All Implemented Interfaces:

org.veupathdb.lib.blast.common.BlastCLI , org.veupathdb.lib.blast.serial.BlastCommand
```
public interface BlastFormatter
 implements BlastCLI
                    
```
Stand-alone BLAST formatter client, version 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 RID`	`getRid()`	-rid `<String>`
`abstract Unit`	`setRid(RID rid)`	-rid `<String>`
`abstract Archive`	`getArchive()`	-archive `<File_In>`
`abstract Unit`	`setArchive(Archive archive)`	-archive `<File_In>`
`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

getRid
```
 abstract RID getRid()
```
-rid <String>

setRid
```
 abstract Unit setRid(RID rid)
```
-rid <String>

getArchive
```
 abstract Archive getArchive()
```
-archive <File_In>

setArchive

 abstract Unit setArchive(Archive archive)

-archive <File_In>

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 BlastFormatter

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

Method Detail

getRid

setRid

getArchive

setArchive

getTool

getShortHelp

setShortHelp

getLongHelp

setLongHelp

getVersion

setVersion

getOutFile

setOutFile

getOutFormat

setOutFormat

getShowGIs