blast-types/org.veupathdb.lib.blast.deltablast/DeltaBlast

DeltaBlast

interface DeltaBlast : BlastQueryWithLists

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

bestHitOverhang

abstract var bestHitOverhang: BestHitOverhang

-best_hit_overhang <Real>

bestHitScoreEdge

abstract var bestHitScoreEdge: BestHitScoreEdge

-best_hit_score_edge <Real>

compBasedStats

abstract var compBasedStats: CompBasedStatsDelta

-comp_based_stats <String>

cullingLimit

abstract var cullingLimit: CullingLimit

-culling_limit <Integer>

dbFile

abstract var dbFile: DBFile

-db <String>

dbSize

abstract var dbSize: DBSize

-dbsize <Int8>

domainInclusionEValueThreshold

abstract var domainInclusionEValueThreshold: DomainInclusionEValueThreshold

-domain_inclusion_ethresh <Real>

entrezQuery

abstract var entrezQuery: EntrezQuery

-entrez_query <String>

expectValue

abstract var expectValue: ExpectValue

-evalue <Real>

exportSearchStrategy

abstract var exportSearchStrategy: ExportSearchStrategy

-export_search_strategy <File_Out>

extensionDropoffFinalGapped

abstract var extensionDropoffFinalGapped: ExtensionDropoffFinalGapped

-xdrop_gap_final <Real>

extensionDropoffPrelimGapped

abstract var extensionDropoffPrelimGapped: ExtensionDropoffPrelimGapped

-xdrop_gap <Real>

extensionDropoffUngapped

abstract var extensionDropoffUngapped: ExtensionDropoffUngapped

-xdrop_ungap <Real>

gapExtend

abstract var gapExtend: GapExtend

-gapextend <Integer>

gapOpen

abstract var gapOpen: GapOpen

-gapopen <Integer>

gapTrigger

abstract var gapTrigger: GapTrigger

-gap_trigger <Real>

giListFile

abstract var giListFile: GIList

-gilist <String>

html

abstract var html: HTML

-html

importSearchStrategy

abstract var importSearchStrategy: ImportSearchStrategy

-import_search_strategy <File_In>

inclusionEValueThreshold

abstract var inclusionEValueThreshold: InclusionEValueThreshold

-inclusion_ethresh <Real>

lineLength

abstract var lineLength: LineLength

-line_length <Integer>

longHelp

abstract var longHelp: HelpLong

-help

lowercaseMasking

abstract var lowercaseMasking: LowercaseMasking

-lcase_masking

matrix

abstract var matrix: MatrixDelta

-matrix <String>

maxHSPs

abstract var maxHSPs: MaxHSPs

-max_hsps <Integer>

maxTargetSeqs

abstract var maxTargetSeqs: MaxTargetSeqs

-max_target_seqs <Integer>

negativeGIListFile

abstract var negativeGIListFile: NegativeGIList

-negative_gilist <String>

negativeSeqIDListFile

abstract var negativeSeqIDListFile: NegativeSeqIDList

-negative_seqidlist <String>

negativeTaxIDListFile

abstract var negativeTaxIDListFile: NegativeTaxIDList

-negative_taxidlist <String>

negativeTaxIDs

abstract var negativeTaxIDs: NegativeTaxIDs

-negative_taxids <String>

numAlignments

abstract var numAlignments: NumAlignments

-num_alignments <Integer>

numCPUCores

abstract var numCPUCores: NumCPUCores

-num_threads <Integer>

numDescriptions

abstract var numDescriptions: NumDescriptions

-num_descriptions <Integer>

numIterations

abstract var numIterations: NumIterations

-num_iterations <Integer>

outASCIIPSSMFile

abstract var outASCIIPSSMFile: OutASCIIPSSMFile

-out_ascii_pssm <File_Out>

outFile

abstract var outFile: OutFile

-out <File_Out>

outFormat

abstract var outFormat: OutFormat

-outfmt <String>

outPSSMFile

abstract var outPSSMFile: OutPSSMFile

-out_pssm <File_Out>

parseDefLines

abstract var parseDefLines: ParseDefLines

-parse_deflines

pseudoCount

abstract var pseudoCount: PseudoCount

-pseudocount <Integer>

queryCoverageHSPPercent

abstract var queryCoverageHSPPercent: QueryCoverageHSPPercent

-qcov_hsp_perc <Real>

queryFile

abstract var queryFile: QueryFile

-query <File_In>

queryLocation

abstract var queryLocation: QueryLocation

-query_loc <String>

remote

abstract var remote: Remote

-remote

rpsDB

abstract var rpsDB: RPSDB

-rpsdb <String>

saveEachPSSM

abstract var saveEachPSSM: SaveEachPSSM

-save_each_pssm

savePSSMAfterLastRound

abstract var savePSSMAfterLastRound: SavePSSMAfterLastRound

-save_pssm_after_last_round

searchSpace

abstract var searchSpace: SearchSpace

-searchsp <Int8>

seg

abstract var seg: SegDelta

-seg <String>

seqIDListFile

abstract var seqIDListFile: SeqIDList

-seqidlist <String>

shortHelp

abstract var shortHelp: HelpShort

-h

showDomainHits

abstract var showDomainHits: ShowDomainHits

-show_domain_hits

showGIs

abstract var showGIs: ShowGIs

-show_gis

softMasking

abstract var softMasking: SoftMaskingDelta

-soft_masking <Boolean>

sortHits

abstract var sortHits: SortHits

-sorthits <Integer>

sortHSPs

abstract var sortHSPs: SortHSPs

-sorthsps <Integer>

subjectBestHit

abstract var subjectBestHit: SubjectBestHit

-subject_besthit

subjectFile

abstract var subjectFile: SubjectFile

-subject <File_In>

subjectLocation

abstract var subjectLocation: SubjectLocation

-subject_loc <String>

sumStats

abstract var sumStats: SumStats

-max_target_seqs <Integer>

taxIDListFile

abstract var taxIDListFile: TaxIDList

-taxidlist <String>

taxIDs

abstract var taxIDs: TaxIDs

-taxids <String>

threshold

abstract var threshold: Threshold

-threshold <Real>

tool

abstract val tool: BlastTool

useSmithWatermanTraceback

abstract var useSmithWatermanTraceback: UseSmithWatermanTraceback

-use_sw_tback

version

abstract var version: Version

-version

windowSize

abstract var windowSize: WindowSize

-window_size <Integer>

wordSize

abstract var wordSize: WordSizeDelta

-word_size <Integer>