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- All Implemented Interfaces:
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org.veupathdb.lib.blast.serial.BlastCommand
public interface BlastCLI implements BlastCommand
Fields common to all BLAST+ tools.
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Method Summary
Modifier and Type Method Description abstract BlastToolgetTool()abstract HelpShortgetShortHelp()-h abstract UnitsetShortHelp(HelpShort shortHelp)-h abstract HelpLonggetLongHelp()-help abstract UnitsetLongHelp(HelpLong longHelp)-help abstract VersiongetVersion()-version abstract UnitsetVersion(Version version)-version abstract OutFilegetOutFile()-out <File_Out>abstract UnitsetOutFile(OutFile outFile)-out <File_Out>abstract OutFormatgetOutFormat()-outfmt <String>abstract UnitsetOutFormat(OutFormat outFormat)-outfmt <String>abstract ShowGIsgetShowGIs()-show_gis abstract UnitsetShowGIs(ShowGIs showGIs)-show_gis abstract NumDescriptionsgetNumDescriptions()-num_descriptions <Integer>abstract UnitsetNumDescriptions(NumDescriptions numDescriptions)-num_descriptions <Integer>abstract NumAlignmentsgetNumAlignments()-num_alignments <Integer>abstract UnitsetNumAlignments(NumAlignments numAlignments)-num_alignments <Integer>abstract LineLengthgetLineLength()-line_length <Integer>abstract UnitsetLineLength(LineLength lineLength)-line_length <Integer>abstract HTMLgetHtml()-html abstract UnitsetHtml(HTML html)-html abstract SortHitsgetSortHits()-sorthits <Integer>abstract UnitsetSortHits(SortHits sortHits)-sorthits <Integer>abstract SortHSPsgetSortHSPs()-sorthsps <Integer>abstract UnitsetSortHSPs(SortHSPs sortHSPs)-sorthsps <Integer>abstract MaxTargetSeqsgetMaxTargetSeqs()-max_target_seqs <Integer>abstract UnitsetMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)-max_target_seqs <Integer>abstract ParseDefLinesgetParseDefLines()-parse_deflines abstract UnitsetParseDefLines(ParseDefLines parseDefLines)-parse_deflines -
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Method Detail
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getShortHelp
abstract HelpShort getShortHelp()
-h
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setShortHelp
abstract Unit setShortHelp(HelpShort shortHelp)
-h
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getLongHelp
abstract HelpLong getLongHelp()
-help
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setLongHelp
abstract Unit setLongHelp(HelpLong longHelp)
-help
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getVersion
abstract Version getVersion()
-version
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setVersion
abstract Unit setVersion(Version version)
-version
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getOutFile
abstract OutFile getOutFile()
-out
<File_Out>
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setOutFile
abstract Unit setOutFile(OutFile outFile)
-out
<File_Out>
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getOutFormat
abstract OutFormat getOutFormat()
-outfmt
<String>
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setOutFormat
abstract Unit setOutFormat(OutFormat outFormat)
-outfmt
<String>
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getShowGIs
abstract ShowGIs getShowGIs()
-show_gis
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setShowGIs
abstract Unit setShowGIs(ShowGIs showGIs)
-show_gis
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getNumDescriptions
abstract NumDescriptions getNumDescriptions()
-num_descriptions
<Integer>
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setNumDescriptions
abstract Unit setNumDescriptions(NumDescriptions numDescriptions)
-num_descriptions
<Integer>
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getNumAlignments
abstract NumAlignments getNumAlignments()
-num_alignments
<Integer>
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setNumAlignments
abstract Unit setNumAlignments(NumAlignments numAlignments)
-num_alignments
<Integer>
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getLineLength
abstract LineLength getLineLength()
-line_length
<Integer>
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setLineLength
abstract Unit setLineLength(LineLength lineLength)
-line_length
<Integer>
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getSortHits
abstract SortHits getSortHits()
-sorthits
<Integer>
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setSortHits
abstract Unit setSortHits(SortHits sortHits)
-sorthits
<Integer>
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getSortHSPs
abstract SortHSPs getSortHSPs()
-sorthsps
<Integer>
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setSortHSPs
abstract Unit setSortHSPs(SortHSPs sortHSPs)
-sorthsps
<Integer>
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getMaxTargetSeqs
abstract MaxTargetSeqs getMaxTargetSeqs()
-max_target_seqs
<Integer>
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setMaxTargetSeqs
abstract Unit setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)
-max_target_seqs
<Integer>
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getParseDefLines
abstract ParseDefLines getParseDefLines()
-parse_deflines
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setParseDefLines
abstract Unit setParseDefLines(ParseDefLines parseDefLines)
-parse_deflines
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