blast-types/org.veupathdb.lib.blast.common

Package org.veupathdb.lib.blast.common

Types

interface BlastCLI : BlastCommand

Fields common to all BLAST+ tools.

interface BlastQueryBase : BlastCLI

Basic fields common to all BLAST+ query tools.

BlastQueryWithIPG

interface BlastQueryWithIPG : BlastQueryWithLists

BlastQueryWithLists

interface BlastQueryWithLists : BlastQueryBase

List fields common to most BLAST+ query tools.

Properties

const val FlagArchive: String

FlagBestHitOverhang

const val FlagBestHitOverhang: String

FlagBestHitScoreEdge

const val FlagBestHitScoreEdge: String

FlagCompBasedStats

const val FlagCompBasedStats: String

FlagCullingLimit

const val FlagCullingLimit: String

const val FlagDBFile: String

const val FlagDBGenCode: String

const val FlagDBHardMask: String

const val FlagDBSize: String

const val FlagDBSoftMask: String

FlagDomainInclusionEThresh

const val FlagDomainInclusionEThresh: String

const val FlagDust: String

FlagEntrezQuery

const val FlagEntrezQuery: String

FlagExpectValue

const val FlagExpectValue: String

FlagExportSearchStrategy

const val FlagExportSearchStrategy: String

FlagFilteringDB

const val FlagFilteringDB: String

const val FlagGapExtend: String

const val FlagGapOpen: String

const val FlagGapTrigger: String

const val FlagGIList: String

const val FlagHelpLong: String

const val FlagHelpShort: String

const val FlagHTML: String

FlagIgnoreMSAMaster

const val FlagIgnoreMSAMaster: String

FlagImportSearchStrategy

const val FlagImportSearchStrategy: String

FlagInclusionEThresh

const val FlagInclusionEThresh: String

const val FlagIndexName: String

const val FlagInMSA: String

const val FlagInPSSM: String

const val FlagIPGList: String

const val FlagLineLength: String

FlagLowercaseMasking

const val FlagLowercaseMasking: String

const val FlagMatrix: String

const val FlagMaxHSPs: String

FlagMaxIntronLength

const val FlagMaxIntronLength: String

FlagMaxTargetSeqs

const val FlagMaxTargetSeqs: String

FlagMinRawGappedScore

const val FlagMinRawGappedScore: String

FlagMSAMasterIndex

const val FlagMSAMasterIndex: String

FlagMultiThreadingMode

const val FlagMultiThreadingMode: String

FlagNegativeGIList

const val FlagNegativeGIList: String

FlagNegativeIPGList

const val FlagNegativeIPGList: String

FlagNegativeSeqIDList

const val FlagNegativeSeqIDList: String

FlagNegativeTaxIDList

const val FlagNegativeTaxIDList: String

FlagNegativeTaxIDs

const val FlagNegativeTaxIDs: String

const val FlagNonGreedy: String

FlagNumAlignments

const val FlagNumAlignments: String

FlagNumDescriptions

const val FlagNumDescriptions: String

FlagNumIterations

const val FlagNumIterations: String

const val FlagNumThreads: String

FlagOffDiagonalRange

const val FlagOffDiagonalRange: String

const val FlagOut: String

FlagOutASCIIPSSM

const val FlagOutASCIIPSSM: String

const val FlagOutFormat: String

const val FlagOutPSSM: String

FlagParseDefLines

const val FlagParseDefLines: String

const val FlagPenalty: String

FlagPercentIdentity

const val FlagPercentIdentity: String

const val FlagPHIPattern: String

FlagPseudoCount

const val FlagPseudoCount: String

FlagQueryCoverageHSPPercent

const val FlagQueryCoverageHSPPercent: String

const val FlagQueryFile: String

FlagQueryGenCode

const val FlagQueryGenCode: String

FlagQueryLocation

const val FlagQueryLocation: String

const val FlagRemote: String

const val FlagReward: String

const val FlagRID: String

const val FlagRPSDB: String

FlagSaveEachPSSM

const val FlagSaveEachPSSM: String

FlagSavePSSMAfterLastRound

const val FlagSavePSSMAfterLastRound: String

FlagSearchSpace

const val FlagSearchSpace: String

const val FlagSeg: String

const val FlagSeqIDList: String

FlagShowDomainHits

const val FlagShowDomainHits: String

const val FlagShowGIs: String

FlagSoftMasking

const val FlagSoftMasking: String

const val FlagSortHits: String

const val FlagSortHSPs: String

const val FlagStrand: String

FlagSubjectBestHit

const val FlagSubjectBestHit: String

FlagSubjectFile

const val FlagSubjectFile: String

FlagSubjectLocation

const val FlagSubjectLocation: String

const val FlagSumStats: String

const val FlagTask: String

const val FlagTaxIDList: String

const val FlagTaxIDs: String

FlagTemplateLength

const val FlagTemplateLength: String

FlagTemplateType

const val FlagTemplateType: String

const val FlagThreshold: String

const val FlagUngapped: String

const val FlagUseIndex: String

const val FlagUseSWTBack: String

const val FlagVersion: String

FlagWindowMaskerDB

const val FlagWindowMaskerDB: String

FlagWindowMaskerTaxID

const val FlagWindowMaskerTaxID: String

const val FlagWindowSize: String

const val FlagWordSize: String

FlagXDropFinalGap

const val FlagXDropFinalGap: String

FlagXDropPrelimGap

const val FlagXDropPrelimGap: String

const val FlagXDropUngap: String