names.hpp File Reference

Names used in blast4 network communications. More...

#include <utility>
#include <string>
#include <corelib/ncbistl.hpp>
#include <corelib/ncbi_safe_static.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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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

enum 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 57 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 448 of file names.cpp.

References string, and rapidjson::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().