All Implemented Interfaces:

org.veupathdb.lib.blast.common.BlastCLI , org.veupathdb.lib.blast.common.BlastQueryBase , org.veupathdb.lib.blast.serial.BlastCommand
```
public interface RPSTBlastN
 implements BlastQueryBase
                    
```
Translated Reverse Position Specific 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 QueryGenCode`	`getQueryGenCode()`	-query_gencode `<Integer>`
`abstract Unit`	`setQueryGenCode(QueryGenCode queryGenCode)`	-query_gencode `<Integer>`
`abstract Strand`	`getStrand()`	-strand `<String>`
`abstract Unit`	`setStrand(Strand strand)`	-strand `<String>`
`abstract CompBasedStatsRPSTN`	`getCompBasedStats()`	-comp_based_stats `<String>`
`abstract Unit`	`setCompBasedStats(CompBasedStatsRPSTN compBasedStats)`	-comp_based_stats `<String>`
`abstract SegRPSTN`	`getSeg()`	-seg `<String>`
`abstract Unit`	`setSeg(SegRPSTN seg)`	-seg `<String>`
`abstract SoftMaskingRPSTN`	`getSoftMasking()`	-soft_masking `<Boolean>`
`abstract Unit`	`setSoftMasking(SoftMaskingRPSTN softMasking)`	-soft_masking `<Boolean>`
`abstract QueryCoverageHSPPercent`	`getQueryCoverageHSPPercent()`	-qcov_hsp_perc `<Real>`
`abstract Unit`	`setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)`	-qcov_hsp_perc `<Real>`
`abstract SumStats`	`getSumStats()`	-sum_stats `<Boolean>`
`abstract Unit`	`setSumStats(SumStats sumStats)`	-sum_stats `<Boolean>`
`abstract ExtensionDropoffPrelimGapped`	`getExtensionDropoffPrelimGapped()`	-xdrop_gap `<Real>`
`abstract Unit`	`setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped extensionDropoffPrelimGapped)`	-xdrop_gap `<Real>`
`abstract ExtensionDropoffFinalGapped`	`getExtensionDropoffFinalGapped()`	-xdrop_gap_final `<Real>`
`abstract Unit`	`setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped extensionDropoffFinalGapped)`	-xdrop_gap_final `<Real>`
`abstract UngappedAlignmentsOnly`	`getUngappedAlignmentsOnly()`	-ungapped
`abstract Unit`	`setUngappedAlignmentsOnly(UngappedAlignmentsOnly ungappedAlignmentsOnly)`	-ungapped
`abstract AutoCPUCores`	`getAutoCPUCores()`	-num_threads `<Integer>`
`abstract Unit`	`setAutoCPUCores(AutoCPUCores autoCPUCores)`	-num_threads `<Integer>`
`abstract MultiThreadingMode`	`getMultiThreadingMode()`	-mt_mode `<Integer>`
`abstract Unit`	`setMultiThreadingMode(MultiThreadingMode multiThreadingMode)`	-mt_mode `<Integer>`
`abstract UseSmithWatermanTraceback`	`getUseSmithWatermanTraceback()`	-use_sw_tback
`abstract Unit`	`setUseSmithWatermanTraceback(UseSmithWatermanTraceback useSmithWatermanTraceback)`	-use_sw_tback
`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

getQueryGenCode

 abstract QueryGenCode getQueryGenCode()

-query_gencode <Integer>

setQueryGenCode

 abstract Unit setQueryGenCode(QueryGenCode queryGenCode)

-query_gencode <Integer>

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

setStrand

 abstract Unit setStrand(Strand strand)

-strand <String>

getCompBasedStats

 abstract CompBasedStatsRPSTN getCompBasedStats()

-comp_based_stats <String>

setCompBasedStats

 abstract Unit setCompBasedStats(CompBasedStatsRPSTN compBasedStats)

-comp_based_stats <String>

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

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

getSoftMasking

 abstract SoftMaskingRPSTN getSoftMasking()

-soft_masking <Boolean>

setSoftMasking

 abstract Unit setSoftMasking(SoftMaskingRPSTN softMasking)

-soft_masking <Boolean>

getQueryCoverageHSPPercent

 abstract QueryCoverageHSPPercent getQueryCoverageHSPPercent()

-qcov_hsp_perc <Real>

setQueryCoverageHSPPercent

 abstract Unit setQueryCoverageHSPPercent(QueryCoverageHSPPercent queryCoverageHSPPercent)

-qcov_hsp_perc <Real>

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

setSumStats

 abstract Unit setSumStats(SumStats sumStats)

-sum_stats <Boolean>

getExtensionDropoffPrelimGapped

 abstract ExtensionDropoffPrelimGapped getExtensionDropoffPrelimGapped()

-xdrop_gap <Real>

setExtensionDropoffPrelimGapped

 abstract Unit setExtensionDropoffPrelimGapped(ExtensionDropoffPrelimGapped extensionDropoffPrelimGapped)

-xdrop_gap <Real>

getExtensionDropoffFinalGapped

 abstract ExtensionDropoffFinalGapped getExtensionDropoffFinalGapped()

-xdrop_gap_final <Real>

setExtensionDropoffFinalGapped

 abstract Unit setExtensionDropoffFinalGapped(ExtensionDropoffFinalGapped extensionDropoffFinalGapped)

-xdrop_gap_final <Real>

getUngappedAlignmentsOnly

 abstract UngappedAlignmentsOnly getUngappedAlignmentsOnly()

-ungapped

setUngappedAlignmentsOnly

 abstract Unit setUngappedAlignmentsOnly(UngappedAlignmentsOnly ungappedAlignmentsOnly)

-ungapped

getAutoCPUCores

 abstract AutoCPUCores getAutoCPUCores()

-num_threads <Integer>

setAutoCPUCores

 abstract Unit setAutoCPUCores(AutoCPUCores autoCPUCores)

-num_threads <Integer>

getMultiThreadingMode

 abstract MultiThreadingMode getMultiThreadingMode()

-mt_mode <Integer>

setMultiThreadingMode

 abstract Unit setMultiThreadingMode(MultiThreadingMode multiThreadingMode)

-mt_mode <Integer>

getUseSmithWatermanTraceback

 abstract UseSmithWatermanTraceback getUseSmithWatermanTraceback()

-use_sw_tback

setUseSmithWatermanTraceback

 abstract Unit setUseSmithWatermanTraceback(UseSmithWatermanTraceback useSmithWatermanTraceback)

-use_sw_tback

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)