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

Package org.veupathdb.lib.blast.common.fields

Types

AutoCPUCores

@JvmInline

value class AutoCPUCores(value: AutoCPUCoresValue) : BlastField

-num_threads <Integer, >=0>

AutoCPUCoresValue

enum AutoCPUCoresValue : Enum<AutoCPUCoresValue>

BestHitOverhang

@JvmInline

value class BestHitOverhang(value: Double) : BlastField

-best_hit_overhang <Real, (>0 and <0.5)>

BestHitScoreEdge

@JvmInline

value class BestHitScoreEdge(value: Double) : BlastField

-best_hit_score_edge <Real, (>0 and <0.5)>

CullingLimit

@JvmInline

value class CullingLimit(value: UInt) : BlastField

-culling_limit <Integer, >=0>

DBFile

@JvmInline

value class DBFile(file: String) : BlastField

-db <String>

DBGenCode

@JvmInline

value class DBGenCode(value: UByte) : BlastField

-db_gencode <Integer>

DBHardMask

@JvmInline

value class DBHardMask(value: String) : BlastField

-db_hard_mask <String>

DBSize

@JvmInline

value class DBSize(value: Byte) : BlastField

-dbsize <Int8>

DBSoftMask

@JvmInline

value class DBSoftMask(value: String) : BlastField

-db_soft_mask <String>

EntrezQuery

@JvmInline

value class EntrezQuery(value: String) : BlastField

-entrez_query <String>

ExpectValue

@JvmInline

value class ExpectValue(value: String) : BlastField

-evalue <Real>

ExportSearchStrategy

@JvmInline

value class ExportSearchStrategy(file: String) : BlastField

ExtensionDropoffFinalGapped

@JvmInline

value class ExtensionDropoffFinalGapped(value: Double) : BlastField

-xdrop_gap_final <Real>

ExtensionDropoffPrelimGapped

@JvmInline

value class ExtensionDropoffPrelimGapped(value: Double) : BlastField

-xdrop_gap <Real>

ExtensionDropoffUngapped

@JvmInline

value class ExtensionDropoffUngapped(value: Double) : BlastField

-xdrop_ungap <Real>

FormatDelimiter

@JvmInline

value class FormatDelimiter(value: String)

FormatField

enum FormatField : Enum<FormatField>

FormatFields

@JvmInline

value class FormatFields(value: List<FormatField>)

FormatType

enum FormatType : Enum<FormatType>

GapExtend

@JvmInline

value class GapExtend(value: Int) : BlastField

-gapextend <Integer>

GapOpen

@JvmInline

value class GapOpen(value: Int) : BlastField

-gapopen <Integer>

GapTrigger

@JvmInline

value class GapTrigger(value: Double) : BlastField

-gap_trigger <Real>

GIList

@JvmInline

value class GIList(file: String) : BlastField

-gilist <String>

HelpLong

@JvmInline

value class HelpLong(value: Boolean) : BlastField

-help

HelpShort

@JvmInline

value class HelpShort(value: Boolean) : BlastField

-h

HitSorting

enum HitSorting : Enum<HitSorting>

HSPSorting

enum HSPSorting : Enum<HSPSorting>

HTML

@JvmInline

value class HTML(value: Boolean) : BlastField

-html

ImportSearchStrategy

@JvmInline

value class ImportSearchStrategy(file: String) : BlastField

-import_search_strategy <File_In>

InclusionEValueThreshold

@JvmInline

value class InclusionEValueThreshold(value: Double) : BlastField

-inclusion_ethresh <Real>

InPSSMFile

@JvmInline

value class InPSSMFile(file: String) : BlastField

-in_pssm <File_In>

IPGList

@JvmInline

value class IPGList(file: String) : BlastField

-ipglist <String>

LineLength

@JvmInline

value class LineLength(value: UInt) : BlastField

-line_length <Integer, >=1>

LowercaseMasking

@JvmInline

value class LowercaseMasking(value: Boolean) : BlastField

-lcase_masking

MaxHSPs

@JvmInline

value class MaxHSPs(value: UInt) : BlastField

-max_hsps <Integer, >=1>

MaxIntronLength

@JvmInline

value class MaxIntronLength(value: UInt) : BlastField

-max_intron_length <Integer, >=0>

MaxTargetSeqs

@JvmInline

value class MaxTargetSeqs(value: UInt) : BlastField

-max_target_seqs <Integer, >=1>

MultiThreadingMode

@JvmInline

value class MultiThreadingMode(value: MultiThreadingModeValue) : BlastField

-mt_mode <Integer, (>=0 and =<1)>

MultiThreadingModeValue

enum MultiThreadingModeValue : Enum<MultiThreadingModeValue>

NegativeGIList

@JvmInline

value class NegativeGIList(file: String) : BlastField

-negative_gilist <String>

NegativeIPGList

@JvmInline

value class NegativeIPGList(file: String) : BlastField

-negative_ipglist <String>

NegativeSeqIDList

@JvmInline

value class NegativeSeqIDList(file: String) : BlastField

-negative_seqidlist <String>

NegativeTaxIDList

@JvmInline

value class NegativeTaxIDList(file: String) : BlastField

-negative_taxidlist <String>

NegativeTaxIDs

@JvmInline

value class NegativeTaxIDs(value: List<String>) : BlastField

-negative_taxids <String>

NumAlignments

@JvmInline

value class NumAlignments(value: UInt) : BlastField

-num_alignments <Integer, >=0>

NumCPUCores

@JvmInline

value class NumCPUCores(value: UByte) : BlastField

NumDescriptions

@JvmInline

value class NumDescriptions(value: UInt) : BlastField

-num_descriptions <Integer, >=0>

NumIterations

@JvmInline

value class NumIterations(value: UByte) : BlastField

-num_iterations <Integer, >=0>

OutASCIIPSSMFile

@JvmInline

value class OutASCIIPSSMFile(file: String) : BlastField

-out_ascii_pssm <File_Out>

OutFile

@JvmInline

value class OutFile(file: String) : BlastField

-out <File_Out>

OutFormat

data class OutFormat(type: FormatType, delimiter: FormatDelimiter, fields: FormatFields) : BlastField

-outfmt <String>

OutPSSMFile

@JvmInline

value class OutPSSMFile(file: String) : BlastField

-out_pssm <File_Out>

ParseDefLines

@JvmInline

value class ParseDefLines(value: Boolean) : BlastField

-parse_deflines

PseudoCount

@JvmInline

value class PseudoCount(value: Int) : BlastField

-pseudocount <Integer>

QueryCoverageHSPPercent

@JvmInline

value class QueryCoverageHSPPercent(value: Double) : BlastField

-qcov_hsp_perc <Real, 0..100>

QueryFile

@JvmInline

value class QueryFile(file: String) : BlastField

-query <File_In>

QueryGenCode

@JvmInline

value class QueryGenCode(value: UByte) : BlastField

-query_gencode <Integer>

QueryLocation

data class QueryLocation(start: UInt, stop: UInt) : BlastField

-query_loc <String>

Remote

@JvmInline

value class Remote(value: Boolean) : BlastField

-remote

SaveEachPSSM

@JvmInline

value class SaveEachPSSM(value: Boolean) : BlastField

-save_each_pssm

SavePSSMAfterLastRound

@JvmInline

value class SavePSSMAfterLastRound(value: Boolean) : BlastField

-save_pssm_after_last_round

SearchSpace

@JvmInline

value class SearchSpace(value: Byte) : BlastField

-searchsp <Int8, >=0>

Seg

interface Seg : BlastField

Low complexity region masker based on the SEG algorithm.

SeqIDList

@JvmInline

value class SeqIDList(value: String) : BlastField

-seqidlist <String>

ShowGIs

@JvmInline

value class ShowGIs(value: Boolean) : BlastField

-show_gis

SortHits

@JvmInline

value class SortHits(value: HitSorting) : BlastField

-sorthits <Integer, (>=0 and =<4)>

SortHSPs

@JvmInline

value class SortHSPs(value: HSPSorting) : BlastField

-sorthsps <Integer, (>=0 and =<4)>

Strand

@JvmInline

value class Strand(value: StrandType) : BlastField

-strand <String>

StrandType

enum StrandType : Enum<StrandType>

SubjectBestHit

@JvmInline

value class SubjectBestHit(value: Boolean) : BlastField

-subject_besthit

SubjectFile

@JvmInline

value class SubjectFile(file: String) : BlastField

-subject <File_In>

SubjectLocation

data class SubjectLocation(start: UInt, stop: UInt) : BlastField

-subject_loc <String>

SumStats

@JvmInline

value class SumStats(value: Boolean) : BlastField

-sum_stats <Boolean>

TaxIDList

@JvmInline

value class TaxIDList(file: String) : BlastField

-taxidlist <String>

TaxIDs

@JvmInline

value class TaxIDs(value: List<String>) : BlastField

-taxids <String>

Threshold

@JvmInline

value class Threshold(value: Double) : BlastField

-threshold <Real, >=0>

UngappedAlignmentsOnly

@JvmInline

value class UngappedAlignmentsOnly(value: Boolean) : BlastField

-ungapped

UseSmithWatermanTraceback

@JvmInline

value class UseSmithWatermanTraceback(value: Boolean) : BlastField

-use_sw_tback

Version

@JvmInline

value class Version(value: Boolean) : BlastField

-version

WindowSize

@JvmInline

value class WindowSize(value: UInt) : BlastField

-window_size <Integer, >=0>