blast-types/org.veupathdb.lib.blast.rpsblast/RPSBlast

RPSBlast

interface RPSBlast : BlastQueryBase
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Reverse Position Specific BLAST 2.11.0+

Functions

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abstract fun toCliArray(): Array<String>
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Converts the current BlastCommand to an array of strings making up a CLI call.

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abstract fun toCliString(): String
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Renders the current BlastCommand as a CLI call string.

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abstract fun toJson(): ObjectNode
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Serializes the current BlastCommand to a JSON ObjectNode.

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abstract fun validate(): ErrorMap
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Validates this Blast+ config checking for flags that are incompatible and values that are out of range or invalid.

Properties

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abstract var autoCPUCores: AutoCPUCores
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-num_threads <Integer>

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abstract var bestHitOverhang: BestHitOverhang
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-best_hit_overhang <Real>

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abstract var bestHitScoreEdge: BestHitScoreEdge
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-best_hit_score_edge <Real>

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abstract var compBasedStats: CompBasedStatsRPS
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-comp_based_stats <String>

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abstract var cullingLimit: CullingLimit
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-culling_limit <Integer>

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abstract var dbFile: DBFile
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-db <String>

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abstract var dbSize: DBSize
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-dbsize <Int8>

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abstract var entrezQuery: EntrezQuery
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-entrez_query <String>

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abstract var expectValue: ExpectValue
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-evalue <Real>

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abstract var exportSearchStrategy: ExportSearchStrategy
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-export_search_strategy <File_Out>

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abstract var extensionDropoffFinalGapped: ExtensionDropoffFinalGapped
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-xdrop_gap_final <Real>

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abstract var extensionDropoffPrelimGapped: ExtensionDropoffPrelimGapped
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-xdrop_gap <Real>

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abstract var extensionDropoffUngapped: ExtensionDropoffUngapped
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-xdrop_ungap <Real>

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abstract var html: HTML
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-html

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abstract var importSearchStrategy: ImportSearchStrategy
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-import_search_strategy <File_In>

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abstract var lineLength: LineLength
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-line_length <Integer>

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abstract var longHelp: HelpLong
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-help

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abstract var lowercaseMasking: LowercaseMasking
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-lcase_masking

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abstract var maxHSPs: MaxHSPs
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-max_hsps <Integer>

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abstract var maxTargetSeqs: MaxTargetSeqs
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-max_target_seqs <Integer>

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abstract var multiThreadingMode: MultiThreadingMode
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-mt_mode <Integer>

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abstract var numAlignments: NumAlignments
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-num_alignments <Integer>

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abstract var numDescriptions: NumDescriptions
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-num_descriptions <Integer>

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abstract var outFile: OutFile
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-out <File_Out>

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abstract var outFormat: OutFormat
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-outfmt <String>

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abstract var parseDefLines: ParseDefLines
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-parse_deflines

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abstract var queryCoverageHSPPercent: QueryCoverageHSPPercent
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-qcov_hsp_perc <Real>

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abstract var queryFile: QueryFile
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-query <File_In>

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abstract var queryLocation: QueryLocation
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-query_loc <String>

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abstract var remote: Remote
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-remote

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abstract var searchSpace: SearchSpace
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-searchsp <Int8>

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abstract var seg: SegRPS
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-seg <String>

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abstract var shortHelp: HelpShort
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-h

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abstract var showGIs: ShowGIs
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-show_gis

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abstract var softMasking: SoftMaskingRPS
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-soft_masking <Boolean>

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abstract var sortHits: SortHits
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-sorthits <Integer>

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abstract var sortHSPs: SortHSPs
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-sorthsps <Integer>

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abstract var subjectBestHit: SubjectBestHit
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-subject_besthit

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abstract var sumStats: SumStats
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-sum_stats <Boolean>

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abstract val tool: BlastTool
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abstract var useSmithWatermanTraceback: UseSmithWatermanTraceback
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-use_sw_tback

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abstract var version: Version
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-version

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abstract var windowSize: WindowSize
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-window_size <Integer>