefaultOutIndexFile()

static const string kDefaultOutIndexFile ( "true"  )
static

◆ kExcludeInvalid()

static const string kExcludeInvalid ( "exclude_invalid"  )
static

◆ kInPssmList()

static const string kInPssmList ( "in"  )
static

◆ kLogFile()

static const string kLogFile ( "logfile"  )
static

◆ kMaxSmpFilesPerVol()

static const string kMaxSmpFilesPerVol ( "max_smp_vol"  )
static

◆ kObsrThreshold()

static const string kObsrThreshold ( "obsr_threshold"  )
static

◆ kOutDbName()

static const string kOutDbName ( "out"  )
static

◆ kOutDbType()

static const string kOutDbType ( "dbtype"  )
static

◆ kOutIndexFile()

static const string kOutIndexFile ( "index"  )
static

◆ kPssmScaleFactor()

static const string kPssmScaleFactor ( "scale"  )
static

◆ kUseCmdlineThreshold()

static const string kUseCmdlineThreshold ( "force"  )
static

◆ main()

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

Definition at line 1947 of file makeprofiledb.cpp.

References CNcbiApplicationAPI::AppMain().

◆ s_DeleteMakeprofileDb()

static bool s_DeleteMakeprofileDb ( const string name)
static

◆ s_GenerateBlastDefline()

static CRef<CBlast_def_line_set> s_GenerateBlastDefline ( const CBioseq bio)
static

◆ s_HasDefline()

static bool s_HasDefline ( const CBioseq bio)
static

Definition at line 1336 of file makeprofiledb.cpp.

References CBioseq_Base::CanGetDescr().

Referenced by CMakeProfileDBApp::x_MakeVol().

◆ s_WriteInt4List()

static void s_WriteInt4List ( CNcbiOfstream ostr,
const list< Int4 > &  l 
)
static

Definition at line 1521 of file makeprofiledb.cpp.

References ITERATE.

Referenced by CMakeProfileDBApp::x_WrapUpDelta().

◆ s_WriteUint4List()

static void s_WriteUint4List ( CNcbiOfstream ostr,
const list< Uint4 > &  l 
)
static

Definition at line 1529 of file makeprofiledb.cpp.

References ITERATE.

Referenced by CMakeProfileDBApp::x_UpdateDelta().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ kFixedPointScaleFactor

const Uint4 kFixedPointScaleFactor = 1000
static

Definition at line 113 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_UpdateDelta().

◆ kMatrixBLOSUM45

const string kMatrixBLOSUM45 = "BLOSUM45"
static

Definition at line 96 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixBLOSUM50

const string kMatrixBLOSUM50 = "BLOSUM50"
static

Definition at line 95 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixBLOSUM62

const string kMatrixBLOSUM62 = "BLOSUM62"
static

Definition at line 93 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixBLOSUM80

const string kMatrixBLOSUM80 = "BLOSUM80"
static

Definition at line 94 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixBLOSUM90

const string kMatrixBLOSUM90 = "BLOSUM90"
static

Definition at line 97 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixPAM250

const string kMatrixPAM250 = "PAM250"
static

Definition at line 98 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixPAM30

const string kMatrixPAM30 = "PAM30"
static

Definition at line 99 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kMatrixPAM70

const string kMatrixPAM70 = "PAM70"
static

Definition at line 100 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kOutDbCobalt

const string kOutDbCobalt = "cobalt"
static

◆ kOutDbDelta

const string kOutDbDelta = "delta"
static

◆ kOutDbRps

const string kOutDbRps = "rps"
static

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 67 of file makeprofiledb.cpp.

Modified on Tue Jul 23 17:48:19 2024 by modify_doxy.py rev. 669887