Constructor Detail

Method Detail

• getWordSize

   abstract WordSizePSI getWordSize()

  -word_size <Integer>

• setWordSize

   abstract Unit setWordSize(WordSizePSI wordSize)

  -word_size <Integer>

• getGapOpen

   abstract GapOpen getGapOpen()

  -gapopen <Integer>

• setGapOpen

   abstract Unit setGapOpen(GapOpen gapOpen)

  -gapopen <Integer>

• getGapExtend

   abstract GapExtend getGapExtend()

  -gapextend <Integer>

• setGapExtend

   abstract Unit setGapExtend(GapExtend gapExtend)

  -gapextend <Integer>

• getMatrix

   abstract MatrixPSI getMatrix()

  -matrix <String>

• setMatrix

   abstract Unit setMatrix(MatrixPSI matrix)

  -matrix <String>

• getThreshold

   abstract Threshold getThreshold()

  -threshold <Real>

• setThreshold

   abstract Unit setThreshold(Threshold threshold)

  -threshold <Real>

• getCompBasedStats

   abstract CompBasedStatsPSI getCompBasedStats()

  -comp_based_stats <String>

• setCompBasedStats

   abstract Unit setCompBasedStats(CompBasedStatsPSI compBasedStats)

  -comp_based_stats <String>

• getSubjectFile

   abstract SubjectFile getSubjectFile()

  -subject <File_In>

• setSubjectFile

   abstract Unit setSubjectFile(SubjectFile subjectFile)

  -subject <File_In>

• getSubjectLocation

   abstract SubjectLocation getSubjectLocation()

  -subject_loc <String>

• setSubjectLocation

   abstract Unit setSubjectLocation(SubjectLocation subjectLocation)

  -subject_loc <String>

• getSeg

   abstract SegPSI getSeg()

  -seg <String>

• setSeg

   abstract Unit setSeg(SegPSI seg)

  -seg <String>

• getSoftMasking

   abstract SoftMaskingPSI getSoftMasking()

  -soft_masking <Boolean>

• setSoftMasking

   abstract Unit setSoftMasking(SoftMaskingPSI softMasking)

  -soft_masking <Boolean>

• getQueryCoverageHSPPercent

   abstract QueryCoverageHSPPercent getQueryCoverageHSPPercent()

  -qcov_hsp_perc <Real>

• setQueryCoverageHSPPercent

   abstract Unit setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)

  -qcov_hsp_perc <Real>

• getCullingLimit

   abstract CullingLimit getCullingLimit()

  -culling_limit <Integer>

• setCullingLimit

   abstract Unit setCullingLimit(CullingLimit cullingLimit)

  -culling_limit <Integer>

• getBestHitOverhang

   abstract BestHitOverhang getBestHitOverhang()

  -best_hit_overhang <Real>

• setBestHitOverhang

   abstract Unit setBestHitOverhang(BestHitOverhang bestHitOverhang)

  -best_hit_overhang <Real>

• getBestHitScoreEdge

   abstract BestHitScoreEdge getBestHitScoreEdge()

  -best_hit_score_edge <Real>

• setBestHitScoreEdge

   abstract Unit setBestHitScoreEdge(BestHitScoreEdge bestHitScoreEdge)

  -best_hit_score_edge <Real>

• getSubjectBestHit

   abstract SubjectBestHit getSubjectBestHit()

  -subject_besthit

• setSubjectBestHit

   abstract Unit setSubjectBestHit(SubjectBestHit subjectBestHit)

  -subject_besthit

• getSumStats

   abstract SumStats getSumStats()

  -sum_stats <Boolean>

• setSumStats

   abstract Unit setSumStats(SumStats sumStats)

  -sum_stats <Boolean>

• getExtensionDropoffPrelimGapped

   abstract ExtensionDropoffPrelimGapped getExtensionDropoffPrelimGapped()

  -xdrop_gap <Real>

• setExtensionDropoffPrelimGapped

   abstract Unit setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped extensionDropoffPrelimGapped)

  -xdrop_gap <Real>

• getExtensionDropoffFinalGapped

   abstract ExtensionDropoffFinalGapped getExtensionDropoffFinalGapped()

  -xdrop_gap_final <Real>

• setExtensionDropoffFinalGapped

   abstract Unit setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped extensionDropoffFinalGapped)

  -xdrop_gap_final <Real>

• getGapTrigger

   abstract GapTrigger getGapTrigger()

  -gap_trigger <Real>

• setGapTrigger

   abstract Unit setGapTrigger(GapTrigger gapTrigger)

  -gap_trigger <Real>

• getNumCPUCores

   abstract NumCPUCores getNumCPUCores()

  -num_threads <Integer>

• setNumCPUCores

   abstract Unit setNumCPUCores(NumCPUCores numCPUCores)

  -num_threads <Integer>

• getUseSmithWatermanTraceback

   abstract UseSmithWatermanTraceback getUseSmithWatermanTraceback()

  -use_sw_tback

• setUseSmithWatermanTraceback

   abstract Unit setUseSmithWatermanTraceback(UseSmithWatermanTraceback useSmithWatermanTraceback)

  -use_sw_tback

• getNumIterations

   abstract NumIterations getNumIterations()

  -num_iterations <Integer>

• setNumIterations

   abstract Unit setNumIterations(NumIterations numIterations)

  -num_iterations <Integer>

• getOutPSSMFile

   abstract OutPSSMFile getOutPSSMFile()

  -out_pssm <File_Out>

• setOutPSSMFile

   abstract Unit setOutPSSMFile(OutPSSMFile outPSSMFile)

  -out_pssm <File_Out>

• getOutASCIIPSSMFile

   abstract OutASCIIPSSMFile getOutASCIIPSSMFile()

  -out_ascii_pssm <File_Out>

• setOutASCIIPSSMFile

   abstract Unit setOutASCIIPSSMFile(OutASCIIPSSMFile outASCIIPSSMFile)

  -out_ascii_pssm <File_Out>

• getSavePSSMAfterLastRound

   abstract SavePSSMAfterLastRound getSavePSSMAfterLastRound()

  -save_pssm_after_last_round

• setSavePSSMAfterLastRound

   abstract Unit setSavePSSMAfterLastRound(SavePSSMAfterLastRound savePSSMAfterLastRound)

  -save_pssm_after_last_round

• getSaveEachPSSM

   abstract SaveEachPSSM getSaveEachPSSM()

  -save_each_pssm

• setSaveEachPSSM

   abstract Unit setSaveEachPSSM(SaveEachPSSM saveEachPSSM)

  -save_each_pssm

• getInMSAFile

   abstract InMSAFile getInMSAFile()

  -in_msa <File_In>

• setInMSAFile

   abstract Unit setInMSAFile(InMSAFile inMSAFile)

  -in_msa <File_In>

• getMsaMasterIndex

   abstract MSAMasterIndex getMsaMasterIndex()

  -msa_master_idx <Integer>

• setMsaMasterIndex

   abstract Unit setMsaMasterIndex(MSAMasterIndex msaMasterIndex)

  -msa_master_idx <Integer>

• getIgnoreMSAMaster

   abstract IgnoreMSAMaster getIgnoreMSAMaster()

  -ignore_msa_master

• setIgnoreMSAMaster

   abstract Unit setIgnoreMSAMaster(IgnoreMSAMaster ignoreMSAMaster)

  -ignore_msa_master

• getInPSSMFile

   abstract InPSSMFile getInPSSMFile()

  -in_pssm <File_In>

• setInPSSMFile

   abstract Unit setInPSSMFile(InPSSMFile inPSSMFile)

  -in_pssm <File_In>

• getPseudoCount

   abstract PseudoCount getPseudoCount()

  -pseudocount <Integer>

• setPseudoCount

   abstract Unit setPseudoCount(PseudoCount pseudoCount)

  -pseudocount <Integer>

• getInclusionEValueThreshold

   abstract InclusionEValueThreshold getInclusionEValueThreshold()

  -inclusion_ethresh <Real>

• setInclusionEValueThreshold

   abstract Unit setInclusionEValueThreshold(InclusionEValueThreshold inclusionEValueThreshold)

  -inclusion_ethresh <Real>

• getPhiPatternFile

   abstract PHIPatternFile getPhiPatternFile()

  -phi_pattern <File_In>

• setPhiPatternFile

   abstract Unit setPhiPatternFile(PHIPatternFile phiPatternFile)

  -phi_pattern <File_In>

• getIpgListFile

   abstract IPGList getIpgListFile()

  -ipglist <String>

• setIpgListFile

   abstract Unit setIpgListFile(IPGList ipgListFile)

  -ipglist <String>

• getNegativeIPGListFile

   abstract NegativeIPGList getNegativeIPGListFile()

  -negative_ipglist <String>

• setNegativeIPGListFile

   abstract Unit setNegativeIPGListFile(NegativeIPGList negativeIPGListFile)

  -negative_ipglist <String>

• getGiListFile

   abstract GIList getGiListFile()

  -gilist <String>

• setGiListFile

   abstract Unit setGiListFile(GIList giListFile)

  -gilist <String>

• getNegativeGIListFile

   abstract NegativeGIList getNegativeGIListFile()

  -negative_gilist <String>

• setNegativeGIListFile

   abstract Unit setNegativeGIListFile(NegativeGIList negativeGIListFile)

  -negative_gilist <String>

• getSeqIDListFile

   abstract SeqIDList getSeqIDListFile()

  -seqidlist <String>

• setSeqIDListFile

   abstract Unit setSeqIDListFile(SeqIDList seqIDListFile)

  -seqidlist <String>

• getNegativeSeqIDListFile

   abstract NegativeSeqIDList getNegativeSeqIDListFile()

  -negative_seqidlist <String>

• setNegativeSeqIDListFile

   abstract Unit setNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)

  -negative_seqidlist <String>

• getTaxIDListFile

   abstract TaxIDList getTaxIDListFile()

  -taxidlist <String>

• setTaxIDListFile

   abstract Unit setTaxIDListFile(TaxIDList taxIDListFile)

  -taxidlist <String>

• getNegativeTaxIDListFile

   abstract NegativeTaxIDList getNegativeTaxIDListFile()

  -negative_taxidlist <String>

• setNegativeTaxIDListFile

   abstract Unit setNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)

  -negative_taxidlist <String>

• getTaxIDs

   abstract TaxIDs getTaxIDs()

  -taxids <String>

• setTaxIDs

   abstract Unit setTaxIDs(TaxIDs taxIDs)

  -taxids <String>

• getNegativeTaxIDs

   abstract NegativeTaxIDs getNegativeTaxIDs()

  -negative_taxids <String>

• setNegativeTaxIDs

   abstract Unit setNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)

  -negative_taxids <String>

• getQueryFile

   abstract QueryFile getQueryFile()

  -query <File_In>

• setQueryFile

   abstract Unit setQueryFile(QueryFile queryFile)

  -query <File_In>

• getQueryLocation

   abstract QueryLocation getQueryLocation()

  -query_loc <String>

• setQueryLocation

   abstract Unit setQueryLocation(QueryLocation queryLocation)

  -query_loc <String>

• getDbFile

   abstract DBFile getDbFile()

  -db <String>

• setDbFile

   abstract Unit setDbFile(DBFile dbFile)

  -db <String>

• getExpectValue

   abstract ExpectValue getExpectValue()

  -evalue <Real>

• setExpectValue

   abstract Unit setExpectValue(ExpectValue expectValue)

  -evalue <Real>

• getLowercaseMasking

   abstract LowercaseMasking getLowercaseMasking()

  -lcase_masking

• setLowercaseMasking

   abstract Unit setLowercaseMasking(LowercaseMasking lowercaseMasking)

  -lcase_masking

• getEntrezQuery

   abstract EntrezQuery getEntrezQuery()

  -entrez_query <String>

• setEntrezQuery

   abstract Unit setEntrezQuery(EntrezQuery entrezQuery)

  -entrez_query <String>

• getMaxHSPs

   abstract MaxHSPs getMaxHSPs()

  -max_hsps <Integer>

• setMaxHSPs

   abstract Unit setMaxHSPs(MaxHSPs maxHSPs)

  -max_hsps <Integer>

• getDbSize

   abstract DBSize getDbSize()

  -dbsize <Int8>

• setDbSize

   abstract Unit setDbSize(DBSize dbSize)

  -dbsize <Int8>

• getSearchSpace

   abstract SearchSpace getSearchSpace()

  -searchsp <Int8>

• setSearchSpace

   abstract Unit setSearchSpace(SearchSpace searchSpace)

  -searchsp <Int8>

• getImportSearchStrategy

   abstract ImportSearchStrategy getImportSearchStrategy()

  -import_search_strategy <File_In>

• setImportSearchStrategy

   abstract Unit setImportSearchStrategy(ImportSearchStrategy importSearchStrategy)

  -import_search_strategy <File_In>

• getExportSearchStrategy

   abstract ExportSearchStrategy getExportSearchStrategy()

  -export_search_strategy <File_Out>

• setExportSearchStrategy

   abstract Unit setExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)

  -export_search_strategy <File_Out>

• getExtensionDropoffUngapped

   abstract ExtensionDropoffUngapped getExtensionDropoffUngapped()

  -xdrop_ungap <Real>

• setExtensionDropoffUngapped

   abstract Unit setExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)

  -xdrop_ungap <Real>

• getWindowSize

   abstract WindowSize getWindowSize()

  -window_size <Integer>

• setWindowSize

   abstract Unit setWindowSize(WindowSize windowSize)

  -window_size <Integer>

• getRemote

   abstract Remote getRemote()

  -remote

• setRemote

   abstract Unit setRemote(Remote remote)

  -remote

• getTool

   abstract BlastTool getTool()

• getShortHelp

   abstract HelpShort getShortHelp()

  -h

• setShortHelp

   abstract Unit setShortHelp(HelpShort shortHelp)

  -h

• getLongHelp

   abstract HelpLong getLongHelp()

  -help

• setLongHelp

   abstract Unit setLongHelp(HelpLong longHelp)

  -help

• getVersion

   abstract Version getVersion()

  -version

• setVersion

   abstract Unit setVersion(Version version)

  -version

• getOutFile

   abstract OutFile getOutFile()

  -out <File_Out>

• setOutFile

   abstract Unit setOutFile(OutFile outFile)

  -out <File_Out>

• getOutFormat

   abstract OutFormat getOutFormat()

  -outfmt <String>

• setOutFormat

   abstract Unit setOutFormat(OutFormat outFormat)

  -outfmt <String>

• getShowGIs

   abstract ShowGIs getShowGIs()

  -show_gis

• setShowGIs

   abstract Unit setShowGIs(ShowGIs showGIs)

  -show_gis

• getNumDescriptions

   abstract NumDescriptions getNumDescriptions()

  -num_descriptions <Integer>

• setNumDescriptions

   abstract Unit setNumDescriptions(NumDescriptions numDescriptions)

  -num_descriptions <Integer>

• getNumAlignments

   abstract NumAlignments getNumAlignments()

  -num_alignments <Integer>

• setNumAlignments

   abstract Unit setNumAlignments(NumAlignments numAlignments)

  -num_alignments <Integer>

• getLineLength

   abstract LineLength getLineLength()

  -line_length <Integer>

• setLineLength

   abstract Unit setLineLength(LineLength lineLength)

  -line_length <Integer>

• getHtml

   abstract HTML getHtml()

  -html

• setHtml

   abstract Unit setHtml(HTML html)

  -html

• getSortHits

   abstract SortHits getSortHits()

  -sorthits <Integer>

• setSortHits

   abstract Unit setSortHits(SortHits sortHits)

  -sorthits <Integer>

• getSortHSPs

   abstract SortHSPs getSortHSPs()

  -sorthsps <Integer>

• setSortHSPs

   abstract Unit setSortHSPs(SortHSPs sortHSPs)

  -sorthsps <Integer>

• getMaxTargetSeqs

   abstract MaxTargetSeqs getMaxTargetSeqs()

  -max_target_seqs <Integer>

• setMaxTargetSeqs

   abstract Unit setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)

  -max_target_seqs <Integer>

• getParseDefLines

   abstract ParseDefLines getParseDefLines()

  -parse_deflines

• setParseDefLines

   abstract Unit setParseDefLines(ParseDefLines parseDefLines)

  -parse_deflines