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- SaveEachPSSM - class in org.veupathdb.lib.blast.common.fields
- -save_each_pssmSave PSSM after each iteration (file name is given in -save_pssm or -save_ascii_pssm options)
- SavePSSMAfterLastRound - class in org.veupathdb.lib.blast.common.fields
- -save_pssm_after_last_roundSave PSSM after the last database search
- ScoringMatrixP - class in org.veupathdb.lib.blast.blastp.field
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - ScoringMatrixPType - class in org.veupathdb.lib.blast.blastp.field
- ScoringMatrixTN - class in org.veupathdb.lib.blast.tblastn.fields
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - ScoringMatrixTNType - class in org.veupathdb.lib.blast.tblastn.fields
- ScoringMatrixTX - class in org.veupathdb.lib.blast.tblastx.fields
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - ScoringMatrixTXType - class in org.veupathdb.lib.blast.tblastx.fields
- ScoringMatrixX - class in org.veupathdb.lib.blast.blastx.field
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - ScoringMatrixXType - class in org.veupathdb.lib.blast.blastx.field
- SearchSpace - class in org.veupathdb.lib.blast.common.fields
- -searchsp
<Int8, >=0>Effective length of the search space - Seg - class in org.veupathdb.lib.blast.common.fields
- Low complexity region masker based on the SEG algorithm.
- SegDelta - class in org.veupathdb.lib.blast.deltablast.fields
- SegDelta.Companion - class in org.veupathdb.lib.blast.deltablast.fields.SegDelta
- SegP - class in org.veupathdb.lib.blast.blastp.field
- -seg
<String>Filter query sequence with SEGFormat:yes
"window locut hicut"
no (to disable)
no - SegP.Companion - class in org.veupathdb.lib.blast.blastp.field.SegP
- SegPSI - class in org.veupathdb.lib.blast.psiblast.fields
- SegPSI.Companion - class in org.veupathdb.lib.blast.psiblast.fields.SegPSI
- SegRPS - class in org.veupathdb.lib.blast.rpsblast.fields
- -seg <String>Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)Default =
no - SegRPS.Companion - class in org.veupathdb.lib.blast.rpsblast.fields.SegRPS
- SegRPSTN - class in org.veupathdb.lib.blast.rpstblastn.fields
- -seg <String>Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)Default =
no - SegRPSTN.Companion - class in org.veupathdb.lib.blast.rpstblastn.fields.SegRPSTN
- SegTN - class in org.veupathdb.lib.blast.tblastn.fields
- -seg
<String>Filter query sequence with SEGFormat:yes
"window locut hicut"
no (to disable)
12 2.2 2.5 - SegTN.Companion - class in org.veupathdb.lib.blast.tblastn.fields.SegTN
- SegTX - class in org.veupathdb.lib.blast.tblastx.fields
- -seg
<String>Filter query sequence with SEGFormat:yes
"window locut hicut"
no (to disable)
12 2.2 2.5 - SegTX.Companion - class in org.veupathdb.lib.blast.tblastx.fields.SegTX
- SegX - class in org.veupathdb.lib.blast.blastx.field
- -seg
<String>Filter query sequence with SEG. - SegX.Companion - class in org.veupathdb.lib.blast.blastx.field.SegX
- SeqAlignBinaryASN1 - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- SeqAlignJSON - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- SeqAlignTextASN1 - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- SeqIDList - class in org.veupathdb.lib.blast.common.fields
- -seqidlist
<String>Restrict search of database to list of SeqIDs - SequenceAlignmentMap - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- setArchive(Archive) - function in org.veupathdb.lib.blast.formatter.BlastFormatter
- -archive
<File_In> - setAutoCPUCores(AutoCPUCores) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -num_threads
<Integer> - setAutoCPUCores(AutoCPUCores) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -num_threads
<Integer> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.blastn.BlastN
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.blastp.BlastP
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.blastx.BlastX
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -best_hit_overhang
<Real> - setBestHitOverhang(BestHitOverhang) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -best_hit_overhang
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.blastn.BlastN
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.blastp.BlastP
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.blastx.BlastX
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -best_hit_score_edge
<Real> - setBestHitScoreEdge(BestHitScoreEdge) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -best_hit_score_edge
<Real> - setCompBasedStats(CompBasedStatsP) - function in org.veupathdb.lib.blast.blastp.BlastP
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsX) - function in org.veupathdb.lib.blast.blastx.BlastX
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsDelta) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsPSI) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsRPS) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsRPSTN) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -comp_based_stats
<String> - setCompBasedStats(CompBasedStatsTN) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -comp_based_stats
<String> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.blastn.BlastN
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.blastp.BlastP
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.blastx.BlastX
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -culling_limit
<Integer> - setCullingLimit(CullingLimit) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -culling_limit
<Integer> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastN
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastP
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastX
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.PSIBlast
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.RPSBlast
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.TBlastN
- -db
<String> - setDbFile(DBFile) - function in org.veupathdb.lib.blast.common.TBlastX
- -db
<String> - setDbGenCode(DBGenCode) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_gencode
<Integer> - setDbGenCode(DBGenCode) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_gencode
<Integer> - setDbHardMask(DBHardMask) - function in org.veupathdb.lib.blast.blastn.BlastN
- -db_hard_mask
<String> - setDbHardMask(DBHardMask) - function in org.veupathdb.lib.blast.blastp.BlastP
- -db_hard_mask
<String> - setDbHardMask(DBHardMask) - function in org.veupathdb.lib.blast.blastx.BlastX
- -db_hard_mask
<String> - setDbHardMask(DBHardMask) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_hard_mask
<String> - setDbHardMask(DBHardMask) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_hard_mask
<String> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastN
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastP
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastX
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.PSIBlast
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.RPSBlast
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.TBlastN
- -dbsize
<Int8> - setDbSize(DBSize) - function in org.veupathdb.lib.blast.common.TBlastX
- -dbsize
<Int8> - setDbSoftMask(DBSoftMask) - function in org.veupathdb.lib.blast.blastn.BlastN
- -db_soft_mask
<String> - setDbSoftMask(DBSoftMask) - function in org.veupathdb.lib.blast.blastp.BlastP
- -db_soft_mask
<String> - setDbSoftMask(DBSoftMask) - function in org.veupathdb.lib.blast.blastx.BlastX
- -db_soft_mask
<String> - setDbSoftMask(DBSoftMask) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_soft_mask
<String> - setDbSoftMask(DBSoftMask) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_soft_mask
<String> - setDelimiter(FormatDelimiter) - function in org.veupathdb.lib.blast.common.fields.OutFormat
- setDomainInclusionEValueThreshold(DomainInclusionEValueThreshold) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -domain_inclusion_ethresh
<Real> - setDust(Dust) - function in org.veupathdb.lib.blast.blastn.BlastN
- -dust
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastN
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastP
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastX
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.PSIBlast
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.RPSBlast
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.TBlastN
- -entrez_query
<String> - setEntrezQuery(EntrezQuery) - function in org.veupathdb.lib.blast.common.TBlastX
- -entrez_query
<String> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastN
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastP
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastX
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.PSIBlast
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.RPSBlast
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.TBlastN
- -evalue
<Real> - setExpectValue(ExpectValue) - function in org.veupathdb.lib.blast.common.TBlastX
- -evalue
<Real> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastN
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastP
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastX
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.PSIBlast
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.RPSBlast
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.TBlastN
- -export_search_strategy
<File_Out> - setExportSearchStrategy(ExportSearchStrategy) - function in org.veupathdb.lib.blast.common.TBlastX
- -export_search_strategy
<File_Out> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.blastn.BlastN
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.blastp.BlastP
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.blastx.BlastX
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -xdrop_gap_final
<Real> - setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -xdrop_gap_final
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.blastn.BlastN
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.blastp.BlastP
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.blastx.BlastX
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -xdrop_gap
<Real> - setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -xdrop_gap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastN
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastP
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastX
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.PSIBlast
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.RPSBlast
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.TBlastN
- -xdrop_ungap
<Real> - setExtensionDropoffUngapped(ExtensionDropoffUngapped) - function in org.veupathdb.lib.blast.common.TBlastX
- -xdrop_ungap
<Real> - setFilteringDBFile(FilteringDB) - function in org.veupathdb.lib.blast.blastn.BlastN
- -filtering_db
<String> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.blastn.BlastN
- -gapextend
<Integer> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.blastp.BlastP
- -gapextend
<Integer> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.blastx.BlastX
- -gapextend
<Integer> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gapextend
<Integer> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gapextend
<Integer> - setGapExtend(GapExtend) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -gapextend
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.blastn.BlastN
- -gapopen
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.blastp.BlastP
- -gapopen
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.blastx.BlastX
- -gapopen
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gapopen
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gapopen
<Integer> - setGapOpen(GapOpen) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -gapopen
<Integer> - setGapTrigger(GapTrigger) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gap_trigger
<Real> - setGapTrigger(GapTrigger) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gap_trigger
<Real> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.BlastN
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.BlastP
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.BlastX
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.TBlastN
- -gilist
<String> - setGiListFile(GIList) - function in org.veupathdb.lib.blast.common.TBlastX
- -gilist
<String> - setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastN
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastP
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastX
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastCLI
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.PSIBlast
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.RPSBlast
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.TBlastN
- -html
- setHtml(HTML) - function in org.veupathdb.lib.blast.common.TBlastX
- -html
- setIgnoreMSAMaster(IgnoreMSAMaster) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -ignore_msa_master
- setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastN
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastP
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastX
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.PSIBlast
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.RPSBlast
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.TBlastN
- -import_search_strategy
<File_In> - setImportSearchStrategy(ImportSearchStrategy) - function in org.veupathdb.lib.blast.common.TBlastX
- -import_search_strategy
<File_In> - setInclusionEValueThreshold(InclusionEValueThreshold) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -inclusion_ethresh
<Real> - setInclusionEValueThreshold(InclusionEValueThreshold) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -inclusion_ethresh
<Real> - setIndexName(IndexName) - function in org.veupathdb.lib.blast.blastn.BlastN
- -index_name
<String> - setInMSAFile(InMSAFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -in_msa
<File_In> - setInPSSMFile(InPSSMFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -in_pssm
<File_In> - setInPSSMFile(InPSSMFile) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -in_pssm
<File_In> - setIpgListFile(IPGList) - function in org.veupathdb.lib.blast.common.BlastP
- -ipglist
<String> - setIpgListFile(IPGList) - function in org.veupathdb.lib.blast.common.BlastX
- -ipglist
<String> - setIpgListFile(IPGList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -ipglist
<String> - setIpgListFile(IPGList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -ipglist
<String> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastN
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastP
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastX
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastCLI
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.PSIBlast
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.RPSBlast
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.TBlastN
- -line_length
<Integer> - setLineLength(LineLength) - function in org.veupathdb.lib.blast.common.TBlastX
- -line_length
<Integer> - setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastN
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastP
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastX
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastCLI
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.PSIBlast
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.RPSBlast
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.TBlastN
- -help
- setLongHelp(HelpLong) - function in org.veupathdb.lib.blast.common.TBlastX
- -help
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastN
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastP
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastX
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.PSIBlast
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.RPSBlast
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.TBlastN
- -lcase_masking
- setLowercaseMasking(LowercaseMasking) - function in org.veupathdb.lib.blast.common.TBlastX
- -lcase_masking
- setMatrix(ScoringMatrixP) - function in org.veupathdb.lib.blast.blastp.BlastP
- -matrix
<String> - setMatrix(ScoringMatrixX) - function in org.veupathdb.lib.blast.blastx.BlastX
- -matrix
<String> - setMatrix(MatrixDelta) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -matrix
<String> - setMatrix(MatrixPSI) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -matrix
<String> - setMatrix(ScoringMatrixTN) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -matrix
<String> - setMatrix(ScoringMatrixTX) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -matrix
<String> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastN
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastP
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastX
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.RPSBlast
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.TBlastN
- -max_hsps
<Integer> - setMaxHSPs(MaxHSPs) - function in org.veupathdb.lib.blast.common.TBlastX
- -max_hsps
<Integer> - setMaxIntronLength(MaxIntronLength) - function in org.veupathdb.lib.blast.blastx.BlastX
- -max_intron_length
<Integer> - setMaxIntronLength(MaxIntronLength) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -max_intron_length
<Integer> - setMaxIntronLength(MaxIntronLength) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -max_intron_length
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastN
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastP
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastX
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastCLI
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.RPSBlast
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.TBlastN
- -max_target_seqs
<Integer> - setMaxTargetSeqs(MaxTargetSeqs) - function in org.veupathdb.lib.blast.common.TBlastX
- -max_target_seqs
<Integer> - setMinRawGappedScore(MinRawGappedScore) - function in org.veupathdb.lib.blast.blastn.BlastN
- -min_raw_gapped_score
<Integer> - setMsaMasterIndex(MSAMasterIndex) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -msa_master_idx
<Integer> - setMultiThreadingMode(MultiThreadingMode) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -mt_mode
<Integer> - setMultiThreadingMode(MultiThreadingMode) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -mt_mode
<Integer> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.BlastN
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.BlastP
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.BlastX
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_gilist
<String> - setNegativeGIListFile(NegativeGIList) - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_gilist
<String> - setNegativeIPGListFile(NegativeIPGList) - function in org.veupathdb.lib.blast.common.BlastP
- -negative_ipglist
<String> - setNegativeIPGListFile(NegativeIPGList) - function in org.veupathdb.lib.blast.common.BlastX
- -negative_ipglist
<String> - setNegativeIPGListFile(NegativeIPGList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_ipglist
<String> - setNegativeIPGListFile(NegativeIPGList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_ipglist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.BlastN
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.BlastP
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.BlastX
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_seqidlist
<String> - setNegativeSeqIDListFile(NegativeSeqIDList) - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_seqidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.BlastN
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.BlastP
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.BlastX
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_taxidlist
<String> - setNegativeTaxIDListFile(NegativeTaxIDList) - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_taxidlist
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.BlastN
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.BlastP
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.BlastX
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_taxids
<String> - setNegativeTaxIDs(NegativeTaxIDs) - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_taxids
<String> - setNonGreedy(NonGreedy) - function in org.veupathdb.lib.blast.blastn.BlastN
- -no_greedy
- setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastN
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastP
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastX
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastCLI
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.PSIBlast
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.RPSBlast
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.TBlastN
- -num_alignments
<Integer> - setNumAlignments(NumAlignments) - function in org.veupathdb.lib.blast.common.TBlastX
- -num_alignments
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.blastn.BlastN
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.blastp.BlastP
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.blastx.BlastX
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -num_threads
<Integer> - setNumCPUCores(NumCPUCores) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -num_threads
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastN
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastP
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastX
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastCLI
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.PSIBlast
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.RPSBlast
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.TBlastN
- -num_descriptions
<Integer> - setNumDescriptions(NumDescriptions) - function in org.veupathdb.lib.blast.common.TBlastX
- -num_descriptions
<Integer> - setNumIterations(NumIterations) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -num_iterations
<Integer> - setNumIterations(NumIterations) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -num_iterations
<Integer> - setOffDiagonalRange(OffDiagonalRange) - function in org.veupathdb.lib.blast.blastn.BlastN
- -off_diagonal_range
<Integer> - setOutASCIIPSSMFile(OutASCIIPSSMFile) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -out_ascii_pssm
<File_Out> - setOutASCIIPSSMFile(OutASCIIPSSMFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -out_ascii_pssm
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastN
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastP
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastX
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastCLI
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.PSIBlast
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.RPSBlast
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.TBlastN
- -out
<File_Out> - setOutFile(OutFile) - function in org.veupathdb.lib.blast.common.TBlastX
- -out
<File_Out> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastN
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastP
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastX
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastCLI
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.PSIBlast
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.RPSBlast
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.TBlastN
- -outfmt
<String> - setOutFormat(OutFormat) - function in org.veupathdb.lib.blast.common.TBlastX
- -outfmt
<String> - setOutPSSMFile(OutPSSMFile) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -out_pssm
<File_Out> - setOutPSSMFile(OutPSSMFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -out_pssm
<File_Out> - setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastN
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastP
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastX
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastCLI
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.PSIBlast
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.RPSBlast
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.TBlastN
- -parse_deflines
- setParseDefLines(ParseDefLines) - function in org.veupathdb.lib.blast.common.TBlastX
- -parse_deflines
- setPenalty(Penalty) - function in org.veupathdb.lib.blast.blastn.BlastN
- -penalty
<Integer> - setPercentIdentity(PercentIdentity) - function in org.veupathdb.lib.blast.blastn.BlastN
- -perc_identity
<Real> - setPhiPatternFile(PHIPatternFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -phi_pattern
<File_In> - setPseudoCount(PseudoCount) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -pseudocount
<Integer> - setPseudoCount(PseudoCount) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -pseudocount
<Integer> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -qcov_hsp_perc
<Real> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -qcov_hsp_perc
<Real> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -qcov_hsp_perc
<Real> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -qcov_hsp_perc
<Real> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -qcov_hsp_perc
<Real> - setQueryCoverageHSPPercent(QueryCoverageHSPPercent) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -qcov_hsp_perc
<Real> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastN
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastP
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastX
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.PSIBlast
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.RPSBlast
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.TBlastN
- -query
<File_In> - setQueryFile(QueryFile) - function in org.veupathdb.lib.blast.common.TBlastX
- -query
<File_In> - setQueryGenCode(QueryGenCode) - function in org.veupathdb.lib.blast.blastx.BlastX
- -query_gencode
<Integer> - setQueryGenCode(QueryGenCode) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -query_gencode
<Integer> - setQueryGenCode(QueryGenCode) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -query_gencode
<Integer> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastN
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastP
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastX
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.PSIBlast
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.RPSBlast
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.TBlastN
- -query_loc
<String> - setQueryLocation(QueryLocation) - function in org.veupathdb.lib.blast.common.TBlastX
- -query_loc
<String> - setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastN
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastP
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastX
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.PSIBlast
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.RPSBlast
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.TBlastN
- -remote
- setRemote(Remote) - function in org.veupathdb.lib.blast.common.TBlastX
- -remote
- setReward(Reward) - function in org.veupathdb.lib.blast.blastn.BlastN
- -reward
<Integer> - setRid(RID) - function in org.veupathdb.lib.blast.formatter.BlastFormatter
- -rid
<String> - setRpsDB(RPSDB) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -rpsdb
<String> - setSaveEachPSSM(SaveEachPSSM) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -save_each_pssm
- setSaveEachPSSM(SaveEachPSSM) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -save_each_pssm
- setSavePSSMAfterLastRound(SavePSSMAfterLastRound) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -save_pssm_after_last_round
- setSavePSSMAfterLastRound(SavePSSMAfterLastRound) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -save_pssm_after_last_round
- setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastN
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastP
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastX
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.PSIBlast
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.RPSBlast
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.TBlastN
- -searchsp
<Int8> - setSearchSpace(SearchSpace) - function in org.veupathdb.lib.blast.common.TBlastX
- -searchsp
<Int8> - setSeg(SegP) - function in org.veupathdb.lib.blast.blastp.BlastP
- -seg
<String> - setSeg(SegX) - function in org.veupathdb.lib.blast.blastx.BlastX
- -seg
<String> - setSeg(SegDelta) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -seg
<String> - setSeg(SegPSI) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -seg
<String> - setSeg(SegRPS) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -seg
<String> - setSeg(SegRPSTN) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -seg
<String> - setSeg(SegTN) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -seg
<String> - setSeg(SegTX) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -seg
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.BlastN
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.BlastP
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.BlastX
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.TBlastN
- -seqidlist
<String> - setSeqIDListFile(SeqIDList) - function in org.veupathdb.lib.blast.common.TBlastX
- -seqidlist
<String> - setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastN
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastP
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastX
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastCLI
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.PSIBlast
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.RPSBlast
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.TBlastN
- -h
- setShortHelp(HelpShort) - function in org.veupathdb.lib.blast.common.TBlastX
- -h
- setShowDomainHits(ShowDomainHits) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -show_domain_hits
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastN
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastP
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastX
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastCLI
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.RPSBlast
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.TBlastN
- -show_gis
- setShowGIs(ShowGIs) - function in org.veupathdb.lib.blast.common.TBlastX
- -show_gis
- setSoftMasking(SoftMaskingN) - function in org.veupathdb.lib.blast.blastn.BlastN
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingP) - function in org.veupathdb.lib.blast.blastp.BlastP
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingX) - function in org.veupathdb.lib.blast.blastx.BlastX
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingDelta) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingPSI) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingRPS) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingRPSTN) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingTN) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -soft_masking
<Boolean> - setSoftMasking(SoftMaskingTX) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -soft_masking
<Boolean> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastN
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastP
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastX
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastCLI
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.PSIBlast
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.RPSBlast
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.TBlastN
- -sorthits
<Integer> - setSortHits(SortHits) - function in org.veupathdb.lib.blast.common.TBlastX
- -sorthits
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastN
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastP
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastX
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastCLI
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.RPSBlast
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.TBlastN
- -sorthsps
<Integer> - setSortHSPs(SortHSPs) - function in org.veupathdb.lib.blast.common.TBlastX
- -sorthsps
<Integer> - setStrand(Strand) - function in org.veupathdb.lib.blast.blastn.BlastN
- -strand
<String> - setStrand(Strand) - function in org.veupathdb.lib.blast.blastx.BlastX
- -strand
<String> - setStrand(Strand) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -strand
<String> - setStrand(Strand) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -strand
<String> - setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject_besthit
- setSubjectBestHit(SubjectBestHit) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject_besthit
- setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject
<File_In> - setSubjectFile(SubjectFile) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject
<File_In> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject_loc
<String> - setSubjectLocation(SubjectLocation) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject_loc
<String> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.blastn.BlastN
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.blastx.BlastX
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -max_target_seqs
<Integer> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -sum_stats
<Boolean> - setSumStats(SumStats) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -sum_stats
<Boolean> - setTask(BlastNTask) - function in org.veupathdb.lib.blast.blastn.BlastN
- -task
<String> - setTask(BlastPTask) - function in org.veupathdb.lib.blast.blastp.BlastP
- -task
<String> - setTask(BlastXTask) - function in org.veupathdb.lib.blast.blastx.BlastX
- -task
<String> - setTask(TBlastNTask) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -task
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.BlastN
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.BlastP
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.BlastX
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.PSIBlast
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.TBlastN
- -taxidlist
<String> - setTaxIDListFile(TaxIDList) - function in org.veupathdb.lib.blast.common.TBlastX
- -taxidlist
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.BlastN
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.BlastP
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.BlastX
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.PSIBlast
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.TBlastN
- -taxids
<String> - setTaxIDs(TaxIDs) - function in org.veupathdb.lib.blast.common.TBlastX
- -taxids
<String> - setTemplateLength(TemplateLength) - function in org.veupathdb.lib.blast.blastn.BlastN
- -template_length
<Integer> - setTemplateType(TemplateType) - function in org.veupathdb.lib.blast.blastn.BlastN
- -template_type
<String> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.blastp.BlastP
- -threshold
<Real> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.blastx.BlastX
- -threshold
<Real> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -threshold
<Real> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -threshold
<Real> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -threshold
<Real> - setThreshold(Threshold) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -threshold
<Real> - setType(FormatType) - function in org.veupathdb.lib.blast.common.fields.OutFormat
- setUngappedAlignmentsOnly(UngappedAlignmentsOnly) - function in org.veupathdb.lib.blast.blastn.BlastN
- -ungapped
- setUngappedAlignmentsOnly(UngappedAlignmentsOnly) - function in org.veupathdb.lib.blast.blastp.BlastP
- -ungapped
- setUngappedAlignmentsOnly(UngappedAlignmentsOnly) - function in org.veupathdb.lib.blast.blastx.BlastX
- -ungapped
- setUngappedAlignmentsOnly(UngappedAlignmentsOnly) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -ungapped
- setUngappedAlignmentsOnly(UngappedAlignmentsOnly) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -ungapped
- setUseIndex(UseIndex) - function in org.veupathdb.lib.blast.blastn.BlastN
- -use_index
<Boolean> - setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.blastp.BlastP
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.blastx.BlastX
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -use_sw_tback
- setUseSmithWatermanTraceback(UseSmithWatermanTraceback) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -use_sw_tback
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastN
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastP
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastX
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastCLI
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.BlastFormatter
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.PSIBlast
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.RPSBlast
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.TBlastN
- -version
- setVersion(Version) - function in org.veupathdb.lib.blast.common.TBlastX
- -version
- setWindowMaskerDBFile(WindowMaskerDB) - function in org.veupathdb.lib.blast.blastn.BlastN
- -window_masker_db
<String> - setWindowMaskerTaxID(WindowMaskerTaxID) - function in org.veupathdb.lib.blast.blastn.BlastN
- -window_masker_taxid
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastN
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastP
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastX
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.DeltaBlast
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.PSIBlast
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.RPSBlast
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.TBlastN
- -window_size
<Integer> - setWindowSize(WindowSize) - function in org.veupathdb.lib.blast.common.TBlastX
- -window_size
<Integer> - setWordSize(WordSizeP) - function in org.veupathdb.lib.blast.blastp.BlastP
- -word_size
<Integer> - setWordSize(WordSizeX) - function in org.veupathdb.lib.blast.blastx.BlastX
- -word_size
<Integer> - setWordSize(WordSizeDelta) - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -word_size
<Integer> - setWordSize(WordSizePSI) - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -word_size
<Integer> - setWordSize(WordSizeTBlastN) - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -word_size
<Integer> - setWordSize(WordSizeTX) - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -word_size
<Integer> - ShowDomainHits - class in org.veupathdb.lib.blast.deltablast.fields
- -show_domain_hitsShow domain hits
- ShowGIs - class in org.veupathdb.lib.blast.common.fields
- -show_gisShow NCBI GIs in deflines?
- SimplifiedCompBasedStats - enum entry in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPSValue
- SingleFileBlastJSON - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- SingleFileBlastXML2 - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- Sixteen - enum entry in org.veupathdb.lib.blast.blastn.fields.TemplateLengthValue
- SoftMaskingDelta - class in org.veupathdb.lib.blast.deltablast.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingN - class in org.veupathdb.lib.blast.blastn.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =true - SoftMaskingP - class in org.veupathdb.lib.blast.blastp.field
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingPSI - class in org.veupathdb.lib.blast.psiblast.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingRPS - class in org.veupathdb.lib.blast.rpsblast.fields
- -soft_masking <Boolean>Apply filtering locations as soft masksDefault =
false - SoftMaskingRPSTN - class in org.veupathdb.lib.blast.rpstblastn.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingTN - class in org.veupathdb.lib.blast.tblastn.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingTX - class in org.veupathdb.lib.blast.tblastx.fields
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SoftMaskingX - class in org.veupathdb.lib.blast.blastx.field
- -soft_masking
<Boolean>Apply filtering locations as soft masksDefault =false - SortHits - class in org.veupathdb.lib.blast.common.fields
- -sorthits
<Integer, (>=0 and =<4)>Sorting option for hits. - SortHSPs - class in org.veupathdb.lib.blast.common.fields
- -sorthsps
<Integer, (>=0 and =<4)>Sorting option for HSPs:0= Sort by hsp evalue1= Sort by hsp score2= Sort by hsp query start3= Sort by hsp percent identity4= Sort by hsp subject start
- SplitByDatabase - enum entry in org.veupathdb.lib.blast.common.fields.MultiThreadingModeValue
- SplitByQuery - enum entry in org.veupathdb.lib.blast.common.fields.MultiThreadingModeValue
- StandardFields - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- StartOfAlignmentInQuery - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- StartOfAlignmentInSubject - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- Statistics - enum entry in org.veupathdb.lib.blast.blastp.field.CompBasedStatsPValue
- Statistics - enum entry in org.veupathdb.lib.blast.blastx.field.CompBasedStatsXValue
- Statistics - enum entry in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSIValue
- Statistics - enum entry in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTNValue
- Strand - class in org.veupathdb.lib.blast.common.fields
- -strand
<String>Permissible values:both
minus
plus
both - StrandType - class in org.veupathdb.lib.blast.common.fields
- SubjectAccession - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectAccessionVersion - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectAsReferenceSeq - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectBestHit - class in org.veupathdb.lib.blast.common.fields
- -subject_besthitTurn on best hit per subject sequence
- SubjectBlastName - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectCommonName - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectFile - class in org.veupathdb.lib.blast.common.fields
- -subject
<File_In>Subject sequence(s) to search - SubjectFrame - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectGI - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectLocation - class in org.veupathdb.lib.blast.common.fields
- -subject_loc
<String>Location on the subject sequence in 1-based offsets (Format: start-stop) - SubjectScientificName - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectSeqID - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectSequenceLength - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectStrand - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectSuperKingdom - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectTaxonomyID - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SubjectTitle - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- SumStats - class in org.veupathdb.lib.blast.common.fields
- -sum_stats
<Boolean>Use sum statistics