All Implemented Interfaces:

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 TBlastX
 implements BlastQueryWithLists
                    
```
Translated Query-Translated Subject BLAST 2.11.0+

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`abstract Strand`	`getStrand()`	-strand `<String>`
`abstract Unit`	`setStrand(Strand strand)`	-strand `<String>`
`abstract QueryGenCode`	`getQueryGenCode()`	-query_gencode `<Integer>`
`abstract Unit`	`setQueryGenCode(QueryGenCode queryGenCode)`	-query_gencode `<Integer>`
`abstract WordSizeTX`	`getWordSize()`	-word_size `<Integer>`
`abstract Unit`	`setWordSize(WordSizeTX wordSize)`	-word_size `<Integer>`
`abstract MaxIntronLength`	`getMaxIntronLength()`	-max_intron_length `<Integer>`
`abstract Unit`	`setMaxIntronLength(MaxIntronLength maxIntronLength)`	-max_intron_length `<Integer>`
`abstract ScoringMatrixTX`	`getMatrix()`	-matrix `<String>`
`abstract Unit`	`setMatrix(ScoringMatrixTX matrix)`	-matrix `<String>`
`abstract Threshold`	`getThreshold()`	-threshold `<Real>`
`abstract Unit`	`setThreshold(Threshold threshold)`	-threshold `<Real>`
`abstract DBGenCode`	`getDbGenCode()`	-db_gencode `<Integer>`
`abstract Unit`	`setDbGenCode(DBGenCode dbGenCode)`	-db_gencode `<Integer>`
`abstract SubjectFile`	`getSubjectFile()`	-subject `<File_In>`
`abstract Unit`	`setSubjectFile(SubjectFile subjectFile)`	-subject `<File_In>`
`abstract SubjectLocation`	`getSubjectLocation()`	-subject_loc `<String>`
`abstract Unit`	`setSubjectLocation(SubjectLocation subjectLocation)`	-subject_loc `<String>`
`abstract SegTX`	`getSeg()`	-seg `<String>`
`abstract Unit`	`setSeg(SegTX seg)`	-seg `<String>`
`abstract SoftMaskingTX`	`getSoftMasking()`	-soft_masking `<Boolean>`
`abstract Unit`	`setSoftMasking(SoftMaskingTX softMasking)`	-soft_masking `<Boolean>`
`abstract DBSoftMask`	`getDbSoftMask()`	-db_soft_mask `<String>`
`abstract Unit`	`setDbSoftMask(DBSoftMask dbSoftMask)`	-db_soft_mask `<String>`
`abstract DBHardMask`	`getDbHardMask()`	-db_hard_mask `<String>`
`abstract Unit`	`setDbHardMask(DBHardMask dbHardMask)`	-db_hard_mask `<String>`
`abstract QueryCoverageHSPPercent`	`getQueryCoverageHSPPercent()`	-qcov_hsp_perc `<Real>`
`abstract Unit`	`setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)`	-qcov_hsp_perc `<Real>`
`abstract CullingLimit`	`getCullingLimit()`	-culling_limit `<Integer>`
`abstract Unit`	`setCullingLimit(CullingLimit cullingLimit)`	-culling_limit `<Integer>`
`abstract BestHitOverhang`	`getBestHitOverhang()`	-best_hit_overhang `<Real>`
`abstract Unit`	`setBestHitOverhang(BestHitOverhang bestHitOverhang)`	-best_hit_overhang `<Real>`
`abstract BestHitScoreEdge`	`getBestHitScoreEdge()`	-best_hit_score_edge `<Real>`
`abstract Unit`	`setBestHitScoreEdge(BestHitScoreEdge bestHitScoreEdge)`	-best_hit_score_edge `<Real>`
`abstract SubjectBestHit`	`getSubjectBestHit()`	-subject_besthit
`abstract Unit`	`setSubjectBestHit(SubjectBestHit subjectBestHit)`	-subject_besthit
`abstract SumStats`	`getSumStats()`	-sum_stats `<Boolean>`
`abstract Unit`	`setSumStats(SumStats sumStats)`	-sum_stats `<Boolean>`
`abstract NumCPUCores`	`getNumCPUCores()`	-num_threads `<Integer>`
`abstract Unit`	`setNumCPUCores(NumCPUCores numCPUCores)`	-num_threads `<Integer>`
`abstract GIList`	`getGiListFile()`	-gilist `<String>`
`abstract Unit`	`setGiListFile(GIList giListFile)`	-gilist `<String>`
`abstract NegativeGIList`	`getNegativeGIListFile()`	-negative_gilist `<String>`
`abstract Unit`	`setNegativeGIListFile(NegativeGIList negativeGIListFile)`	-negative_gilist `<String>`
`abstract SeqIDList`	`getSeqIDListFile()`	-seqidlist `<String>`
`abstract Unit`	`setSeqIDListFile(SeqIDList seqIDListFile)`	-seqidlist `<String>`
`abstract NegativeSeqIDList`	`getNegativeSeqIDListFile()`	-negative_seqidlist `<String>`
`abstract Unit`	`setNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)`	-negative_seqidlist `<String>`
`abstract TaxIDList`	`getTaxIDListFile()`	-taxidlist `<String>`
`abstract Unit`	`setTaxIDListFile(TaxIDList taxIDListFile)`	-taxidlist `<String>`
`abstract NegativeTaxIDList`	`getNegativeTaxIDListFile()`	-negative_taxidlist `<String>`
`abstract Unit`	`setNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)`	-negative_taxidlist `<String>`
`abstract TaxIDs`	`getTaxIDs()`	-taxids `<String>`
`abstract Unit`	`setTaxIDs(TaxIDs taxIDs)`	-taxids `<String>`
`abstract NegativeTaxIDs`	`getNegativeTaxIDs()`	-negative_taxids `<String>`
`abstract Unit`	`setNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)`	-negative_taxids `<String>`
`abstract QueryFile`	`getQueryFile()`	-query `<File_In>`
`abstract Unit`	`setQueryFile(QueryFile queryFile)`	-query `<File_In>`
`abstract QueryLocation`	`getQueryLocation()`	-query_loc `<String>`
`abstract Unit`	`setQueryLocation(QueryLocation queryLocation)`	-query_loc `<String>`
`abstract DBFile`	`getDbFile()`	-db `<String>`
`abstract Unit`	`setDbFile(DBFile dbFile)`	-db `<String>`
`abstract ExpectValue`	`getExpectValue()`	-evalue `<Real>`
`abstract Unit`	`setExpectValue(ExpectValue expectValue)`	-evalue `<Real>`
`abstract LowercaseMasking`	`getLowercaseMasking()`	-lcase_masking
`abstract Unit`	`setLowercaseMasking(LowercaseMasking lowercaseMasking)`	-lcase_masking
`abstract EntrezQuery`	`getEntrezQuery()`	-entrez_query `<String>`
`abstract Unit`	`setEntrezQuery(EntrezQuery entrezQuery)`	-entrez_query `<String>`
`abstract MaxHSPs`	`getMaxHSPs()`	-max_hsps `<Integer>`
`abstract Unit`	`setMaxHSPs(MaxHSPs maxHSPs)`	-max_hsps `<Integer>`
`abstract DBSize`	`getDbSize()`	-dbsize `<Int8>`
`abstract Unit`	`setDbSize(DBSize dbSize)`	-dbsize `<Int8>`
`abstract SearchSpace`	`getSearchSpace()`	-searchsp `<Int8>`
`abstract Unit`	`setSearchSpace(SearchSpace searchSpace)`	-searchsp `<Int8>`
`abstract ImportSearchStrategy`	`getImportSearchStrategy()`	-import_search_strategy `<File_In>`
`abstract Unit`	`setImportSearchStrategy(ImportSearchStrategy importSearchStrategy)`	-import_search_strategy `<File_In>`
`abstract ExportSearchStrategy`	`getExportSearchStrategy()`	-export_search_strategy `<File_Out>`
`abstract Unit`	`setExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)`	-export_search_strategy `<File_Out>`
`abstract ExtensionDropoffUngapped`	`getExtensionDropoffUngapped()`	-xdrop_ungap `<Real>`
`abstract Unit`	`setExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)`	-xdrop_ungap `<Real>`
`abstract WindowSize`	`getWindowSize()`	-window_size `<Integer>`
`abstract Unit`	`setWindowSize(WindowSize windowSize)`	-window_size `<Integer>`
`abstract Remote`	`getRemote()`	-remote
`abstract Unit`	`setRemote(Remote remote)`	-remote
`abstract BlastTool`	`getTool()`
`abstract HelpShort`	`getShortHelp()`	-h
`abstract Unit`	`setShortHelp(HelpShort shortHelp)`	-h
`abstract HelpLong`	`getLongHelp()`	-help
`abstract Unit`	`setLongHelp(HelpLong longHelp)`	-help
`abstract Version`	`getVersion()`	-version
`abstract Unit`	`setVersion(Version version)`	-version
`abstract OutFile`	`getOutFile()`	-out `<File_Out>`
`abstract Unit`	`setOutFile(OutFile outFile)`	-out `<File_Out>`
`abstract OutFormat`	`getOutFormat()`	-outfmt `<String>`
`abstract Unit`	`setOutFormat(OutFormat outFormat)`	-outfmt `<String>`
`abstract ShowGIs`	`getShowGIs()`	-show_gis
`abstract Unit`	`setShowGIs(ShowGIs showGIs)`	-show_gis
`abstract NumDescriptions`	`getNumDescriptions()`	-num_descriptions `<Integer>`
`abstract Unit`	`setNumDescriptions(NumDescriptions numDescriptions)`	-num_descriptions `<Integer>`
`abstract NumAlignments`	`getNumAlignments()`	-num_alignments `<Integer>`
`abstract Unit`	`setNumAlignments(NumAlignments numAlignments)`	-num_alignments `<Integer>`
`abstract LineLength`	`getLineLength()`	-line_length `<Integer>`
`abstract Unit`	`setLineLength(LineLength lineLength)`	-line_length `<Integer>`
`abstract HTML`	`getHtml()`	-html
`abstract Unit`	`setHtml(HTML html)`	-html
`abstract SortHits`	`getSortHits()`	-sorthits `<Integer>`
`abstract Unit`	`setSortHits(SortHits sortHits)`	-sorthits `<Integer>`
`abstract SortHSPs`	`getSortHSPs()`	-sorthsps `<Integer>`
`abstract Unit`	`setSortHSPs(SortHSPs sortHSPs)`	-sorthsps `<Integer>`
`abstract MaxTargetSeqs`	`getMaxTargetSeqs()`	-max_target_seqs `<Integer>`
`abstract Unit`	`setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)`	-max_target_seqs `<Integer>`
`abstract ParseDefLines`	`getParseDefLines()`	-parse_deflines
`abstract Unit`	`setParseDefLines(ParseDefLines parseDefLines)`	-parse_deflines

Methods inherited from class org.veupathdb.lib.blast.common.BlastCLI
toCliArray, toCliString, toJson, validate
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Method Detail

getStrand
```
 abstract Strand getStrand()
```
-strand <String>

setStrand

 abstract Unit setStrand(Strand strand)

-strand <String>

getQueryGenCode

 abstract QueryGenCode getQueryGenCode()

-query_gencode <Integer>

setQueryGenCode

 abstract Unit setQueryGenCode(QueryGenCode queryGenCode)

-query_gencode <Integer>

getWordSize
```
 abstract WordSizeTX getWordSize()
```
-word_size <Integer>

setWordSize

 abstract Unit setWordSize(WordSizeTX wordSize)

-word_size <Integer>

getMaxIntronLength

 abstract MaxIntronLength getMaxIntronLength()

-max_intron_length <Integer>

setMaxIntronLength

 abstract Unit setMaxIntronLength(MaxIntronLength maxIntronLength)

-max_intron_length <Integer>

getMatrix
```
 abstract ScoringMatrixTX getMatrix()
```
-matrix <String>

setMatrix

 abstract Unit setMatrix(ScoringMatrixTX matrix)

-matrix <String>

getThreshold
```
 abstract Threshold getThreshold()
```
-threshold <Real>

setThreshold

 abstract Unit setThreshold(Threshold threshold)

-threshold <Real>

getDbGenCode
```
 abstract DBGenCode getDbGenCode()
```
-db_gencode <Integer>

setDbGenCode

 abstract Unit setDbGenCode(DBGenCode dbGenCode)

-db_gencode <Integer>

getSubjectFile
```
 abstract SubjectFile getSubjectFile()
```
-subject <File_In>

setSubjectFile

 abstract Unit setSubjectFile(SubjectFile subjectFile)

-subject <File_In>

getSubjectLocation

 abstract SubjectLocation getSubjectLocation()

-subject_loc <String>

setSubjectLocation

 abstract Unit setSubjectLocation(SubjectLocation subjectLocation)

-subject_loc <String>

getSeg
```
 abstract SegTX getSeg()
```
-seg <String>

setSeg
```
 abstract Unit setSeg(SegTX seg)
```
-seg <String>

getSoftMasking

 abstract SoftMaskingTX getSoftMasking()

-soft_masking <Boolean>

setSoftMasking

 abstract Unit setSoftMasking(SoftMaskingTX softMasking)

-soft_masking <Boolean>

getDbSoftMask
```
 abstract DBSoftMask getDbSoftMask()
```
-db_soft_mask <String>

setDbSoftMask

 abstract Unit setDbSoftMask(DBSoftMask dbSoftMask)

-db_soft_mask <String>

getDbHardMask
```
 abstract DBHardMask getDbHardMask()
```
-db_hard_mask <String>

setDbHardMask

 abstract Unit setDbHardMask(DBHardMask dbHardMask)

-db_hard_mask <String>

getQueryCoverageHSPPercent

 abstract QueryCoverageHSPPercent getQueryCoverageHSPPercent()

-qcov_hsp_perc <Real>

setQueryCoverageHSPPercent

 abstract Unit setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)

-qcov_hsp_perc <Real>

getCullingLimit

 abstract CullingLimit getCullingLimit()

-culling_limit <Integer>

setCullingLimit

 abstract Unit setCullingLimit(CullingLimit cullingLimit)

-culling_limit <Integer>

getBestHitOverhang

 abstract BestHitOverhang getBestHitOverhang()

-best_hit_overhang <Real>

setBestHitOverhang

 abstract Unit setBestHitOverhang(BestHitOverhang bestHitOverhang)

-best_hit_overhang <Real>

getBestHitScoreEdge

 abstract BestHitScoreEdge getBestHitScoreEdge()

-best_hit_score_edge <Real>

setBestHitScoreEdge

 abstract Unit setBestHitScoreEdge(BestHitScoreEdge bestHitScoreEdge)

-best_hit_score_edge <Real>

getSubjectBestHit

 abstract SubjectBestHit getSubjectBestHit()

-subject_besthit

setSubjectBestHit

 abstract Unit setSubjectBestHit(SubjectBestHit subjectBestHit)

-subject_besthit

getSumStats
```
 abstract SumStats getSumStats()
```
-sum_stats <Boolean>

setSumStats

 abstract Unit setSumStats(SumStats sumStats)

-sum_stats <Boolean>

getNumCPUCores
```
 abstract NumCPUCores getNumCPUCores()
```
-num_threads <Integer>

setNumCPUCores

 abstract Unit setNumCPUCores(NumCPUCores numCPUCores)

-num_threads <Integer>

getGiListFile
```
 abstract GIList getGiListFile()
```
-gilist <String>

setGiListFile

 abstract Unit setGiListFile(GIList giListFile)

-gilist <String>

getNegativeGIListFile

 abstract NegativeGIList getNegativeGIListFile()

-negative_gilist <String>

setNegativeGIListFile

 abstract Unit setNegativeGIListFile(NegativeGIList negativeGIListFile)

-negative_gilist <String>

getSeqIDListFile
```
 abstract SeqIDList getSeqIDListFile()
```
-seqidlist <String>

setSeqIDListFile

 abstract Unit setSeqIDListFile(SeqIDList seqIDListFile)

-seqidlist <String>

getNegativeSeqIDListFile

 abstract NegativeSeqIDList getNegativeSeqIDListFile()

-negative_seqidlist <String>

setNegativeSeqIDListFile

 abstract Unit setNegativeSeqIDListFile(NegativeSeqIDList negativeSeqIDListFile)

-negative_seqidlist <String>

getTaxIDListFile
```
 abstract TaxIDList getTaxIDListFile()
```
-taxidlist <String>

setTaxIDListFile

 abstract Unit setTaxIDListFile(TaxIDList taxIDListFile)

-taxidlist <String>

getNegativeTaxIDListFile

 abstract NegativeTaxIDList getNegativeTaxIDListFile()

-negative_taxidlist <String>

setNegativeTaxIDListFile

 abstract Unit setNegativeTaxIDListFile(NegativeTaxIDList negativeTaxIDListFile)

-negative_taxidlist <String>

getTaxIDs
```
 abstract TaxIDs getTaxIDs()
```
-taxids <String>

setTaxIDs

 abstract Unit setTaxIDs(TaxIDs taxIDs)

-taxids <String>

getNegativeTaxIDs

 abstract NegativeTaxIDs getNegativeTaxIDs()

-negative_taxids <String>

setNegativeTaxIDs

 abstract Unit setNegativeTaxIDs(NegativeTaxIDs negativeTaxIDs)

-negative_taxids <String>

getQueryFile
```
 abstract QueryFile getQueryFile()
```
-query <File_In>

setQueryFile

 abstract Unit setQueryFile(QueryFile queryFile)

-query <File_In>

getQueryLocation

 abstract QueryLocation getQueryLocation()

-query_loc <String>

setQueryLocation

 abstract Unit setQueryLocation(QueryLocation queryLocation)

-query_loc <String>

getDbFile
```
 abstract DBFile getDbFile()
```
-db <String>

setDbFile

 abstract Unit setDbFile(DBFile dbFile)

-db <String>

getExpectValue
```
 abstract ExpectValue getExpectValue()
```
-evalue <Real>

setExpectValue

 abstract Unit setExpectValue(ExpectValue expectValue)

-evalue <Real>

getLowercaseMasking

 abstract LowercaseMasking getLowercaseMasking()

-lcase_masking

setLowercaseMasking

 abstract Unit setLowercaseMasking(LowercaseMasking lowercaseMasking)

-lcase_masking

getEntrezQuery
```
 abstract EntrezQuery getEntrezQuery()
```
-entrez_query <String>

setEntrezQuery

 abstract Unit setEntrezQuery(EntrezQuery entrezQuery)

-entrez_query <String>

getMaxHSPs
```
 abstract MaxHSPs getMaxHSPs()
```
-max_hsps <Integer>

setMaxHSPs

 abstract Unit setMaxHSPs(MaxHSPs maxHSPs)

-max_hsps <Integer>

getDbSize
```
 abstract DBSize getDbSize()
```
-dbsize <Int8>

setDbSize

 abstract Unit setDbSize(DBSize dbSize)

-dbsize <Int8>

getSearchSpace
```
 abstract SearchSpace getSearchSpace()
```
-searchsp <Int8>

setSearchSpace

 abstract Unit setSearchSpace(SearchSpace searchSpace)

-searchsp <Int8>

getImportSearchStrategy

 abstract ImportSearchStrategy getImportSearchStrategy()

-import_search_strategy <File_In>

setImportSearchStrategy

 abstract Unit setImportSearchStrategy(ImportSearchStrategy importSearchStrategy)

-import_search_strategy <File_In>

getExportSearchStrategy

 abstract ExportSearchStrategy getExportSearchStrategy()

-export_search_strategy <File_Out>

setExportSearchStrategy

 abstract Unit setExportSearchStrategy(ExportSearchStrategy exportSearchStrategy)

-export_search_strategy <File_Out>

getExtensionDropoffUngapped

 abstract ExtensionDropoffUngapped getExtensionDropoffUngapped()

-xdrop_ungap <Real>

setExtensionDropoffUngapped

 abstract Unit setExtensionDropoffUngapped(ExtensionDropoffUngapped extensionDropoffUngapped)

-xdrop_ungap <Real>

getWindowSize
```
 abstract WindowSize getWindowSize()
```
-window_size <Integer>

setWindowSize

 abstract Unit setWindowSize(WindowSize windowSize)

-window_size <Integer>

getRemote
```
 abstract Remote getRemote()
```
-remote

setRemote

 abstract Unit setRemote(Remote remote)

-remote

getTool
```
 abstract BlastTool getTool()
```

getShortHelp
```
 abstract HelpShort getShortHelp()
```
-h

setShortHelp

 abstract Unit setShortHelp(HelpShort shortHelp)

-h

getLongHelp
```
 abstract HelpLong getLongHelp()
```
-help

setLongHelp

 abstract Unit setLongHelp(HelpLong longHelp)

-help

getVersion
```
 abstract Version getVersion()
```
-version

setVersion

 abstract Unit setVersion(Version version)

-version

getOutFile
```
 abstract OutFile getOutFile()
```
-out <File_Out>

setOutFile

 abstract Unit setOutFile(OutFile outFile)

-out <File_Out>

getOutFormat
```
 abstract OutFormat getOutFormat()
```
-outfmt <String>

setOutFormat

 abstract Unit setOutFormat(OutFormat outFormat)

-outfmt <String>

getShowGIs
```
 abstract ShowGIs getShowGIs()
```
-show_gis

setShowGIs

 abstract Unit setShowGIs(ShowGIs showGIs)

-show_gis

getNumDescriptions

 abstract NumDescriptions getNumDescriptions()

-num_descriptions <Integer>

setNumDescriptions

 abstract Unit setNumDescriptions(NumDescriptions numDescriptions)

-num_descriptions <Integer>

getNumAlignments

 abstract NumAlignments getNumAlignments()

-num_alignments <Integer>

setNumAlignments

 abstract Unit setNumAlignments(NumAlignments numAlignments)

-num_alignments <Integer>

getLineLength
```
 abstract LineLength getLineLength()
```
-line_length <Integer>

setLineLength

 abstract Unit setLineLength(LineLength lineLength)

-line_length <Integer>

getHtml
```
 abstract HTML getHtml()
```
-html

setHtml
```
 abstract Unit setHtml(HTML html)
```
-html

getSortHits
```
 abstract SortHits getSortHits()
```
-sorthits <Integer>

setSortHits

 abstract Unit setSortHits(SortHits sortHits)

-sorthits <Integer>

getSortHSPs
```
 abstract SortHSPs getSortHSPs()
```
-sorthsps <Integer>

setSortHSPs

 abstract Unit setSortHSPs(SortHSPs sortHSPs)

-sorthsps <Integer>

getMaxTargetSeqs

 abstract MaxTargetSeqs getMaxTargetSeqs()

-max_target_seqs <Integer>

setMaxTargetSeqs

 abstract Unit setMaxTargetSeqs(MaxTargetSeqs maxTargetSeqs)

-max_target_seqs <Integer>

getParseDefLines

 abstract ParseDefLines getParseDefLines()

-parse_deflines

setParseDefLines

 abstract Unit setParseDefLines(ParseDefLines parseDefLines)

-parse_deflines

Interface TBlastX

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class org.veupathdb.lib.blast.common.BlastCLI

Methods inherited from class java.lang.Object

Constructor Detail