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- All Implemented Interfaces:
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org.veupathdb.lib.blast.common.BlastCLI,org.veupathdb.lib.blast.common.BlastQueryBase,org.veupathdb.lib.blast.common.BlastQueryWithLists,org.veupathdb.lib.blast.serial.BlastCommand
public interface BlastQueryWithIPG implements BlastQueryWithLists
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Method Summary
Modifier and Type Method Description abstract IPGListgetIpgListFile()-ipglist <String>abstract UnitsetIpgListFile(IPGList ipgListFile)-ipglist <String>abstract NegativeIPGListgetNegativeIPGListFile()-negative_ipglist <String>abstract UnitsetNegativeIPGListFile(NegativeIPGList negativeIPGListFile)-negative_ipglist <String>abstract GIListgetGiListFile()-gilist <String>abstract UnitsetGiListFile(GIList giListFile)-gilist <String>abstract NegativeGIListgetNegativeGIListFile()-negative_gilist <String>abstract UnitsetNegativeGIListFile(NegativeGIList negativeGIListFile)-negative_gilist <String>abstract SeqIDListgetSeqIDListFile()-seqidlist <String>abstract UnitsetSeqIDListFile(SeqIDList seqIDListFile)-seqidlist <String>abstract NegativeSeqIDListgetNegativeSeqIDListFile()-negative_seqidlist <String>abstract UnitsetNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)-negative_seqidlist <String>abstract TaxIDListgetTaxIDListFile()-taxidlist <String>abstract UnitsetTaxIDListFile(TaxIDList taxIDListFile)-taxidlist <String>abstract NegativeTaxIDListgetNegativeTaxIDListFile()-negative_taxidlist <String>abstract UnitsetNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)-negative_taxidlist <String>abstract TaxIDsgetTaxIDs()-taxids <String>abstract UnitsetTaxIDs(TaxIDs taxIDs)-taxids <String>abstract NegativeTaxIDsgetNegativeTaxIDs()-negative_taxids <String>abstract UnitsetNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)-negative_taxids <String>abstract QueryFilegetQueryFile()-query <File_In>abstract UnitsetQueryFile(QueryFile queryFile)-query <File_In>abstract QueryLocationgetQueryLocation()-query_loc <String>abstract UnitsetQueryLocation(QueryLocation queryLocation)-query_loc <String>abstract DBFilegetDbFile()-db <String>abstract UnitsetDbFile(DBFile dbFile)-db <String>abstract ExpectValuegetExpectValue()-evalue <Real>abstract UnitsetExpectValue(ExpectValue expectValue)-evalue <Real>abstract LowercaseMaskinggetLowercaseMasking()-lcase_masking abstract UnitsetLowercaseMasking(LowercaseMasking lowercaseMasking)-lcase_masking abstract EntrezQuerygetEntrezQuery()-entrez_query <String>abstract UnitsetEntrezQuery(EntrezQuery entrezQuery)-entrez_query <String>abstract MaxHSPsgetMaxHSPs()-max_hsps <Integer>abstract UnitsetMaxHSPs(MaxHSPs maxHSPs)-max_hsps <Integer>abstract DBSizegetDbSize()-dbsize <Int8>abstract UnitsetDbSize(DBSize dbSize)-dbsize <Int8>abstract SearchSpacegetSearchSpace()-searchsp <Int8>abstract UnitsetSearchSpace(SearchSpace searchSpace)-searchsp <Int8>abstract ImportSearchStrategygetImportSearchStrategy()-import_search_strategy <File_In>abstract UnitsetImportSearchStrategy(ImportSearchStrategy importSearchStrategy)-import_search_strategy <File_In>abstract ExportSearchStrategygetExportSearchStrategy()-export_search_strategy <File_Out>abstract UnitsetExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)-export_search_strategy <File_Out>abstract ExtensionDropoffUngappedgetExtensionDropoffUngapped()-xdrop_ungap <Real>abstract UnitsetExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)-xdrop_ungap <Real>abstract WindowSizegetWindowSize()-window_size <Integer>abstract UnitsetWindowSize(WindowSize windowSize)-window_size <Integer>abstract RemotegetRemote()-remote abstract UnitsetRemote(Remote remote)-remote abstract BlastToolgetTool()abstract HelpShortgetShortHelp()-h abstract UnitsetShortHelp(HelpShort shortHelp)-h abstract HelpLonggetLongHelp()-help abstract UnitsetLongHelp(HelpLong longHelp)-help abstract VersiongetVersion()-version abstract UnitsetVersion(Version version)-version abstract OutFilegetOutFile()-out <File_Out>abstract UnitsetOutFile(OutFile outFile)-out <File_Out>abstract OutFormatgetOutFormat()-outfmt <String>abstract UnitsetOutFormat(OutFormat outFormat)-outfmt <String>abstract ShowGIsgetShowGIs()-show_gis abstract UnitsetShowGIs(ShowGIs showGIs)-show_gis abstract NumDescriptionsgetNumDescriptions()-num_descriptions <Integer>abstract UnitsetNumDescriptions(NumDescriptions numDescriptions)-num_descriptions <Integer>abstract NumAlignmentsgetNumAlignments()-num_alignments <Integer>abstract UnitsetNumAlignments(NumAlignments numAlignments)-num_alignments <Integer>abstract LineLengthgetLineLength()-line_length <Integer>abstract UnitsetLineLength(LineLength lineLength)-line_length <Integer>abstract HTMLgetHtml()-html abstract UnitsetHtml(HTML html)-html abstract SortHitsgetSortHits()-sorthits <Integer>abstract UnitsetSortHits(SortHits sortHits)-sorthits <Integer>abstract SortHSPsgetSortHSPs()-sorthsps <Integer>abstract UnitsetSortHSPs(SortHSPs sortHSPs)-sorthsps <Integer>abstract MaxTargetSeqsgetMaxTargetSeqs()-max_target_seqs <Integer>abstract UnitsetMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)-max_target_seqs <Integer>abstract ParseDefLinesgetParseDefLines()-parse_deflines abstract UnitsetParseDefLines(ParseDefLines parseDefLines)-parse_deflines -
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Method Detail
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getIpgListFile
abstract IPGList getIpgListFile()
-ipglist
<String>
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setIpgListFile
abstract Unit setIpgListFile(IPGList ipgListFile)
-ipglist
<String>
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getNegativeIPGListFile
abstract NegativeIPGList getNegativeIPGListFile()
-negative_ipglist
<String>
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setNegativeIPGListFile
abstract Unit setNegativeIPGListFile(NegativeIPGList negativeIPGListFile)
-negative_ipglist
<String>
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getGiListFile
abstract GIList getGiListFile()
-gilist
<String>
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setGiListFile
abstract Unit setGiListFile(GIList giListFile)
-gilist
<String>
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getNegativeGIListFile
abstract NegativeGIList getNegativeGIListFile()
-negative_gilist
<String>
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setNegativeGIListFile
abstract Unit setNegativeGIListFile(NegativeGIList negativeGIListFile)
-negative_gilist
<String>
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getSeqIDListFile
abstract SeqIDList getSeqIDListFile()
-seqidlist
<String>
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setSeqIDListFile
abstract Unit setSeqIDListFile(SeqIDList seqIDListFile)
-seqidlist
<String>
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getNegativeSeqIDListFile
abstract NegativeSeqIDList getNegativeSeqIDListFile()
-negative_seqidlist
<String>
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setNegativeSeqIDListFile
abstract Unit setNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)
-negative_seqidlist
<String>
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getTaxIDListFile
abstract TaxIDList getTaxIDListFile()
-taxidlist
<String>
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setTaxIDListFile
abstract Unit setTaxIDListFile(TaxIDList taxIDListFile)
-taxidlist
<String>
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getNegativeTaxIDListFile
abstract NegativeTaxIDList getNegativeTaxIDListFile()
-negative_taxidlist
<String>
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setNegativeTaxIDListFile
abstract Unit setNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)
-negative_taxidlist
<String>
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getNegativeTaxIDs
abstract NegativeTaxIDs getNegativeTaxIDs()
-negative_taxids
<String>
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setNegativeTaxIDs
abstract Unit setNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)
-negative_taxids
<String>
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getQueryFile
abstract QueryFile getQueryFile()
-query
<File_In>
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setQueryFile
abstract Unit setQueryFile(QueryFile queryFile)
-query
<File_In>
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getQueryLocation
abstract QueryLocation getQueryLocation()
-query_loc
<String>
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setQueryLocation
abstract Unit setQueryLocation(QueryLocation queryLocation)
-query_loc
<String>
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getExpectValue
abstract ExpectValue getExpectValue()
-evalue
<Real>
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setExpectValue
abstract Unit setExpectValue(ExpectValue expectValue)
-evalue
<Real>
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getLowercaseMasking
abstract LowercaseMasking getLowercaseMasking()
-lcase_masking
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setLowercaseMasking
abstract Unit setLowercaseMasking(LowercaseMasking lowercaseMasking)
-lcase_masking
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getEntrezQuery
abstract EntrezQuery getEntrezQuery()
-entrez_query
<String>
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setEntrezQuery
abstract Unit setEntrezQuery(EntrezQuery entrezQuery)
-entrez_query
<String>
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getMaxHSPs
abstract MaxHSPs getMaxHSPs()
-max_hsps
<Integer>
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setMaxHSPs
abstract Unit setMaxHSPs(MaxHSPs maxHSPs)
-max_hsps
<Integer>
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getSearchSpace
abstract SearchSpace getSearchSpace()
-searchsp
<Int8>
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setSearchSpace
abstract Unit setSearchSpace(SearchSpace searchSpace)
-searchsp
<Int8>
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getImportSearchStrategy
abstract ImportSearchStrategy getImportSearchStrategy()
-import_search_strategy
<File_In>
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setImportSearchStrategy
abstract Unit setImportSearchStrategy(ImportSearchStrategy importSearchStrategy)
-import_search_strategy
<File_In>
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getExportSearchStrategy
abstract ExportSearchStrategy getExportSearchStrategy()
-export_search_strategy
<File_Out>
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setExportSearchStrategy
abstract Unit setExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)
-export_search_strategy
<File_Out>
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getExtensionDropoffUngapped
abstract ExtensionDropoffUngapped getExtensionDropoffUngapped()
-xdrop_ungap
<Real>
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setExtensionDropoffUngapped
abstract Unit setExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)
-xdrop_ungap
<Real>
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getWindowSize
abstract WindowSize getWindowSize()
-window_size
<Integer>
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setWindowSize
abstract Unit setWindowSize(WindowSize windowSize)
-window_size
<Integer>
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getShortHelp
abstract HelpShort getShortHelp()
-h
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setShortHelp
abstract Unit setShortHelp(HelpShort shortHelp)
-h
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getLongHelp
abstract HelpLong getLongHelp()
-help
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setLongHelp
abstract Unit setLongHelp(HelpLong longHelp)
-help
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getVersion
abstract Version getVersion()
-version
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setVersion
abstract Unit setVersion(Version version)
-version
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getOutFile
abstract OutFile getOutFile()
-out
<File_Out>
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setOutFile
abstract Unit setOutFile(OutFile outFile)
-out
<File_Out>
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getOutFormat
abstract OutFormat getOutFormat()
-outfmt
<String>
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setOutFormat
abstract Unit setOutFormat(OutFormat outFormat)
-outfmt
<String>
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getShowGIs
abstract ShowGIs getShowGIs()
-show_gis
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setShowGIs
abstract Unit setShowGIs(ShowGIs showGIs)
-show_gis
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getNumDescriptions
abstract NumDescriptions getNumDescriptions()
-num_descriptions
<Integer>
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setNumDescriptions
abstract Unit setNumDescriptions(NumDescriptions numDescriptions)
-num_descriptions
<Integer>
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getNumAlignments
abstract NumAlignments getNumAlignments()
-num_alignments
<Integer>
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setNumAlignments
abstract Unit setNumAlignments(NumAlignments numAlignments)
-num_alignments
<Integer>
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getLineLength
abstract LineLength getLineLength()
-line_length
<Integer>
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setLineLength
abstract Unit setLineLength(LineLength lineLength)
-line_length
<Integer>
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getSortHits
abstract SortHits getSortHits()
-sorthits
<Integer>
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setSortHits
abstract Unit setSortHits(SortHits sortHits)
-sorthits
<Integer>
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getSortHSPs
abstract SortHSPs getSortHSPs()
-sorthsps
<Integer>
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setSortHSPs
abstract Unit setSortHSPs(SortHSPs sortHSPs)
-sorthsps
<Integer>
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getMaxTargetSeqs
abstract MaxTargetSeqs getMaxTargetSeqs()
-max_target_seqs
<Integer>
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setMaxTargetSeqs
abstract Unit setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)
-max_target_seqs
<Integer>
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getParseDefLines
abstract ParseDefLines getParseDefLines()
-parse_deflines
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setParseDefLines
abstract Unit setParseDefLines(ParseDefLines parseDefLines)
-parse_deflines
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