blast-types/org.veupathdb.lib.blast.common/BlastCLI

BlastCLI

interface BlastCLI : BlastCommand

Fields common to all BLAST+ tools.

Functions

toCliArray

abstract fun toCliArray(): Array<String>

Converts the current BlastCommand to an array of strings making up a CLI call.

toCliString

abstract fun toCliString(): String

Renders the current BlastCommand as a CLI call string.

toJson

abstract fun toJson(): ObjectNode

Serializes the current BlastCommand to a JSON ObjectNode.

validate

abstract fun validate(): ErrorMap

Validates this Blast+ config checking for flags that are incompatible and values that are out of range or invalid.

Properties

html

abstract var html: HTML

-html

lineLength

abstract var lineLength: LineLength

-line_length <Integer>

longHelp

abstract var longHelp: HelpLong

-help

maxTargetSeqs

abstract var maxTargetSeqs: MaxTargetSeqs

-max_target_seqs <Integer>

numAlignments

abstract var numAlignments: NumAlignments

-num_alignments <Integer>

numDescriptions

abstract var numDescriptions: NumDescriptions

-num_descriptions <Integer>

outFile

abstract var outFile: OutFile

-out <File_Out>

outFormat

abstract var outFormat: OutFormat

-outfmt <String>

parseDefLines

abstract var parseDefLines: ParseDefLines

-parse_deflines

shortHelp

abstract var shortHelp: HelpShort

-h

showGIs

abstract var showGIs: ShowGIs

-show_gis

sortHits

abstract var sortHits: SortHits

-sorthits <Integer>

sortHSPs

abstract var sortHSPs: SortHSPs

-sorthsps <Integer>

tool

abstract val tool: BlastTool

version

abstract var version: Version

-version

Inheritors

BlastQueryBase

BlastFormatter