NCBI C++ ToolKit
Typedefs | Functions | Variables
blast_search_params.cpp File Reference
#include <ncbi_pch.hpp>
#include <gui/packages/pkg_alignment/blast_search_params.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <algo/blast/api/blast_options.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/blast_prot_options.hpp>
#include <algo/blast/api/blastx_options.hpp>
#include <algo/blast/api/tblastx_options.hpp>
#include <algo/blast/api/tblastn_options.hpp>
#include <algo/blast/blastinput/blastn_args.hpp>
#include <algo/blast/blastinput/blastp_args.hpp>
#include <algo/blast/blastinput/blastx_args.hpp>
#include <algo/blast/blastinput/tblastn_args.hpp>
#include <algo/blast/blastinput/tblastx_args.hpp>
#include <corelib/ncbi_system.hpp>
+ Include dependency graph for blast_search_params.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Typedefs

typedef SStaticPair< const char *, const char * > TRepeatName
 
typedef CStaticPairArrayMap< const char *, const char *, PNocase_CStrTRepeatMap
 

Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (blast)
 
static CBLASTParams::SProgParams s_DefaultParams (blast::EProgram prg)
 
 DEFINE_STATIC_ARRAY_MAP (TRepeatMap, sc_RepeatMap, sc_RepeatLibs)
 
static void s_NextToken (string::const_iterator &begin, string::const_iterator end, string::const_iterator &tok_begin, string::const_iterator &tok_end)
 

Variables

static const CBLASTParams::SProgInfo sc_ProgPairs []
 
static TRepeatName sc_RepeatLibs []
 
static const char * kBLASTParamsTag = "BLAST Params"
 
static const char * kNucProgTag = "Nuc Program"
 
static const char * kProtProgTag = "Prot Program"
 
static const char * kNucDBTag = "Nuc DB"
 
static const char * kProtDBTag = "Prot DB"
 
static const char * kNucMRUDBsTag = "Nuc MRU DBs"
 
static const char * kProtMRUDBsTag = "Prot MRU DBs"
 
static const char * kEntrezQueryTag = "Entrez Query"
 
static const char * kAdvParamsTag = "Advanced Params"
 
static const char * kJobTitleTag = "Job Title"
 
static const char * kLocalNucDB = "LocalNucDB"
 
static const char * kLocalProtDB = "LocalProtDB"
 
static const char * kSubjectType = "SubjectType"
 
static const char * kLocalDBLoader = "LocalDBLoader"
 
static const char * kThresholdTag = "Threshold"
 
static const char * kWordSizeTag = "WordSize"
 
static const char * keValueTag = "eValue"
 
static const char * kFilterLowComplexTag = "FilterLowComplex"
 
static const char * kGeneticCodeTag = "GeneticCode"
 
static const char * kDbGeneticCodeTag = "DbGeneticCode"
 
static const char * kMaskLowercaseTag = "MaskLowercase"
 
static const char * kMaskRepeatsTag = "MaskRepeats"
 

Typedef Documentation

◆ TRepeatMap

Definition at line 380 of file blast_search_params.cpp.

◆ TRepeatName

typedef SStaticPair<const char*, const char*> TRepeatName

Definition at line 361 of file blast_search_params.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP ( TRepeatMap  ,
sc_RepeatMap  ,
sc_RepeatLibs   
)

◆ s_DefaultParams()

static CBLASTParams::SProgParams s_DefaultParams ( blast::EProgram  prg)
static

◆ s_NextToken()

static void s_NextToken ( string::const_iterator &  begin,
string::const_iterator  end,
string::const_iterator &  tok_begin,
string::const_iterator &  tok_end 
)
static

Definition at line 716 of file blast_search_params.cpp.

Referenced by CBLASTParams::x_ArgsToBlastOptions().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ kAdvParamsTag

const char* kAdvParamsTag = "Advanced Params"
static

◆ kBLASTParamsTag

const char* kBLASTParamsTag = "BLAST Params"
static

◆ kDbGeneticCodeTag

const char* kDbGeneticCodeTag = "DbGeneticCode"
static

◆ kEntrezQueryTag

const char* kEntrezQueryTag = "Entrez Query"
static

◆ keValueTag

const char* keValueTag = "eValue"
static

◆ kFilterLowComplexTag

const char* kFilterLowComplexTag = "FilterLowComplex"
static

◆ kGeneticCodeTag

const char* kGeneticCodeTag = "GeneticCode"
static

◆ kJobTitleTag

const char* kJobTitleTag = "Job Title"
static

◆ kLocalDBLoader

const char* kLocalDBLoader = "LocalDBLoader"
static

◆ kLocalNucDB

const char* kLocalNucDB = "LocalNucDB"
static

◆ kLocalProtDB

const char* kLocalProtDB = "LocalProtDB"
static

◆ kMaskLowercaseTag

const char* kMaskLowercaseTag = "MaskLowercase"
static

◆ kMaskRepeatsTag

const char* kMaskRepeatsTag = "MaskRepeats"
static

◆ kNucDBTag

const char* kNucDBTag = "Nuc DB"
static

◆ kNucMRUDBsTag

const char* kNucMRUDBsTag = "Nuc MRU DBs"
static

◆ kNucProgTag

const char* kNucProgTag = "Nuc Program"
static

◆ kProtDBTag

const char* kProtDBTag = "Prot DB"
static

◆ kProtMRUDBsTag

const char* kProtMRUDBsTag = "Prot MRU DBs"
static

◆ kProtProgTag

const char* kProtProgTag = "Prot Program"
static

◆ kSubjectType

const char* kSubjectType = "SubjectType"
static

◆ kThresholdTag

const char* kThresholdTag = "Threshold"
static

◆ kWordSizeTag

const char* kWordSizeTag = "WordSize"
static

◆ sc_ProgPairs

const CBLASTParams::SProgInfo sc_ProgPairs[]
static
Initial value:
= {
{ blast::eBlastn, "Nucleotide-Nucleotide (BLASTn)",
true, true, false, false, false, true },
{ blast::eMegablast, "Nucleotide-Nucleotide (MegaBLAST)",
true, true, false, false, false, true },
{ blast::eDiscMegablast, "Nucleotide-Nucleotide (Discontiguous MegaBLAST)",
true, true, false, false, false, true },
{ blast::eBlastp, "Protein-Protein (BLASTp)",
false, false, true, false, false, false },
{ blast::eBlastx, "Translated Nucleotide-Protein (BLASTx)",
true, false, true, true, false, false },
{ blast::eTblastn, "Protein-Translated Nucleotide (tBLASTn)",
false, true, true, false, true, false },
{ blast::eTblastx, "Translated Nucleotide-Translated Nucleotide (tBLASTx)",
true, true, true, true, true, false }
}
@ eTblastx
Translated nucl-Translated nucl.
Definition: blast_types.hpp:62
@ eBlastn
Nucl-Nucl (traditional blastn)
Definition: blast_types.hpp:58
@ eBlastp
Protein-Protein.
Definition: blast_types.hpp:59
@ eTblastn
Protein-Translated nucl.
Definition: blast_types.hpp:61
@ eMegablast
Nucl-Nucl (traditional megablast)
Definition: blast_types.hpp:65
@ eDiscMegablast
Nucl-Nucl using discontiguous megablast.
Definition: blast_types.hpp:66
@ eBlastx
Translated nucl-Protein.
Definition: blast_types.hpp:60

Definition at line 60 of file blast_search_params.cpp.

Referenced by CBLASTParams::CBLASTParams().

◆ sc_RepeatLibs

TRepeatName sc_RepeatLibs[]
static
Initial value:
= {
{ "Anopheles gambiae", "repeat/repeat_7165" },
{ "Arabidopsis thaliana", "repeat/repeat_3702" },
{ "bony fishes", "repeat/repeat_31032" },
{ "Caenorhabditis briggsae", "repeat/repeat_6238" },
{ "Caenorhabditis elegans", "repeat/repeat_6239" },
{ "Chlamydomonas reinhardtii", "repeat/repeat_3055" },
{ "Ciona intestinalis", "repeat/repeat_7719" },
{ "Danio rerio", "repeat/repeat_7955" },
{ "Drosophila melanogaster", "repeat/repeat_7227" },
{ "fungi", "repeat/repeat_4751" },
{ "human", "repeat/repeat_9606" },
{ "mammals", "repeat/repeat_40674" },
{ "Oryza sativa", "repeat/repeat_4530" },
{ "rodents", "repeat/repeat_9989" },
{ "Thalassiosira pseudonana", "repeat/repeat_35128" }
}

Definition at line 362 of file blast_search_params.cpp.

Modified on Fri Mar 01 10:07:20 2024 by modify_doxy.py rev. 669887