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G
- GapExtend - class in org.veupathdb.lib.blast.common.fields
- -gapextend
<Integer>Cost to extend a gap - GapOpen - class in org.veupathdb.lib.blast.common.fields
- -gapopen
<Integer>Cost to open a gap - GapTrigger - class in org.veupathdb.lib.blast.common.fields
- -gap_trigger
<Real>Number of bits to trigger gappingDefault =22 - getArchive() - function in org.veupathdb.lib.blast.formatter.BlastFormatter
- -archive
<File_In> - getAutoCPUCores() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -num_threads
<Integer> - getAutoCPUCores() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -num_threads
<Integer> - getBestHitOverhang() - function in org.veupathdb.lib.blast.blastn.BlastN
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.blastp.BlastP
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.blastx.BlastX
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -best_hit_overhang
<Real> - getBestHitOverhang() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -best_hit_overhang
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.blastn.BlastN
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.blastp.BlastP
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.blastx.BlastX
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -best_hit_score_edge
<Real> - getBestHitScoreEdge() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -best_hit_score_edge
<Real> - getCompBasedStats() - function in org.veupathdb.lib.blast.blastp.BlastP
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.blastx.BlastX
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -comp_based_stats
<String> - getCompBasedStats() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -comp_based_stats
<String> - getCullingLimit() - function in org.veupathdb.lib.blast.blastn.BlastN
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.blastp.BlastP
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.blastx.BlastX
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -culling_limit
<Integer> - getCullingLimit() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -culling_limit
<Integer> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastN
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastP
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastX
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.RPSBlast
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -db
<String> - getDbFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -db
<String> - getDbGenCode() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_gencode
<Integer> - getDbGenCode() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_gencode
<Integer> - getDbHardMask() - function in org.veupathdb.lib.blast.blastn.BlastN
- -db_hard_mask
<String> - getDbHardMask() - function in org.veupathdb.lib.blast.blastp.BlastP
- -db_hard_mask
<String> - getDbHardMask() - function in org.veupathdb.lib.blast.blastx.BlastX
- -db_hard_mask
<String> - getDbHardMask() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_hard_mask
<String> - getDbHardMask() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_hard_mask
<String> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastN
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastP
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastX
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.PSIBlast
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.RPSBlast
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.TBlastN
- -dbsize
<Int8> - getDbSize() - function in org.veupathdb.lib.blast.common.TBlastX
- -dbsize
<Int8> - getDbSoftMask() - function in org.veupathdb.lib.blast.blastn.BlastN
- -db_soft_mask
<String> - getDbSoftMask() - function in org.veupathdb.lib.blast.blastp.BlastP
- -db_soft_mask
<String> - getDbSoftMask() - function in org.veupathdb.lib.blast.blastx.BlastX
- -db_soft_mask
<String> - getDbSoftMask() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -db_soft_mask
<String> - getDbSoftMask() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -db_soft_mask
<String> - getDelimiter() - function in org.veupathdb.lib.blast.common.fields.OutFormat
- getDomainInclusionEValueThreshold() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -domain_inclusion_ethresh
<Real> - getDust() - function in org.veupathdb.lib.blast.blastn.BlastN
- -dust
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastN
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastP
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastX
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.PSIBlast
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.RPSBlast
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.TBlastN
- -entrez_query
<String> - getEntrezQuery() - function in org.veupathdb.lib.blast.common.TBlastX
- -entrez_query
<String> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastN
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastP
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastX
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.PSIBlast
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.RPSBlast
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.TBlastN
- -evalue
<Real> - getExpectValue() - function in org.veupathdb.lib.blast.common.TBlastX
- -evalue
<Real> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastN
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastP
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastX
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.PSIBlast
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.RPSBlast
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.TBlastN
- -export_search_strategy
<File_Out> - getExportSearchStrategy() - function in org.veupathdb.lib.blast.common.TBlastX
- -export_search_strategy
<File_Out> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.blastn.BlastN
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.blastp.BlastP
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.blastx.BlastX
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -xdrop_gap_final
<Real> - getExtensionDropoffFinalGapped() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -xdrop_gap_final
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.blastn.BlastN
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.blastp.BlastP
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.blastx.BlastX
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -xdrop_gap
<Real> - getExtensionDropoffPrelimGapped() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -xdrop_gap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastN
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastP
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastX
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.PSIBlast
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.RPSBlast
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.TBlastN
- -xdrop_ungap
<Real> - getExtensionDropoffUngapped() - function in org.veupathdb.lib.blast.common.TBlastX
- -xdrop_ungap
<Real> - getFields() - function in org.veupathdb.lib.blast.common.fields.OutFormat
- getFile() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerDB
- getFile() - function in org.veupathdb.lib.blast.common.fields.DBFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.GIList
- getFile() - function in org.veupathdb.lib.blast.common.fields.IPGList
- getFile() - function in org.veupathdb.lib.blast.common.fields.InPSSMFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.NegativeGIList
- getFile() - function in org.veupathdb.lib.blast.common.fields.NegativeIPGList
- getFile() - function in org.veupathdb.lib.blast.common.fields.NegativeSeqIDList
- getFile() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDList
- getFile() - function in org.veupathdb.lib.blast.common.fields.OutASCIIPSSMFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.OutFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.OutPSSMFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.QueryFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.ImportSearchStrategy
- getFile() - function in org.veupathdb.lib.blast.common.fields.ExportSearchStrategy
- getFile() - function in org.veupathdb.lib.blast.common.fields.SubjectFile
- getFile() - function in org.veupathdb.lib.blast.common.fields.TaxIDList
- getFile() - function in org.veupathdb.lib.blast.formatter.fields.Archive
- getFile() - function in org.veupathdb.lib.blast.psiblast.fields.InMSAFile
- getFilteringDBFile() - function in org.veupathdb.lib.blast.blastn.BlastN
- -filtering_db
<String> - getGapExtend() - function in org.veupathdb.lib.blast.blastn.BlastN
- -gapextend
<Integer> - getGapExtend() - function in org.veupathdb.lib.blast.blastp.BlastP
- -gapextend
<Integer> - getGapExtend() - function in org.veupathdb.lib.blast.blastx.BlastX
- -gapextend
<Integer> - getGapExtend() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gapextend
<Integer> - getGapExtend() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gapextend
<Integer> - getGapExtend() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -gapextend
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.blastn.BlastN
- -gapopen
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.blastp.BlastP
- -gapopen
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.blastx.BlastX
- -gapopen
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gapopen
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gapopen
<Integer> - getGapOpen() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -gapopen
<Integer> - getGapTrigger() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -gap_trigger
<Real> - getGapTrigger() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -gap_trigger
<Real> - getGiListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -gilist
<String> - getGiListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -gilist
<String> - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegP
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegX
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.Seg
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegDelta
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegPSI
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegRPS
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegRPSTN
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegTN
- SEG hicutDefault =
2.5 - getHicut() - function in org.veupathdb.lib.blast.common.fields.SegTX
- SEG hicutDefault =
2.5 - getHtml() - function in org.veupathdb.lib.blast.common.BlastN
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastP
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastX
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastCLI
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.PSIBlast
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.RPSBlast
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.TBlastN
- -html
- getHtml() - function in org.veupathdb.lib.blast.common.TBlastX
- -html
- getIgnoreMSAMaster() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -ignore_msa_master
- getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastN
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastP
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastX
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.PSIBlast
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.RPSBlast
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.TBlastN
- -import_search_strategy
<File_In> - getImportSearchStrategy() - function in org.veupathdb.lib.blast.common.TBlastX
- -import_search_strategy
<File_In> - getInclusionEValueThreshold() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -inclusion_ethresh
<Real> - getInclusionEValueThreshold() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -inclusion_ethresh
<Real> - getIndexName() - function in org.veupathdb.lib.blast.blastn.BlastN
- -index_name
<String> - getInMSAFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -in_msa
<File_In> - getInPSSMFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -in_pssm
<File_In> - getInPSSMFile() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -in_pssm
<File_In> - getIpgListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -ipglist
<String> - getIpgListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -ipglist
<String> - getIpgListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -ipglist
<String> - getIpgListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -ipglist
<String> - getIsDefault() - function in org.veupathdb.lib.blast.serial.Dust
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.FilteringDB
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.IndexName
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.MinRawGappedScore
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.NonGreedy
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.OffDiagonalRange
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.Penalty
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.PercentIdentity
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.Reward
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.SoftMaskingN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.BlastNTask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.TemplateLength
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.TemplateType
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.UseIndex
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerDB
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerTaxID
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastp.field.BlastPTask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsP
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixP
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegP
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastp.field.SoftMaskingP
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastp.field.WordSizeP
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastx.field.BlastXTask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastx.field.SoftMaskingX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.blastx.field.WordSizeX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.AutoCPUCores
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.BestHitOverhang
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.BestHitScoreEdge
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.CullingLimit
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.DBFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.DBGenCode
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.DBHardMask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.DBSize
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.DBSoftMask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.EntrezQuery
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ExpectValue
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.GIList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.GapExtend
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.GapOpen
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.GapTrigger
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.HTML
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.HelpLong
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.HelpShort
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.IPGList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.InPSSMFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.InclusionEValueThreshold
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.LineLength
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.LowercaseMasking
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.MaxHSPs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.MaxIntronLength
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.MaxTargetSeqs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.MultiThreadingMode
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NegativeGIList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NegativeIPGList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NegativeSeqIDList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NumAlignments
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NumCPUCores
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NumDescriptions
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.NumIterations
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.OutASCIIPSSMFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.OutFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.OutFormat
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.FormatDelimiter
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.FormatFields
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.FormatType
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.FormatField
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.OutPSSMFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ParseDefLines
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.PseudoCount
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.QueryCoverageHSPPercent
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.QueryFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.QueryGenCode
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.QueryLocation
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.Remote
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SaveEachPSSM
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SavePSSMAfterLastRound
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SearchSpace
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ImportSearchStrategy
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ExportSearchStrategy
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.Seg
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SeqIDList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ShowGIs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SortHSPs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SortHits
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.Strand
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SubjectBestHit
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SubjectFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SubjectLocation
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.SumStats
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.TaxIDList
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.TaxIDs
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.Threshold
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.UngappedAlignmentsOnly
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.UseSmithWatermanTraceback
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.Version
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.WindowSize
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffUngapped
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffPrelimGapped
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffFinalGapped
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDelta
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.DomainInclusionEValueThreshold
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDelta
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.RPSDB
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegDelta
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.ShowDomainHits
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.SoftMaskingDelta
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.deltablast.fields.WordSizeDelta
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.formatter.fields.Archive
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.formatter.fields.RID
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSI
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.IgnoreMSAMaster
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.InMSAFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.MSAMasterIndex
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSI
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.PHIPatternFile
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegPSI
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.SoftMaskingPSI
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.psiblast.fields.WordSizePSI
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPS
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegRPS
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.rpsblast.fields.SoftMaskingRPS
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegRPSTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.rpstblastn.fields.SoftMaskingRPSTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.BlastField
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastn.fields.SoftMaskingTN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTask
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastn.fields.WordSizeTBlastN
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.serial.SegTX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastx.fields.SoftMaskingTX
- Indicates whether the field is currently set to its default value.
- getIsDefault() - function in org.veupathdb.lib.blast.tblastx.fields.WordSizeTX
- Indicates whether the field is currently set to its default value.
- getIsNo() - function in org.veupathdb.lib.blast.blastn.fields.Dust
- Indicates whether this Dust value is
"no". - getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegP
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegX
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.Seg
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegDelta
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegPSI
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegRPS
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegRPSTN
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegTN
- Indicates whether this SEG value equals "no".
- getIsNo() - function in org.veupathdb.lib.blast.common.fields.SegTX
- Indicates whether this SEG value equals "no".
- getIsYes() - function in org.veupathdb.lib.blast.blastn.fields.Dust
- Indicates whether this Dust value is
"yes". - getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegP
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegX
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.Seg
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegDelta
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegPSI
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegRPS
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegRPSTN
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegTN
- Indicates whether this SEG value equals "yes".
- getIsYes() - function in org.veupathdb.lib.blast.common.fields.SegTX
- Indicates whether this SEG value equals "yes".
- getLevel() - function in org.veupathdb.lib.blast.blastn.fields.Dust
- The level value for a value based Dust value.
- getLineLength() - function in org.veupathdb.lib.blast.common.BlastN
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastP
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastX
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastCLI
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.PSIBlast
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.RPSBlast
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.TBlastN
- -line_length
<Integer> - getLineLength() - function in org.veupathdb.lib.blast.common.TBlastX
- -line_length
<Integer> - getLinker() - function in org.veupathdb.lib.blast.blastn.fields.Dust
- The linker value for a value based Dust value.
- getLocut() - function in org.veupathdb.lib.blast.common.fields.SegP
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegX
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.Seg
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegDelta
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegPSI
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegRPS
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegRPSTN
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegTN
- SEG locutDefault =
2.2 - getLocut() - function in org.veupathdb.lib.blast.common.fields.SegTX
- SEG locutDefault =
2.2 - getLongHelp() - function in org.veupathdb.lib.blast.common.BlastN
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastP
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastX
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastCLI
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.PSIBlast
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.RPSBlast
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.TBlastN
- -help
- getLongHelp() - function in org.veupathdb.lib.blast.common.TBlastX
- -help
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastN
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastP
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastX
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.PSIBlast
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.RPSBlast
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.TBlastN
- -lcase_masking
- getLowercaseMasking() - function in org.veupathdb.lib.blast.common.TBlastX
- -lcase_masking
- getMatrix() - function in org.veupathdb.lib.blast.blastp.BlastP
- -matrix
<String> - getMatrix() - function in org.veupathdb.lib.blast.blastx.BlastX
- -matrix
<String> - getMatrix() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -matrix
<String> - getMatrix() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -matrix
<String> - getMatrix() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -matrix
<String> - getMatrix() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -matrix
<String> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastN
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastP
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastX
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.RPSBlast
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.TBlastN
- -max_hsps
<Integer> - getMaxHSPs() - function in org.veupathdb.lib.blast.common.TBlastX
- -max_hsps
<Integer> - getMaxIntronLength() - function in org.veupathdb.lib.blast.blastx.BlastX
- -max_intron_length
<Integer> - getMaxIntronLength() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -max_intron_length
<Integer> - getMaxIntronLength() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -max_intron_length
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastN
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastP
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastX
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastCLI
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.RPSBlast
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.TBlastN
- -max_target_seqs
<Integer> - getMaxTargetSeqs() - function in org.veupathdb.lib.blast.common.TBlastX
- -max_target_seqs
<Integer> - getMinRawGappedScore() - function in org.veupathdb.lib.blast.blastn.BlastN
- -min_raw_gapped_score
<Integer> - getMsaMasterIndex() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -msa_master_idx
<Integer> - getMultiThreadingMode() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -mt_mode
<Integer> - getMultiThreadingMode() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -mt_mode
<Integer> - getName() - function in kotlin.BlastTool
- getName() - function in org.veupathdb.lib.blast.serial.Dust
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.FilteringDB
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.IndexName
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.MinRawGappedScore
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.NonGreedy
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.OffDiagonalRange
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.Penalty
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.PercentIdentity
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.Reward
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.SoftMaskingN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.BlastNTask
- The name of this field.
- getName() - function in kotlin.BlastNTaskType
- getName() - function in org.veupathdb.lib.blast.blastn.fields.TemplateLength
- The name of this field.
- getName() - function in kotlin.TemplateLengthValue
- getName() - function in org.veupathdb.lib.blast.blastn.fields.TemplateType
- The name of this field.
- getName() - function in kotlin.TemplateTypeType
- getName() - function in org.veupathdb.lib.blast.blastn.fields.UseIndex
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerDB
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerTaxID
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastp.field.BlastPTask
- The name of this field.
- getName() - function in kotlin.BlastPTaskType
- getName() - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsP
- The name of this field.
- getName() - function in kotlin.CompBasedStatsPValue
- getName() - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixP
- The name of this field.
- getName() - function in kotlin.ScoringMatrixPType
- getName() - function in org.veupathdb.lib.blast.serial.SegP
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastp.field.SoftMaskingP
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastp.field.WordSizeP
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastx.field.BlastXTask
- The name of this field.
- getName() - function in kotlin.BlastXTaskType
- getName() - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsX
- The name of this field.
- getName() - function in kotlin.CompBasedStatsXValue
- getName() - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixX
- The name of this field.
- getName() - function in kotlin.ScoringMatrixXType
- getName() - function in org.veupathdb.lib.blast.serial.SegX
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastx.field.SoftMaskingX
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.blastx.field.WordSizeX
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.AutoCPUCores
- The name of this field.
- getName() - function in kotlin.AutoCPUCoresValue
- getName() - function in org.veupathdb.lib.blast.common.fields.BestHitOverhang
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.BestHitScoreEdge
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.CullingLimit
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.DBFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.DBGenCode
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.DBHardMask
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.DBSize
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.DBSoftMask
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.EntrezQuery
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ExpectValue
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.GIList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.GapExtend
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.GapOpen
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.GapTrigger
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.HTML
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.HelpLong
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.HelpShort
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.IPGList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.InPSSMFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.InclusionEValueThreshold
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.LineLength
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.LowercaseMasking
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.MaxHSPs
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.MaxIntronLength
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.MaxTargetSeqs
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.MultiThreadingMode
- The name of this field.
- getName() - function in kotlin.MultiThreadingModeValue
- getName() - function in org.veupathdb.lib.blast.common.fields.NegativeGIList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NegativeIPGList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NegativeSeqIDList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDs
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NumAlignments
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NumCPUCores
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NumDescriptions
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.NumIterations
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.OutASCIIPSSMFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.OutFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.OutFormat
- The name of this field.
- getName() - function in kotlin.FormatType
- getName() - function in kotlin.FormatField
- getName() - function in org.veupathdb.lib.blast.common.fields.OutPSSMFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ParseDefLines
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.PseudoCount
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.QueryCoverageHSPPercent
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.QueryFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.QueryGenCode
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.QueryLocation
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.Remote
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SaveEachPSSM
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SavePSSMAfterLastRound
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SearchSpace
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ImportSearchStrategy
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ExportSearchStrategy
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.serial.Seg
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SeqIDList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ShowGIs
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SortHSPs
- The name of this field.
- getName() - function in kotlin.HSPSorting
- getName() - function in org.veupathdb.lib.blast.common.fields.SortHits
- The name of this field.
- getName() - function in kotlin.HitSorting
- getName() - function in org.veupathdb.lib.blast.common.fields.Strand
- The name of this field.
- getName() - function in kotlin.StrandType
- getName() - function in org.veupathdb.lib.blast.common.fields.SubjectBestHit
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SubjectFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SubjectLocation
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.SumStats
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.TaxIDList
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.TaxIDs
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.Threshold
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.UngappedAlignmentsOnly
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.UseSmithWatermanTraceback
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.Version
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.WindowSize
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffUngapped
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffPrelimGapped
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffFinalGapped
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDelta
- The name of this field.
- getName() - function in kotlin.CompBasedStatsDeltaValue
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.DomainInclusionEValueThreshold
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDelta
- The name of this field.
- getName() - function in kotlin.MatrixDeltaType
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.RPSDB
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.serial.SegDelta
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.ShowDomainHits
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.SoftMaskingDelta
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.deltablast.fields.WordSizeDelta
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.formatter.fields.Archive
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.formatter.fields.RID
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSI
- The name of this field.
- getName() - function in kotlin.CompBasedStatsPSIValue
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.IgnoreMSAMaster
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.InMSAFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.MSAMasterIndex
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSI
- The name of this field.
- getName() - function in kotlin.MatrixPSIType
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.PHIPatternFile
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.serial.SegPSI
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.SoftMaskingPSI
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.psiblast.fields.WordSizePSI
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPS
- The name of this field.
- getName() - function in kotlin.CompBasedStatsRPSValue
- getName() - function in org.veupathdb.lib.blast.serial.SegRPS
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.rpsblast.fields.SoftMaskingRPS
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTN
- The name of this field.
- getName() - function in kotlin.CompBasedStatsRPSTNValue
- getName() - function in org.veupathdb.lib.blast.serial.SegRPSTN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.rpstblastn.fields.SoftMaskingRPSTN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.serial.BlastField
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTN
- The name of this field.
- getName() - function in kotlin.CompBasedStatsTNValue
- getName() - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTN
- The name of this field.
- getName() - function in kotlin.ScoringMatrixTNType
- getName() - function in org.veupathdb.lib.blast.serial.SegTN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastn.fields.SoftMaskingTN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTask
- The name of this field.
- getName() - function in kotlin.TBlastNTaskValue
- getName() - function in org.veupathdb.lib.blast.tblastn.fields.WordSizeTBlastN
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTX
- The name of this field.
- getName() - function in kotlin.ScoringMatrixTXType
- getName() - function in org.veupathdb.lib.blast.serial.SegTX
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastx.fields.SoftMaskingTX
- The name of this field.
- getName() - function in org.veupathdb.lib.blast.tblastx.fields.WordSizeTX
- The name of this field.
- getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_gilist
<String> - getNegativeGIListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_gilist
<String> - getNegativeIPGListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -negative_ipglist
<String> - getNegativeIPGListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -negative_ipglist
<String> - getNegativeIPGListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_ipglist
<String> - getNegativeIPGListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_ipglist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_seqidlist
<String> - getNegativeSeqIDListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_seqidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_taxidlist
<String> - getNegativeTaxIDListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_taxidlist
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.BlastN
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.BlastP
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.BlastX
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.TBlastN
- -negative_taxids
<String> - getNegativeTaxIDs() - function in org.veupathdb.lib.blast.common.TBlastX
- -negative_taxids
<String> - getNonGreedy() - function in org.veupathdb.lib.blast.blastn.BlastN
- -no_greedy
- getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastN
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastP
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastX
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastCLI
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.PSIBlast
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.RPSBlast
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.TBlastN
- -num_alignments
<Integer> - getNumAlignments() - function in org.veupathdb.lib.blast.common.TBlastX
- -num_alignments
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.blastn.BlastN
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.blastp.BlastP
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.blastx.BlastX
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -num_threads
<Integer> - getNumCPUCores() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -num_threads
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastN
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastP
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastX
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastCLI
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.PSIBlast
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.RPSBlast
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.TBlastN
- -num_descriptions
<Integer> - getNumDescriptions() - function in org.veupathdb.lib.blast.common.TBlastX
- -num_descriptions
<Integer> - getNumIterations() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -num_iterations
<Integer> - getNumIterations() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -num_iterations
<Integer> - getOffDiagonalRange() - function in org.veupathdb.lib.blast.blastn.BlastN
- -off_diagonal_range
<Integer> - getOrdinal() - function in kotlin.BlastTool
- getOrdinal() - function in kotlin.BlastNTaskType
- getOrdinal() - function in kotlin.TemplateLengthValue
- getOrdinal() - function in kotlin.TemplateTypeType
- getOrdinal() - function in kotlin.BlastPTaskType
- getOrdinal() - function in kotlin.CompBasedStatsPValue
- getOrdinal() - function in kotlin.ScoringMatrixPType
- getOrdinal() - function in kotlin.BlastXTaskType
- getOrdinal() - function in kotlin.CompBasedStatsXValue
- getOrdinal() - function in kotlin.ScoringMatrixXType
- getOrdinal() - function in kotlin.AutoCPUCoresValue
- getOrdinal() - function in kotlin.MultiThreadingModeValue
- getOrdinal() - function in kotlin.FormatType
- getOrdinal() - function in kotlin.FormatField
- getOrdinal() - function in kotlin.HSPSorting
- getOrdinal() - function in kotlin.HitSorting
- getOrdinal() - function in kotlin.StrandType
- getOrdinal() - function in kotlin.CompBasedStatsDeltaValue
- getOrdinal() - function in kotlin.MatrixDeltaType
- getOrdinal() - function in kotlin.CompBasedStatsPSIValue
- getOrdinal() - function in kotlin.MatrixPSIType
- getOrdinal() - function in kotlin.CompBasedStatsRPSValue
- getOrdinal() - function in kotlin.CompBasedStatsRPSTNValue
- getOrdinal() - function in kotlin.CompBasedStatsTNValue
- getOrdinal() - function in kotlin.ScoringMatrixTNType
- getOrdinal() - function in kotlin.TBlastNTaskValue
- getOrdinal() - function in kotlin.ScoringMatrixTXType
- getOutASCIIPSSMFile() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -out_ascii_pssm
<File_Out> - getOutASCIIPSSMFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -out_ascii_pssm
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastN
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastP
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastX
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastCLI
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.RPSBlast
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -out
<File_Out> - getOutFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -out
<File_Out> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastN
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastP
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastX
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastCLI
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.PSIBlast
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.RPSBlast
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.TBlastN
- -outfmt
<String> - getOutFormat() - function in org.veupathdb.lib.blast.common.TBlastX
- -outfmt
<String> - getOutPSSMFile() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -out_pssm
<File_Out> - getOutPSSMFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -out_pssm
<File_Out> - getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastN
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastP
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastX
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastCLI
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.PSIBlast
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.RPSBlast
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.TBlastN
- -parse_deflines
- getParseDefLines() - function in org.veupathdb.lib.blast.common.TBlastX
- -parse_deflines
- getPenalty() - function in org.veupathdb.lib.blast.blastn.BlastN
- -penalty
<Integer> - getPercentIdentity() - function in org.veupathdb.lib.blast.blastn.BlastN
- -perc_identity
<Real> - getPhiPatternFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -phi_pattern
<File_In> - getPseudoCount() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -pseudocount
<Integer> - getPseudoCount() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -pseudocount
<Integer> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -qcov_hsp_perc
<Real> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -qcov_hsp_perc
<Real> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -qcov_hsp_perc
<Real> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -qcov_hsp_perc
<Real> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -qcov_hsp_perc
<Real> - getQueryCoverageHSPPercent() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -qcov_hsp_perc
<Real> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastN
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastP
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastX
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.RPSBlast
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -query
<File_In> - getQueryFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -query
<File_In> - getQueryGenCode() - function in org.veupathdb.lib.blast.blastx.BlastX
- -query_gencode
<Integer> - getQueryGenCode() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -query_gencode
<Integer> - getQueryGenCode() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -query_gencode
<Integer> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastN
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastP
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastX
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.PSIBlast
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.RPSBlast
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.TBlastN
- -query_loc
<String> - getQueryLocation() - function in org.veupathdb.lib.blast.common.TBlastX
- -query_loc
<String> - getRemote() - function in org.veupathdb.lib.blast.common.BlastN
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.BlastP
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.BlastX
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.PSIBlast
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.RPSBlast
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.TBlastN
- -remote
- getRemote() - function in org.veupathdb.lib.blast.common.TBlastX
- -remote
- getReward() - function in org.veupathdb.lib.blast.blastn.BlastN
- -reward
<Integer> - getRid() - function in org.veupathdb.lib.blast.formatter.BlastFormatter
- -rid
<String> - getRpsDB() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -rpsdb
<String> - getSaveEachPSSM() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -save_each_pssm
- getSaveEachPSSM() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -save_each_pssm
- getSavePSSMAfterLastRound() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -save_pssm_after_last_round
- getSavePSSMAfterLastRound() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -save_pssm_after_last_round
- getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastN
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastP
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastX
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.PSIBlast
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.RPSBlast
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.TBlastN
- -searchsp
<Int8> - getSearchSpace() - function in org.veupathdb.lib.blast.common.TBlastX
- -searchsp
<Int8> - getSeg() - function in org.veupathdb.lib.blast.blastp.BlastP
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.blastx.BlastX
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -seg
<String> - getSeg() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -seg
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -seqidlist
<String> - getSeqIDListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -seqidlist
<String> - getShortHelp() - function in org.veupathdb.lib.blast.common.BlastN
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastP
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastX
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastCLI
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.PSIBlast
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.RPSBlast
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.TBlastN
- -h
- getShortHelp() - function in org.veupathdb.lib.blast.common.TBlastX
- -h
- getShowDomainHits() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -show_domain_hits
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastN
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastP
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastX
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastCLI
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.RPSBlast
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.TBlastN
- -show_gis
- getShowGIs() - function in org.veupathdb.lib.blast.common.TBlastX
- -show_gis
- getSoftMasking() - function in org.veupathdb.lib.blast.blastn.BlastN
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.blastp.BlastP
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.blastx.BlastX
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -soft_masking
<Boolean> - getSoftMasking() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -soft_masking
<Boolean> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastN
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastP
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastX
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastCLI
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.PSIBlast
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.RPSBlast
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.TBlastN
- -sorthits
<Integer> - getSortHits() - function in org.veupathdb.lib.blast.common.TBlastX
- -sorthits
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastN
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastP
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastX
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastCLI
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.RPSBlast
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.TBlastN
- -sorthsps
<Integer> - getSortHSPs() - function in org.veupathdb.lib.blast.common.TBlastX
- -sorthsps
<Integer> - getStart() - function in org.veupathdb.lib.blast.common.fields.QueryLocation
- getStart() - function in org.veupathdb.lib.blast.common.fields.SubjectLocation
- getStop() - function in org.veupathdb.lib.blast.common.fields.QueryLocation
- getStop() - function in org.veupathdb.lib.blast.common.fields.SubjectLocation
- getStrand() - function in org.veupathdb.lib.blast.blastn.BlastN
- -strand
<String> - getStrand() - function in org.veupathdb.lib.blast.blastx.BlastX
- -strand
<String> - getStrand() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -strand
<String> - getStrand() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -strand
<String> - getSubjectBestHit() - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject_besthit
- getSubjectBestHit() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject_besthit
- getSubjectFile() - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject
<File_In> - getSubjectFile() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject
<File_In> - getSubjectLocation() - function in org.veupathdb.lib.blast.blastn.BlastN
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.blastp.BlastP
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.blastx.BlastX
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -subject_loc
<String> - getSubjectLocation() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -subject_loc
<String> - getSumStats() - function in org.veupathdb.lib.blast.blastn.BlastN
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.blastx.BlastX
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -max_target_seqs
<Integer> - getSumStats() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -sum_stats
<Boolean> - getSumStats() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -sum_stats
<Boolean> - getTask() - function in org.veupathdb.lib.blast.blastn.BlastN
- -task
<String> - getTask() - function in org.veupathdb.lib.blast.blastp.BlastP
- -task
<String> - getTask() - function in org.veupathdb.lib.blast.blastx.BlastX
- -task
<String> - getTask() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -task
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastN
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastP
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastX
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.PSIBlast
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.TBlastN
- -taxidlist
<String> - getTaxIDListFile() - function in org.veupathdb.lib.blast.common.TBlastX
- -taxidlist
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.BlastN
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.BlastP
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.BlastX
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.PSIBlast
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.TBlastN
- -taxids
<String> - getTaxIDs() - function in org.veupathdb.lib.blast.common.TBlastX
- -taxids
<String> - getTemplateLength() - function in org.veupathdb.lib.blast.blastn.BlastN
- -template_length
<Integer> - getTemplateType() - function in org.veupathdb.lib.blast.blastn.BlastN
- -template_type
<String> - getThreshold() - function in org.veupathdb.lib.blast.blastp.BlastP
- -threshold
<Real> - getThreshold() - function in org.veupathdb.lib.blast.blastx.BlastX
- -threshold
<Real> - getThreshold() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -threshold
<Real> - getThreshold() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -threshold
<Real> - getThreshold() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -threshold
<Real> - getThreshold() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -threshold
<Real> - getTool() - function in org.veupathdb.lib.blast.common.BlastN
- getTool() - function in org.veupathdb.lib.blast.common.BlastP
- getTool() - function in org.veupathdb.lib.blast.common.BlastX
- getTool() - function in org.veupathdb.lib.blast.common.BlastCLI
- getTool() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- getTool() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- getTool() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- getTool() - function in org.veupathdb.lib.blast.common.DeltaBlast
- getTool() - function in org.veupathdb.lib.blast.common.BlastFormatter
- getTool() - function in org.veupathdb.lib.blast.common.PSIBlast
- getTool() - function in org.veupathdb.lib.blast.common.RPSBlast
- getTool() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- getTool() - function in org.veupathdb.lib.blast.common.TBlastN
- getTool() - function in org.veupathdb.lib.blast.common.TBlastX
- getType() - function in org.veupathdb.lib.blast.common.fields.OutFormat
- getUngappedAlignmentsOnly() - function in org.veupathdb.lib.blast.blastn.BlastN
- -ungapped
- getUngappedAlignmentsOnly() - function in org.veupathdb.lib.blast.blastp.BlastP
- -ungapped
- getUngappedAlignmentsOnly() - function in org.veupathdb.lib.blast.blastx.BlastX
- -ungapped
- getUngappedAlignmentsOnly() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -ungapped
- getUngappedAlignmentsOnly() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -ungapped
- getUseIndex() - function in org.veupathdb.lib.blast.blastn.BlastN
- -use_index
<Boolean> - getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.blastp.BlastP
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.blastx.BlastX
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.rpsblast.RPSBlast
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.rpstblastn.RPSTBlastN
- -use_sw_tback
- getUseSmithWatermanTraceback() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -use_sw_tback
- getValue() - function in org.veupathdb.lib.blast.BlastTool
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.FilteringDB
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.IndexName
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.MinRawGappedScore
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.NonGreedy
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.OffDiagonalRange
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.Penalty
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.PercentIdentity
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.Reward
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.SoftMaskingN
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.BlastNTask
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.BlastNTaskType
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.TemplateLength
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.TemplateLengthValue
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.TemplateType
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.TemplateTypeType
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.UseIndex
- getValue() - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerTaxID
- getValue() - function in org.veupathdb.lib.blast.blastp.field.BlastPTask
- getValue() - function in org.veupathdb.lib.blast.blastp.field.BlastPTaskType
- getValue() - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsP
- getValue() - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsPValue
- getValue() - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixP
- getValue() - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType
- getValue() - function in org.veupathdb.lib.blast.blastp.field.SoftMaskingP
- getValue() - function in org.veupathdb.lib.blast.blastp.field.WordSizeP
- getValue() - function in org.veupathdb.lib.blast.blastx.field.BlastXTask
- getValue() - function in org.veupathdb.lib.blast.blastx.field.BlastXTaskType
- getValue() - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsX
- getValue() - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsXValue
- getValue() - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixX
- getValue() - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType
- getValue() - function in org.veupathdb.lib.blast.blastx.field.SoftMaskingX
- getValue() - function in org.veupathdb.lib.blast.blastx.field.WordSizeX
- getValue() - function in org.veupathdb.lib.blast.common.fields.AutoCPUCores
- getValue() - function in org.veupathdb.lib.blast.common.fields.BestHitOverhang
- getValue() - function in org.veupathdb.lib.blast.common.fields.BestHitScoreEdge
- getValue() - function in org.veupathdb.lib.blast.common.fields.CullingLimit
- getValue() - function in org.veupathdb.lib.blast.common.fields.DBGenCode
- getValue() - function in org.veupathdb.lib.blast.common.fields.DBHardMask
- getValue() - function in org.veupathdb.lib.blast.common.fields.DBSize
- getValue() - function in org.veupathdb.lib.blast.common.fields.DBSoftMask
- getValue() - function in org.veupathdb.lib.blast.common.fields.EntrezQuery
- getValue() - function in org.veupathdb.lib.blast.common.fields.ExpectValue
- getValue() - function in org.veupathdb.lib.blast.common.fields.GapExtend
- getValue() - function in org.veupathdb.lib.blast.common.fields.GapOpen
- getValue() - function in org.veupathdb.lib.blast.common.fields.GapTrigger
- getValue() - function in org.veupathdb.lib.blast.common.fields.HTML
- getValue() - function in org.veupathdb.lib.blast.common.fields.HelpLong
- getValue() - function in org.veupathdb.lib.blast.common.fields.HelpShort
- getValue() - function in org.veupathdb.lib.blast.common.fields.InclusionEValueThreshold
- getValue() - function in org.veupathdb.lib.blast.common.fields.LineLength
- getValue() - function in org.veupathdb.lib.blast.common.fields.LowercaseMasking
- getValue() - function in org.veupathdb.lib.blast.common.fields.MaxHSPs
- getValue() - function in org.veupathdb.lib.blast.common.fields.MaxIntronLength
- getValue() - function in org.veupathdb.lib.blast.common.fields.MaxTargetSeqs
- getValue() - function in org.veupathdb.lib.blast.common.fields.MultiThreadingMode
- getValue() - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDs
- getValue() - function in org.veupathdb.lib.blast.common.fields.NumAlignments
- getValue() - function in org.veupathdb.lib.blast.common.fields.NumCPUCores
- getValue() - function in org.veupathdb.lib.blast.common.fields.NumDescriptions
- getValue() - function in org.veupathdb.lib.blast.common.fields.NumIterations
- getValue() - function in org.veupathdb.lib.blast.common.fields.FormatDelimiter
- getValue() - function in org.veupathdb.lib.blast.common.fields.FormatFields
- getValue() - function in org.veupathdb.lib.blast.common.fields.FormatType
- getValue() - function in org.veupathdb.lib.blast.common.fields.FormatField
- getValue() - function in org.veupathdb.lib.blast.common.fields.ParseDefLines
- getValue() - function in org.veupathdb.lib.blast.common.fields.PseudoCount
- getValue() - function in org.veupathdb.lib.blast.common.fields.QueryCoverageHSPPercent
- getValue() - function in org.veupathdb.lib.blast.common.fields.QueryGenCode
- getValue() - function in org.veupathdb.lib.blast.common.fields.Remote
- getValue() - function in org.veupathdb.lib.blast.common.fields.SaveEachPSSM
- getValue() - function in org.veupathdb.lib.blast.common.fields.SavePSSMAfterLastRound
- getValue() - function in org.veupathdb.lib.blast.common.fields.SearchSpace
- getValue() - function in org.veupathdb.lib.blast.common.fields.SeqIDList
- getValue() - function in org.veupathdb.lib.blast.common.fields.ShowGIs
- getValue() - function in org.veupathdb.lib.blast.common.fields.SortHSPs
- getValue() - function in org.veupathdb.lib.blast.common.fields.HSPSorting
- getValue() - function in org.veupathdb.lib.blast.common.fields.SortHits
- getValue() - function in org.veupathdb.lib.blast.common.fields.HitSorting
- getValue() - function in org.veupathdb.lib.blast.common.fields.Strand
- getValue() - function in org.veupathdb.lib.blast.common.fields.StrandType
- getValue() - function in org.veupathdb.lib.blast.common.fields.SubjectBestHit
- getValue() - function in org.veupathdb.lib.blast.common.fields.SumStats
- getValue() - function in org.veupathdb.lib.blast.common.fields.TaxIDs
- getValue() - function in org.veupathdb.lib.blast.common.fields.Threshold
- getValue() - function in org.veupathdb.lib.blast.common.fields.UngappedAlignmentsOnly
- getValue() - function in org.veupathdb.lib.blast.common.fields.UseSmithWatermanTraceback
- getValue() - function in org.veupathdb.lib.blast.common.fields.Version
- getValue() - function in org.veupathdb.lib.blast.common.fields.WindowSize
- getValue() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffUngapped
- getValue() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffPrelimGapped
- getValue() - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffFinalGapped
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDelta
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDeltaValue
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.DomainInclusionEValueThreshold
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDelta
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.RPSDB
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.ShowDomainHits
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.SoftMaskingDelta
- getValue() - function in org.veupathdb.lib.blast.deltablast.fields.WordSizeDelta
- getValue() - function in org.veupathdb.lib.blast.formatter.fields.RID
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSI
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSIValue
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.IgnoreMSAMaster
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.MSAMasterIndex
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSI
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.PHIPatternFile
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.SoftMaskingPSI
- getValue() - function in org.veupathdb.lib.blast.psiblast.fields.WordSizePSI
- getValue() - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPS
- getValue() - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPSValue
- getValue() - function in org.veupathdb.lib.blast.rpsblast.fields.SoftMaskingRPS
- getValue() - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTN
- getValue() - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTNValue
- getValue() - function in org.veupathdb.lib.blast.rpstblastn.fields.SoftMaskingRPSTN
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTN
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTNValue
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTN
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.SoftMaskingTN
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTask
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTaskValue
- getValue() - function in org.veupathdb.lib.blast.tblastn.fields.WordSizeTBlastN
- getValue() - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTX
- getValue() - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType
- getValue() - function in org.veupathdb.lib.blast.tblastx.fields.SoftMaskingTX
- getValue() - function in org.veupathdb.lib.blast.tblastx.fields.WordSizeTX
- getVersion() - function in org.veupathdb.lib.blast.common.BlastN
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastP
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastX
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastCLI
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.BlastFormatter
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.PSIBlast
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.RPSBlast
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.TBlastN
- -version
- getVersion() - function in org.veupathdb.lib.blast.common.TBlastX
- -version
- getWindow() - function in org.veupathdb.lib.blast.blastn.fields.Dust
- The window value for a value based Dust value.
- getWindow() - function in org.veupathdb.lib.blast.common.fields.SegP
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegX
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.Seg
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegDelta
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegPSI
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegRPS
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegRPSTN
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegTN
- SEG windowDefault =
12 - getWindow() - function in org.veupathdb.lib.blast.common.fields.SegTX
- SEG windowDefault =
12 - getWindowMaskerDBFile() - function in org.veupathdb.lib.blast.blastn.BlastN
- -window_masker_db
<String> - getWindowMaskerTaxID() - function in org.veupathdb.lib.blast.blastn.BlastN
- -window_masker_taxid
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastN
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastP
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastX
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastQueryBase
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastQueryWithIPG
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.BlastQueryWithLists
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.DeltaBlast
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.PSIBlast
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.RPSBlast
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.RPSTBlastN
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.TBlastN
- -window_size
<Integer> - getWindowSize() - function in org.veupathdb.lib.blast.common.TBlastX
- -window_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.blastp.BlastP
- -word_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.blastx.BlastX
- -word_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.deltablast.DeltaBlast
- -word_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.psiblast.PSIBlast
- -word_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.tblastn.TBlastN
- -word_size
<Integer> - getWordSize() - function in org.veupathdb.lib.blast.tblastx.TBlastX
- -word_size
<Integer> - GIList - class in org.veupathdb.lib.blast.common.fields
- -gilist
<String>Restrict search of database to list of GIs