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- All Implemented Interfaces:
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org.veupathdb.lib.blast.common.BlastCLI,org.veupathdb.lib.blast.common.BlastQueryBase,org.veupathdb.lib.blast.common.BlastQueryWithLists,org.veupathdb.lib.blast.serial.BlastCommand
public interface DeltaBlast implements BlastQueryWithLists
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Method Summary
Modifier and Type Method Description abstract WordSizeDeltagetWordSize()-word_size <Integer>abstract UnitsetWordSize(WordSizeDelta wordSize)-word_size <Integer>abstract GapOpengetGapOpen()-gapopen <Integer>abstract UnitsetGapOpen(GapOpen gapOpen)-gapopen <Integer>abstract GapExtendgetGapExtend()-gapextend <Integer>abstract UnitsetGapExtend(GapExtend gapExtend)-gapextend <Integer>abstract MatrixDeltagetMatrix()-matrix <String>abstract UnitsetMatrix(MatrixDelta matrix)-matrix <String>abstract ThresholdgetThreshold()-threshold <Real>abstract UnitsetThreshold(Threshold threshold)-threshold <Real>abstract CompBasedStatsDeltagetCompBasedStats()-comp_based_stats <String>abstract UnitsetCompBasedStats(CompBasedStatsDelta compBasedStats)-comp_based_stats <String>abstract SubjectFilegetSubjectFile()-subject <File_In>abstract UnitsetSubjectFile(SubjectFile subjectFile)-subject <File_In>abstract SubjectLocationgetSubjectLocation()-subject_loc <String>abstract UnitsetSubjectLocation(SubjectLocation subjectLocation)-subject_loc <String>abstract SegDeltagetSeg()-seg <String>abstract UnitsetSeg(SegDelta seg)-seg <String>abstract SoftMaskingDeltagetSoftMasking()-soft_masking <Boolean>abstract UnitsetSoftMasking(SoftMaskingDelta softMasking)-soft_masking <Boolean>abstract QueryCoverageHSPPercentgetQueryCoverageHSPPercent()-qcov_hsp_perc <Real>abstract UnitsetQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)-qcov_hsp_perc <Real>abstract CullingLimitgetCullingLimit()-culling_limit <Integer>abstract UnitsetCullingLimit(CullingLimit cullingLimit)-culling_limit <Integer>abstract BestHitOverhanggetBestHitOverhang()-best_hit_overhang <Real>abstract UnitsetBestHitOverhang(BestHitOverhang bestHitOverhang)-best_hit_overhang <Real>abstract BestHitScoreEdgegetBestHitScoreEdge()-best_hit_score_edge <Real>abstract UnitsetBestHitScoreEdge(BestHitScoreEdge bestHitScoreEdge)-best_hit_score_edge <Real>abstract SubjectBestHitgetSubjectBestHit()-subject_besthit abstract UnitsetSubjectBestHit(SubjectBestHit subjectBestHit)-subject_besthit abstract SumStatsgetSumStats()-max_target_seqs <Integer>abstract UnitsetSumStats(SumStats sumStats)-max_target_seqs <Integer>abstract ExtensionDropoffPrelimGappedgetExtensionDropoffPrelimGapped()-xdrop_gap <Real>abstract UnitsetExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped extensionDropoffPrelimGapped)-xdrop_gap <Real>abstract ExtensionDropoffFinalGappedgetExtensionDropoffFinalGapped()-xdrop_gap_final <Real>abstract UnitsetExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped extensionDropoffFinalGapped)-xdrop_gap_final <Real>abstract GapTriggergetGapTrigger()-gap_trigger <Real>abstract UnitsetGapTrigger(GapTrigger gapTrigger)-gap_trigger <Real>abstract NumCPUCoresgetNumCPUCores()-num_threads <Integer>abstract UnitsetNumCPUCores(NumCPUCores numCPUCores)-num_threads <Integer>abstract UseSmithWatermanTracebackgetUseSmithWatermanTraceback()-use_sw_tback abstract UnitsetUseSmithWatermanTraceback(UseSmithWatermanTraceback useSmithWatermanTraceback)-use_sw_tback abstract NumIterationsgetNumIterations()-num_iterations <Integer>abstract UnitsetNumIterations(NumIterations numIterations)-num_iterations <Integer>abstract OutPSSMFilegetOutPSSMFile()-out_pssm <File_Out>abstract UnitsetOutPSSMFile(OutPSSMFile outPSSMFile)-out_pssm <File_Out>abstract OutASCIIPSSMFilegetOutASCIIPSSMFile()-out_ascii_pssm <File_Out>abstract UnitsetOutASCIIPSSMFile(OutASCIIPSSMFile outASCIIPSSMFile)-out_ascii_pssm <File_Out>abstract SavePSSMAfterLastRoundgetSavePSSMAfterLastRound()-save_pssm_after_last_round abstract UnitsetSavePSSMAfterLastRound(SavePSSMAfterLastRound savePSSMAfterLastRound)-save_pssm_after_last_round abstract SaveEachPSSMgetSaveEachPSSM()-save_each_pssm abstract UnitsetSaveEachPSSM(SaveEachPSSM saveEachPSSM)-save_each_pssm abstract PseudoCountgetPseudoCount()-pseudocount <Integer>abstract UnitsetPseudoCount(PseudoCount pseudoCount)-pseudocount <Integer>abstract DomainInclusionEValueThresholdgetDomainInclusionEValueThreshold()-domain_inclusion_ethresh <Real>abstract UnitsetDomainInclusionEValueThreshold(DomainInclusionEValueThreshold domainInclusionEValueThreshold)-domain_inclusion_ethresh <Real>abstract InclusionEValueThresholdgetInclusionEValueThreshold()-inclusion_ethresh <Real>abstract UnitsetInclusionEValueThreshold(InclusionEValueThreshold inclusionEValueThreshold)-inclusion_ethresh <Real>abstract RPSDBgetRpsDB()-rpsdb <String>abstract UnitsetRpsDB(RPSDB rpsDB)-rpsdb <String>abstract ShowDomainHitsgetShowDomainHits()-show_domain_hits abstract UnitsetShowDomainHits(ShowDomainHits showDomainHits)-show_domain_hits abstract GIListgetGiListFile()-gilist <String>abstract UnitsetGiListFile(GIList giListFile)-gilist <String>abstract NegativeGIListgetNegativeGIListFile()-negative_gilist <String>abstract UnitsetNegativeGIListFile(NegativeGIList negativeGIListFile)-negative_gilist <String>abstract SeqIDListgetSeqIDListFile()-seqidlist <String>abstract UnitsetSeqIDListFile(SeqIDList seqIDListFile)-seqidlist <String>abstract NegativeSeqIDListgetNegativeSeqIDListFile()-negative_seqidlist <String>abstract UnitsetNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)-negative_seqidlist <String>abstract TaxIDListgetTaxIDListFile()-taxidlist <String>abstract UnitsetTaxIDListFile(TaxIDList taxIDListFile)-taxidlist <String>abstract NegativeTaxIDListgetNegativeTaxIDListFile()-negative_taxidlist <String>abstract UnitsetNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)-negative_taxidlist <String>abstract TaxIDsgetTaxIDs()-taxids <String>abstract UnitsetTaxIDs(TaxIDs taxIDs)-taxids <String>abstract NegativeTaxIDsgetNegativeTaxIDs()-negative_taxids <String>abstract UnitsetNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)-negative_taxids <String>abstract QueryFilegetQueryFile()-query <File_In>abstract UnitsetQueryFile(QueryFile queryFile)-query <File_In>abstract QueryLocationgetQueryLocation()-query_loc <String>abstract UnitsetQueryLocation(QueryLocation queryLocation)-query_loc <String>abstract DBFilegetDbFile()-db <String>abstract UnitsetDbFile(DBFile dbFile)-db <String>abstract ExpectValuegetExpectValue()-evalue <Real>abstract UnitsetExpectValue(ExpectValue expectValue)-evalue <Real>abstract LowercaseMaskinggetLowercaseMasking()-lcase_masking abstract UnitsetLowercaseMasking(LowercaseMasking lowercaseMasking)-lcase_masking abstract EntrezQuerygetEntrezQuery()-entrez_query <String>abstract UnitsetEntrezQuery(EntrezQuery entrezQuery)-entrez_query <String>abstract MaxHSPsgetMaxHSPs()-max_hsps <Integer>abstract UnitsetMaxHSPs(MaxHSPs maxHSPs)-max_hsps <Integer>abstract DBSizegetDbSize()-dbsize <Int8>abstract UnitsetDbSize(DBSize dbSize)-dbsize <Int8>abstract SearchSpacegetSearchSpace()-searchsp <Int8>abstract UnitsetSearchSpace(SearchSpace searchSpace)-searchsp <Int8>abstract ImportSearchStrategygetImportSearchStrategy()-import_search_strategy <File_In>abstract UnitsetImportSearchStrategy(ImportSearchStrategy importSearchStrategy)-import_search_strategy <File_In>abstract ExportSearchStrategygetExportSearchStrategy()-export_search_strategy <File_Out>abstract UnitsetExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)-export_search_strategy <File_Out>abstract ExtensionDropoffUngappedgetExtensionDropoffUngapped()-xdrop_ungap <Real>abstract UnitsetExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)-xdrop_ungap <Real>abstract WindowSizegetWindowSize()-window_size <Integer>abstract UnitsetWindowSize(WindowSize windowSize)-window_size <Integer>abstract RemotegetRemote()-remote abstract UnitsetRemote(Remote remote)-remote abstract BlastToolgetTool()abstract HelpShortgetShortHelp()-h abstract UnitsetShortHelp(HelpShort shortHelp)-h abstract HelpLonggetLongHelp()-help abstract UnitsetLongHelp(HelpLong longHelp)-help abstract VersiongetVersion()-version abstract UnitsetVersion(Version version)-version abstract OutFilegetOutFile()-out <File_Out>abstract UnitsetOutFile(OutFile outFile)-out <File_Out>abstract OutFormatgetOutFormat()-outfmt <String>abstract UnitsetOutFormat(OutFormat outFormat)-outfmt <String>abstract ShowGIsgetShowGIs()-show_gis abstract UnitsetShowGIs(ShowGIs showGIs)-show_gis abstract NumDescriptionsgetNumDescriptions()-num_descriptions <Integer>abstract UnitsetNumDescriptions(NumDescriptions numDescriptions)-num_descriptions <Integer>abstract NumAlignmentsgetNumAlignments()-num_alignments <Integer>abstract UnitsetNumAlignments(NumAlignments numAlignments)-num_alignments <Integer>abstract LineLengthgetLineLength()-line_length <Integer>abstract UnitsetLineLength(LineLength lineLength)-line_length <Integer>abstract HTMLgetHtml()-html abstract UnitsetHtml(HTML html)-html abstract SortHitsgetSortHits()-sorthits <Integer>abstract UnitsetSortHits(SortHits sortHits)-sorthits <Integer>abstract SortHSPsgetSortHSPs()-sorthsps <Integer>abstract UnitsetSortHSPs(SortHSPs sortHSPs)-sorthsps <Integer>abstract MaxTargetSeqsgetMaxTargetSeqs()-max_target_seqs <Integer>abstract UnitsetMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)-max_target_seqs <Integer>abstract ParseDefLinesgetParseDefLines()-parse_deflines abstract UnitsetParseDefLines(ParseDefLines parseDefLines)-parse_deflines -
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Method Detail
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getWordSize
abstract WordSizeDelta getWordSize()
-word_size
<Integer>
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setWordSize
abstract Unit setWordSize(WordSizeDelta wordSize)
-word_size
<Integer>
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getGapOpen
abstract GapOpen getGapOpen()
-gapopen
<Integer>
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setGapOpen
abstract Unit setGapOpen(GapOpen gapOpen)
-gapopen
<Integer>
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getGapExtend
abstract GapExtend getGapExtend()
-gapextend
<Integer>
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setGapExtend
abstract Unit setGapExtend(GapExtend gapExtend)
-gapextend
<Integer>
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getMatrix
abstract MatrixDelta getMatrix()
-matrix
<String>
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setMatrix
abstract Unit setMatrix(MatrixDelta matrix)
-matrix
<String>
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getThreshold
abstract Threshold getThreshold()
-threshold
<Real>
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setThreshold
abstract Unit setThreshold(Threshold threshold)
-threshold
<Real>
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getCompBasedStats
abstract CompBasedStatsDelta getCompBasedStats()
-comp_based_stats
<String>
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setCompBasedStats
abstract Unit setCompBasedStats(CompBasedStatsDelta compBasedStats)
-comp_based_stats
<String>
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getSubjectFile
abstract SubjectFile getSubjectFile()
-subject
<File_In>
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setSubjectFile
abstract Unit setSubjectFile(SubjectFile subjectFile)
-subject
<File_In>
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getSubjectLocation
abstract SubjectLocation getSubjectLocation()
-subject_loc
<String>
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setSubjectLocation
abstract Unit setSubjectLocation(SubjectLocation subjectLocation)
-subject_loc
<String>
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getSoftMasking
abstract SoftMaskingDelta getSoftMasking()
-soft_masking
<Boolean>
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setSoftMasking
abstract Unit setSoftMasking(SoftMaskingDelta softMasking)
-soft_masking
<Boolean>
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getQueryCoverageHSPPercent
abstract QueryCoverageHSPPercent getQueryCoverageHSPPercent()
-qcov_hsp_perc
<Real>
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setQueryCoverageHSPPercent
abstract Unit setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)
-qcov_hsp_perc
<Real>
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getCullingLimit
abstract CullingLimit getCullingLimit()
-culling_limit
<Integer>
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setCullingLimit
abstract Unit setCullingLimit(CullingLimit cullingLimit)
-culling_limit
<Integer>
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getBestHitOverhang
abstract BestHitOverhang getBestHitOverhang()
-best_hit_overhang
<Real>
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setBestHitOverhang
abstract Unit setBestHitOverhang(BestHitOverhang bestHitOverhang)
-best_hit_overhang
<Real>
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getBestHitScoreEdge
abstract BestHitScoreEdge getBestHitScoreEdge()
-best_hit_score_edge
<Real>
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setBestHitScoreEdge
abstract Unit setBestHitScoreEdge(BestHitScoreEdge bestHitScoreEdge)
-best_hit_score_edge
<Real>
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getSubjectBestHit
abstract SubjectBestHit getSubjectBestHit()
-subject_besthit
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setSubjectBestHit
abstract Unit setSubjectBestHit(SubjectBestHit subjectBestHit)
-subject_besthit
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getSumStats
abstract SumStats getSumStats()
-max_target_seqs
<Integer>
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setSumStats
abstract Unit setSumStats(SumStats sumStats)
-max_target_seqs
<Integer>
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getExtensionDropoffPrelimGapped
abstract ExtensionDropoffPrelimGapped getExtensionDropoffPrelimGapped()
-xdrop_gap
<Real>
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setExtensionDropoffPrelimGapped
abstract Unit setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped extensionDropoffPrelimGapped)
-xdrop_gap
<Real>
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getExtensionDropoffFinalGapped
abstract ExtensionDropoffFinalGapped getExtensionDropoffFinalGapped()
-xdrop_gap_final
<Real>
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setExtensionDropoffFinalGapped
abstract Unit setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped extensionDropoffFinalGapped)
-xdrop_gap_final
<Real>
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getGapTrigger
abstract GapTrigger getGapTrigger()
-gap_trigger
<Real>
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setGapTrigger
abstract Unit setGapTrigger(GapTrigger gapTrigger)
-gap_trigger
<Real>
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getNumCPUCores
abstract NumCPUCores getNumCPUCores()
-num_threads
<Integer>
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setNumCPUCores
abstract Unit setNumCPUCores(NumCPUCores numCPUCores)
-num_threads
<Integer>
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getUseSmithWatermanTraceback
abstract UseSmithWatermanTraceback getUseSmithWatermanTraceback()
-use_sw_tback
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setUseSmithWatermanTraceback
abstract Unit setUseSmithWatermanTraceback(UseSmithWatermanTraceback useSmithWatermanTraceback)
-use_sw_tback
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getNumIterations
abstract NumIterations getNumIterations()
-num_iterations
<Integer>
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setNumIterations
abstract Unit setNumIterations(NumIterations numIterations)
-num_iterations
<Integer>
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getOutPSSMFile
abstract OutPSSMFile getOutPSSMFile()
-out_pssm
<File_Out>
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setOutPSSMFile
abstract Unit setOutPSSMFile(OutPSSMFile outPSSMFile)
-out_pssm
<File_Out>
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getOutASCIIPSSMFile
abstract OutASCIIPSSMFile getOutASCIIPSSMFile()
-out_ascii_pssm
<File_Out>
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setOutASCIIPSSMFile
abstract Unit setOutASCIIPSSMFile(OutASCIIPSSMFile outASCIIPSSMFile)
-out_ascii_pssm
<File_Out>
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getSavePSSMAfterLastRound
abstract SavePSSMAfterLastRound getSavePSSMAfterLastRound()
-save_pssm_after_last_round
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setSavePSSMAfterLastRound
abstract Unit setSavePSSMAfterLastRound(SavePSSMAfterLastRound savePSSMAfterLastRound)
-save_pssm_after_last_round
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getSaveEachPSSM
abstract SaveEachPSSM getSaveEachPSSM()
-save_each_pssm
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setSaveEachPSSM
abstract Unit setSaveEachPSSM(SaveEachPSSM saveEachPSSM)
-save_each_pssm
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getPseudoCount
abstract PseudoCount getPseudoCount()
-pseudocount
<Integer>
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setPseudoCount
abstract Unit setPseudoCount(PseudoCount pseudoCount)
-pseudocount
<Integer>
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getDomainInclusionEValueThreshold
abstract DomainInclusionEValueThreshold getDomainInclusionEValueThreshold()
-domain_inclusion_ethresh
<Real>
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setDomainInclusionEValueThreshold
abstract Unit setDomainInclusionEValueThreshold(DomainInclusionEValueThreshold domainInclusionEValueThreshold)
-domain_inclusion_ethresh
<Real>
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getInclusionEValueThreshold
abstract InclusionEValueThreshold getInclusionEValueThreshold()
-inclusion_ethresh
<Real>
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setInclusionEValueThreshold
abstract Unit setInclusionEValueThreshold(InclusionEValueThreshold inclusionEValueThreshold)
-inclusion_ethresh
<Real>
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getShowDomainHits
abstract ShowDomainHits getShowDomainHits()
-show_domain_hits
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setShowDomainHits
abstract Unit setShowDomainHits(ShowDomainHits showDomainHits)
-show_domain_hits
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getGiListFile
abstract GIList getGiListFile()
-gilist
<String>
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setGiListFile
abstract Unit setGiListFile(GIList giListFile)
-gilist
<String>
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getNegativeGIListFile
abstract NegativeGIList getNegativeGIListFile()
-negative_gilist
<String>
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setNegativeGIListFile
abstract Unit setNegativeGIListFile(NegativeGIList negativeGIListFile)
-negative_gilist
<String>
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getSeqIDListFile
abstract SeqIDList getSeqIDListFile()
-seqidlist
<String>
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setSeqIDListFile
abstract Unit setSeqIDListFile(SeqIDList seqIDListFile)
-seqidlist
<String>
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getNegativeSeqIDListFile
abstract NegativeSeqIDList getNegativeSeqIDListFile()
-negative_seqidlist
<String>
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setNegativeSeqIDListFile
abstract Unit setNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)
-negative_seqidlist
<String>
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getTaxIDListFile
abstract TaxIDList getTaxIDListFile()
-taxidlist
<String>
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setTaxIDListFile
abstract Unit setTaxIDListFile(TaxIDList taxIDListFile)
-taxidlist
<String>
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getNegativeTaxIDListFile
abstract NegativeTaxIDList getNegativeTaxIDListFile()
-negative_taxidlist
<String>
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setNegativeTaxIDListFile
abstract Unit setNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)
-negative_taxidlist
<String>
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getNegativeTaxIDs
abstract NegativeTaxIDs getNegativeTaxIDs()
-negative_taxids
<String>
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setNegativeTaxIDs
abstract Unit setNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)
-negative_taxids
<String>
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getQueryFile
abstract QueryFile getQueryFile()
-query
<File_In>
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setQueryFile
abstract Unit setQueryFile(QueryFile queryFile)
-query
<File_In>
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getQueryLocation
abstract QueryLocation getQueryLocation()
-query_loc
<String>
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setQueryLocation
abstract Unit setQueryLocation(QueryLocation queryLocation)
-query_loc
<String>
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getExpectValue
abstract ExpectValue getExpectValue()
-evalue
<Real>
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setExpectValue
abstract Unit setExpectValue(ExpectValue expectValue)
-evalue
<Real>
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getLowercaseMasking
abstract LowercaseMasking getLowercaseMasking()
-lcase_masking
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setLowercaseMasking
abstract Unit setLowercaseMasking(LowercaseMasking lowercaseMasking)
-lcase_masking
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getEntrezQuery
abstract EntrezQuery getEntrezQuery()
-entrez_query
<String>
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setEntrezQuery
abstract Unit setEntrezQuery(EntrezQuery entrezQuery)
-entrez_query
<String>
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getMaxHSPs
abstract MaxHSPs getMaxHSPs()
-max_hsps
<Integer>
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setMaxHSPs
abstract Unit setMaxHSPs(MaxHSPs maxHSPs)
-max_hsps
<Integer>
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getSearchSpace
abstract SearchSpace getSearchSpace()
-searchsp
<Int8>
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setSearchSpace
abstract Unit setSearchSpace(SearchSpace searchSpace)
-searchsp
<Int8>
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getImportSearchStrategy
abstract ImportSearchStrategy getImportSearchStrategy()
-import_search_strategy
<File_In>
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setImportSearchStrategy
abstract Unit setImportSearchStrategy(ImportSearchStrategy importSearchStrategy)
-import_search_strategy
<File_In>
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getExportSearchStrategy
abstract ExportSearchStrategy getExportSearchStrategy()
-export_search_strategy
<File_Out>
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setExportSearchStrategy
abstract Unit setExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)
-export_search_strategy
<File_Out>
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getExtensionDropoffUngapped
abstract ExtensionDropoffUngapped getExtensionDropoffUngapped()
-xdrop_ungap
<Real>
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setExtensionDropoffUngapped
abstract Unit setExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)
-xdrop_ungap
<Real>
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getWindowSize
abstract WindowSize getWindowSize()
-window_size
<Integer>
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setWindowSize
abstract Unit setWindowSize(WindowSize windowSize)
-window_size
<Integer>
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getShortHelp
abstract HelpShort getShortHelp()
-h
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setShortHelp
abstract Unit setShortHelp(HelpShort shortHelp)
-h
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getLongHelp
abstract HelpLong getLongHelp()
-help
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setLongHelp
abstract Unit setLongHelp(HelpLong longHelp)
-help
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getVersion
abstract Version getVersion()
-version
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setVersion
abstract Unit setVersion(Version version)
-version
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getOutFile
abstract OutFile getOutFile()
-out
<File_Out>
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setOutFile
abstract Unit setOutFile(OutFile outFile)
-out
<File_Out>
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getOutFormat
abstract OutFormat getOutFormat()
-outfmt
<String>
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setOutFormat
abstract Unit setOutFormat(OutFormat outFormat)
-outfmt
<String>
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getShowGIs
abstract ShowGIs getShowGIs()
-show_gis
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setShowGIs
abstract Unit setShowGIs(ShowGIs showGIs)
-show_gis
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getNumDescriptions
abstract NumDescriptions getNumDescriptions()
-num_descriptions
<Integer>
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setNumDescriptions
abstract Unit setNumDescriptions(NumDescriptions numDescriptions)
-num_descriptions
<Integer>
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getNumAlignments
abstract NumAlignments getNumAlignments()
-num_alignments
<Integer>
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setNumAlignments
abstract Unit setNumAlignments(NumAlignments numAlignments)
-num_alignments
<Integer>
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getLineLength
abstract LineLength getLineLength()
-line_length
<Integer>
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setLineLength
abstract Unit setLineLength(LineLength lineLength)
-line_length
<Integer>
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getSortHits
abstract SortHits getSortHits()
-sorthits
<Integer>
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setSortHits
abstract Unit setSortHits(SortHits sortHits)
-sorthits
<Integer>
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getSortHSPs
abstract SortHSPs getSortHSPs()
-sorthsps
<Integer>
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setSortHSPs
abstract Unit setSortHSPs(SortHSPs sortHSPs)
-sorthsps
<Integer>
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getMaxTargetSeqs
abstract MaxTargetSeqs getMaxTargetSeqs()
-max_target_seqs
<Integer>
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setMaxTargetSeqs
abstract Unit setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)
-max_target_seqs
<Integer>
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getParseDefLines
abstract ParseDefLines getParseDefLines()
-parse_deflines
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setParseDefLines
abstract Unit setParseDefLines(ParseDefLines parseDefLines)
-parse_deflines
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-
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