NCBI C++ ToolKit
Classes | Enumerations | Functions | Variables
names.hpp File Reference

Names used in blast4 network communications. More...

#include <utility>
#include <string>
#include <corelib/ncbistl.hpp>
#include <objects/blast/NCBI_Blast4_module.hpp>
#include <objects/blast/Blast4_value.hpp>
#include <objects/blast/Blast4_parameter.hpp>
+ Include dependency graph for names.hpp:
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Go to the source code of this file.

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Classes

class  CBlast4Field
 Field properties for options in a Blast4 parameter list. More...
 

Enumerations

enum  EBlastOptIdx {
  eBlastOpt_Program = 100 , eBlastOpt_WordThreshold , eBlastOpt_LookupTableType , eBlastOpt_WordSize ,
  eBlastOpt_AlphabetSize , eBlastOpt_MBTemplateLength , eBlastOpt_MBTemplateType , eBlastOpt_FilterString ,
  eBlastOpt_MaskAtHash , eBlastOpt_DustFiltering , eBlastOpt_DustFilteringLevel , eBlastOpt_DustFilteringWindow ,
  eBlastOpt_DustFilteringLinker , eBlastOpt_SegFiltering , eBlastOpt_SegFilteringWindow , eBlastOpt_SegFilteringLocut ,
  eBlastOpt_SegFilteringHicut , eBlastOpt_RepeatFiltering , eBlastOpt_RepeatFilteringDB , eBlastOpt_StrandOption ,
  eBlastOpt_QueryGeneticCode , eBlastOpt_WindowSize , eBlastOpt_SeedContainerType , eBlastOpt_SeedExtensionMethod ,
  eBlastOpt_XDropoff , eBlastOpt_GapXDropoff , eBlastOpt_GapXDropoffFinal , eBlastOpt_GapTrigger ,
  eBlastOpt_GapExtnAlgorithm , eBlastOpt_HitlistSize , eBlastOpt_MaxNumHspPerSequence , eBlastOpt_MaxHspsPerSubject ,
  eBlastOpt_CullingLimit , eBlastOpt_EvalueThreshold , eBlastOpt_CutoffScore , eBlastOpt_PercentIdentity ,
  eBlastOpt_QueryCovHspPerc , eBlastOpt_SumStatisticsMode , eBlastOpt_LongestIntronLength , eBlastOpt_GappedMode ,
  eBlastOpt_ComplexityAdjMode , eBlastOpt_MaskLevel , eBlastOpt_MatrixName , eBlastOpt_MatrixPath ,
  eBlastOpt_MatchReward , eBlastOpt_MismatchPenalty , eBlastOpt_GapOpeningCost , eBlastOpt_GapExtensionCost ,
  eBlastOpt_FrameShiftPenalty , eBlastOpt_OutOfFrameMode , eBlastOpt_DbLength , eBlastOpt_DbSeqNum ,
  eBlastOpt_EffectiveSearchSpace , eBlastOpt_DbGeneticCode , eBlastOpt_PHIPattern , eBlastOpt_InclusionThreshold ,
  eBlastOpt_PseudoCount , eBlastOpt_GapTracebackAlgorithm , eBlastOpt_CompositionBasedStats , eBlastOpt_SmithWatermanMode ,
  eBlastOpt_UnifiedP , eBlastOpt_WindowMaskerDatabase , eBlastOpt_WindowMaskerTaxId , eBlastOpt_ForceMbIndex ,
  eBlastOpt_MbIndexName , eBlastOpt_BestHitScoreEdge , eBlastOpt_BestHitOverhang , eBlastOpt_IgnoreMsaMaster ,
  eBlastOpt_DomainInclusionThreshold , eBlastOpt_Culling , eBlastOpt_SubjectBestHit , eBlastOpt_EntrezQuery ,
  eBlastOpt_FinalDbSeq , eBlastOpt_FirstDbSeq , eBlastOpt_GiList , eBlastOpt_DbFilteringAlgorithmId ,
  eBlastOpt_DbFilteringAlgorithmKey , eBlastOpt_SubjectMaskingType , eBlastOpt_HspRangeMax , eBlastOpt_LCaseMask ,
  eBlastOpt_MatrixTable , eBlastOpt_NegativeGiList , eBlastOpt_RequiredEnd , eBlastOpt_RequiredStart ,
  eBlastOpt_UseRealDbSize , eBlastOpt_TaxidList , eBlastOpt_NegativeTaxidList , eBlastOpt_Web_BlastSpecialPage ,
  eBlastOpt_Web_EntrezQuery , eBlastOpt_Web_JobTitle , eBlastOpt_Web_NewWindow , eBlastOpt_Web_OrganismName ,
  eBlastOpt_Web_RunPsiBlast , eBlastOpt_Web_ShortQueryAdjust , eBlastOpt_Web_StepNumber , eBlastOpt_Web_DBInput ,
  eBlastOpt_Web_DBGroup , eBlastOpt_Web_DBSubgroupName , eBlastOpt_Web_DBSubgroup , eBlastOpt_Web_ExclModels ,
  eBlastOpt_Web_ExclSeqUncult , eBlastOpt_MaxValue
}
 Index of remote BLAST options. More...
 

Functions

string Blast4SearchInfo_BuildReplyName (const string &name, const string &value)
 This function builds the reply name token in the get-search-info reply objects, provided a pair of strings such as those defined above (i.e. More...
 

Variables

const char * kBlast4SearchInfoReqName_Search
 Used to retrieve information about the BLAST search. More...
 
const char * kBlast4SearchInfoReqName_Alignment
 Used to retrieve information about the BLAST alignments. More...
 
const char * kBlast4SearchInfoReqValue_Status
 Used to retrieve the BLAST search status. More...
 
const char * kBlast4SearchInfoReqValue_Title
 Used to retrieve the BLAST search title. More...
 
const char * kBlast4SearchInfoReqValue_Subjects
 Used to retrieve the BLAST search subjects. More...
 
const char * kBlast4SearchInfoReqValue_PsiIterationNum
 Used to retrieve the PSI-BLAST iteration number. More...
 

Detailed Description

Names used in blast4 network communications.

This file declares string objects corresponding to names used when specifying options for blast4 network communications protocol.

Definition in file names.hpp.

Enumeration Type Documentation

◆ EBlastOptIdx

Index of remote BLAST options.

The blast4 server only supports a subset of these

Enumerator
eBlastOpt_Program 
eBlastOpt_WordThreshold 
eBlastOpt_LookupTableType 
eBlastOpt_WordSize 
eBlastOpt_AlphabetSize 
eBlastOpt_MBTemplateLength 
eBlastOpt_MBTemplateType 
eBlastOpt_FilterString 
eBlastOpt_MaskAtHash 
eBlastOpt_DustFiltering 
eBlastOpt_DustFilteringLevel 
eBlastOpt_DustFilteringWindow 
eBlastOpt_DustFilteringLinker 
eBlastOpt_SegFiltering 
eBlastOpt_SegFilteringWindow 
eBlastOpt_SegFilteringLocut 
eBlastOpt_SegFilteringHicut 
eBlastOpt_RepeatFiltering 
eBlastOpt_RepeatFilteringDB 
eBlastOpt_StrandOption 
eBlastOpt_QueryGeneticCode 
eBlastOpt_WindowSize 
eBlastOpt_SeedContainerType 
eBlastOpt_SeedExtensionMethod 
eBlastOpt_XDropoff 
eBlastOpt_GapXDropoff 
eBlastOpt_GapXDropoffFinal 
eBlastOpt_GapTrigger 
eBlastOpt_GapExtnAlgorithm 
eBlastOpt_HitlistSize 
eBlastOpt_MaxNumHspPerSequence 
eBlastOpt_MaxHspsPerSubject 
eBlastOpt_CullingLimit 
eBlastOpt_EvalueThreshold 
eBlastOpt_CutoffScore 
eBlastOpt_PercentIdentity 
eBlastOpt_QueryCovHspPerc 
eBlastOpt_SumStatisticsMode 
eBlastOpt_LongestIntronLength 
eBlastOpt_GappedMode 
eBlastOpt_ComplexityAdjMode 
eBlastOpt_MaskLevel 
eBlastOpt_MatrixName 
eBlastOpt_MatrixPath 
eBlastOpt_MatchReward 
eBlastOpt_MismatchPenalty 
eBlastOpt_GapOpeningCost 
eBlastOpt_GapExtensionCost 
eBlastOpt_FrameShiftPenalty 
eBlastOpt_OutOfFrameMode 
eBlastOpt_DbLength 
eBlastOpt_DbSeqNum 
eBlastOpt_EffectiveSearchSpace 
eBlastOpt_DbGeneticCode 
eBlastOpt_PHIPattern 
eBlastOpt_InclusionThreshold 
eBlastOpt_PseudoCount 
eBlastOpt_GapTracebackAlgorithm 
eBlastOpt_CompositionBasedStats 
eBlastOpt_SmithWatermanMode 
eBlastOpt_UnifiedP 
eBlastOpt_WindowMaskerDatabase 
eBlastOpt_WindowMaskerTaxId 
eBlastOpt_ForceMbIndex 
eBlastOpt_MbIndexName 
eBlastOpt_BestHitScoreEdge 
eBlastOpt_BestHitOverhang 
eBlastOpt_IgnoreMsaMaster 
eBlastOpt_DomainInclusionThreshold 
eBlastOpt_Culling 
eBlastOpt_SubjectBestHit 
eBlastOpt_EntrezQuery 
eBlastOpt_FinalDbSeq 
eBlastOpt_FirstDbSeq 
eBlastOpt_GiList 
eBlastOpt_DbFilteringAlgorithmId 
eBlastOpt_DbFilteringAlgorithmKey 
eBlastOpt_SubjectMaskingType 
eBlastOpt_HspRangeMax 
eBlastOpt_LCaseMask 
eBlastOpt_MatrixTable 
eBlastOpt_NegativeGiList 
eBlastOpt_RequiredEnd 
eBlastOpt_RequiredStart 
eBlastOpt_UseRealDbSize 
eBlastOpt_TaxidList 
eBlastOpt_NegativeTaxidList 
eBlastOpt_Web_BlastSpecialPage 
eBlastOpt_Web_EntrezQuery 
eBlastOpt_Web_JobTitle 
eBlastOpt_Web_NewWindow 
eBlastOpt_Web_OrganismName 
eBlastOpt_Web_RunPsiBlast 
eBlastOpt_Web_ShortQueryAdjust 
eBlastOpt_Web_StepNumber 
eBlastOpt_Web_DBInput 
eBlastOpt_Web_DBGroup 
eBlastOpt_Web_DBSubgroupName 
eBlastOpt_Web_DBSubgroup 
eBlastOpt_Web_ExclModels 
eBlastOpt_Web_ExclSeqUncult 
eBlastOpt_MaxValue 

Definition at line 55 of file names.hpp.

Function Documentation

◆ Blast4SearchInfo_BuildReplyName()

string Blast4SearchInfo_BuildReplyName ( const string name,
const string value 
)

This function builds the reply name token in the get-search-info reply objects, provided a pair of strings such as those defined above (i.e.

: kBlast4SearchInfoReq{Name,Value})

This function builds the reply name token in the get-search-info reply objects, provided a pair of strings such as those defined above (i.e.

Definition at line 446 of file names.cpp.

References string, and value.

Referenced by CRemoteBlast::x_GetStringFromSearchInfoReply(), and CRemoteBlast::x_GetSubjects().

Variable Documentation

◆ kBlast4SearchInfoReqName_Alignment

const char* kBlast4SearchInfoReqName_Alignment
extern

Used to retrieve information about the BLAST alignments.

◆ kBlast4SearchInfoReqName_Search

const char* kBlast4SearchInfoReqName_Search
extern

Used to retrieve information about the BLAST search.

Referenced by CRemoteBlast::GetTitle(), CRemoteBlast::x_GetPsiIterationsFromServer(), and CRemoteBlast::x_GetSubjects().

◆ kBlast4SearchInfoReqValue_PsiIterationNum

const char* kBlast4SearchInfoReqValue_PsiIterationNum
extern

Used to retrieve the PSI-BLAST iteration number.

Referenced by CRemoteBlast::x_GetPsiIterationsFromServer().

◆ kBlast4SearchInfoReqValue_Status

const char* kBlast4SearchInfoReqValue_Status
extern

Used to retrieve the BLAST search status.

◆ kBlast4SearchInfoReqValue_Subjects

const char* kBlast4SearchInfoReqValue_Subjects
extern

Used to retrieve the BLAST search subjects.

Referenced by CRemoteBlast::x_GetSubjects().

◆ kBlast4SearchInfoReqValue_Title

const char* kBlast4SearchInfoReqValue_Title
extern

Used to retrieve the BLAST search title.

Referenced by CRemoteBlast::GetTitle().

Modified on Thu Feb 22 17:07:15 2024 by modify_doxy.py rev. 669887