A-index

A B C D E F G H I L M N O P Q R S T U V W Y

A

addError(String,String) - function in org.veupathdb.lib.blast.err.ErrorMap

Appends an error to this ErrorMap.

AlignedPartOfQuerySequence - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AlignedPartOfSubjectSequence - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AlignmentLength - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AllSubjectAccessions - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AllSubjectGIs - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AllSubjectSeqIDs - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

AllSubjectTitles - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.Dust

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.FilteringDB

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.IndexName

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.MinRawGappedScore

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.NonGreedy

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.OffDiagonalRange

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.Penalty

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.PercentIdentity

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.Reward

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.SoftMaskingN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.BlastNTask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.TemplateLength

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.TemplateType

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.UseIndex

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerDB

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerTaxID

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastp.field.BlastPTask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsP

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixP

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegP

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastp.field.SoftMaskingP

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastp.field.WordSizeP

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastx.field.BlastXTask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastx.field.SoftMaskingX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.blastx.field.WordSizeX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.AutoCPUCores

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.BestHitOverhang

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.BestHitScoreEdge

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.CullingLimit

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.DBFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.DBGenCode

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.DBHardMask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.DBSize

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.DBSoftMask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.EntrezQuery

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ExpectValue

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.GIList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.GapExtend

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.GapOpen

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.GapTrigger

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.HTML

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.HelpLong

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.HelpShort

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.IPGList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.InPSSMFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.InclusionEValueThreshold

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.LineLength

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.LowercaseMasking

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.MaxHSPs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.MaxIntronLength

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.MaxTargetSeqs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.MultiThreadingMode

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NegativeGIList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NegativeIPGList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NegativeSeqIDList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NumAlignments

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NumCPUCores

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NumDescriptions

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.NumIterations

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.OutASCIIPSSMFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.OutFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.OutFormat

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.OutPSSMFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ParseDefLines

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.PseudoCount

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.QueryCoverageHSPPercent

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.QueryFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.QueryGenCode

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.QueryLocation

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.Remote

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SaveEachPSSM

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SavePSSMAfterLastRound

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SearchSpace

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ImportSearchStrategy

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ExportSearchStrategy

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.Seg

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SeqIDList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ShowGIs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SortHSPs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SortHits

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.Strand

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SubjectBestHit

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SubjectFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SubjectLocation

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.SumStats

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.TaxIDList

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.TaxIDs

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.Threshold

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.UngappedAlignmentsOnly

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.UseSmithWatermanTraceback

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.Version

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.WindowSize

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffUngapped

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffPrelimGapped

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffFinalGapped

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDelta

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.DomainInclusionEValueThreshold

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDelta

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.RPSDB

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegDelta

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.ShowDomainHits

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.SoftMaskingDelta

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.deltablast.fields.WordSizeDelta

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.formatter.fields.Archive

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.formatter.fields.RID

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSI

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.IgnoreMSAMaster

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.InMSAFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.MSAMasterIndex

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSI

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.PHIPatternFile

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegPSI

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.SoftMaskingPSI

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.psiblast.fields.WordSizePSI

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPS

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegRPS

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.rpsblast.fields.SoftMaskingRPS

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegRPSTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.rpstblastn.fields.SoftMaskingRPSTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.BlastField

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastn.fields.SoftMaskingTN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTask

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastn.fields.WordSizeTBlastN

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.serial.SegTX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastx.fields.SoftMaskingTX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliParts(List) - function in org.veupathdb.lib.blast.tblastx.fields.WordSizeTX

Appends this field to the given MutableList only if it is not set to its default value.

appendCliSegment(TypeAliased(typeAlias=GenericTypeConstructor(dri=kotlin.text/StringBuilder///PointingToDeclaration/, projections=[], presentableName=null, extra=PropertyContainer(map={})), inner=GenericTypeConstructor(dri=java.lang/StringBuilder///PointingToDeclaration/, projections=[], presentableName=null, extra=PropertyContainer(map={})))) - function in org.veupathdb.lib.blast.serial.Dust

Appends this field to the given StringBuilder only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.Dust

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.FilteringDB

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.IndexName

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.MinRawGappedScore

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.NonGreedy

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.OffDiagonalRange

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.Penalty

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.PercentIdentity

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.Reward

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.SoftMaskingN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.BlastNTask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.TemplateLength

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.TemplateType

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.UseIndex

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerDB

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastn.fields.WindowMaskerTaxID

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastp.field.BlastPTask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastp.field.CompBasedStatsP

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastp.field.ScoringMatrixP

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegP

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastp.field.SoftMaskingP

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastp.field.WordSizeP

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastx.field.BlastXTask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastx.field.CompBasedStatsX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastx.field.ScoringMatrixX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastx.field.SoftMaskingX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.blastx.field.WordSizeX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.AutoCPUCores

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.BestHitOverhang

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.BestHitScoreEdge

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.CullingLimit

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.DBFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.DBGenCode

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.DBHardMask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.DBSize

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.DBSoftMask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.EntrezQuery

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ExpectValue

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.GIList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.GapExtend

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.GapOpen

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.GapTrigger

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.HTML

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.HelpLong

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.HelpShort

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.IPGList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.InPSSMFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.InclusionEValueThreshold

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.LineLength

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.LowercaseMasking

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.MaxHSPs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.MaxIntronLength

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.MaxTargetSeqs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.MultiThreadingMode

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NegativeGIList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NegativeIPGList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NegativeSeqIDList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NegativeTaxIDs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NumAlignments

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NumCPUCores

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NumDescriptions

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.NumIterations

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.OutASCIIPSSMFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.OutFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.OutFormat

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.FormatDelimiter

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.FormatFields

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.FormatType

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.OutPSSMFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ParseDefLines

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.PseudoCount

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.QueryCoverageHSPPercent

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.QueryFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.QueryGenCode

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.QueryLocation

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.Remote

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SaveEachPSSM

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SavePSSMAfterLastRound

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SearchSpace

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ImportSearchStrategy

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ExportSearchStrategy

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.Seg

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SeqIDList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ShowGIs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SortHSPs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SortHits

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.Strand

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SubjectBestHit

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SubjectFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SubjectLocation

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.SumStats

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.TaxIDList

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.TaxIDs

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.Threshold

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.UngappedAlignmentsOnly

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.UseSmithWatermanTraceback

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.Version

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.WindowSize

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffUngapped

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffPrelimGapped

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.common.fields.ExtensionDropoffFinalGapped

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDelta

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.DomainInclusionEValueThreshold

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.MatrixDelta

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.RPSDB

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegDelta

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.ShowDomainHits

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.SoftMaskingDelta

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.deltablast.fields.WordSizeDelta

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.formatter.fields.Archive

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.formatter.fields.RID

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSI

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.IgnoreMSAMaster

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.InMSAFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.MSAMasterIndex

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.MatrixPSI

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.PHIPatternFile

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegPSI

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.SoftMaskingPSI

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.psiblast.fields.WordSizePSI

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPS

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegRPS

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.rpsblast.fields.SoftMaskingRPS

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegRPSTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.rpstblastn.fields.SoftMaskingRPSTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.BlastField

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastn.fields.SoftMaskingTN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastn.fields.TBlastNTask

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastn.fields.WordSizeTBlastN

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.serial.SegTX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastx.fields.SoftMaskingTX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

appendJson(ObjectNode) - function in org.veupathdb.lib.blast.tblastx.fields.WordSizeTX

Appends this field to the given JSON ObjectNode only if it is not set to its default value.

Archive - class in org.veupathdb.lib.blast.formatter.fields

-archive <File_In>File containing BLAST Archive format in ASN.1 (i.e.

AutoCPUCores - class in org.veupathdb.lib.blast.common.fields

-num_threads <Integer, >=0>Number of threads to use in RPS BLAST search:

0 (auto = num of databases)
1 (disable)

Max number of threads = num of databasesDefault = 1

AutoCPUCoresValue - class in org.veupathdb.lib.blast.common.fields

A B C D E F G H I L M N O P Q R S T U V W Y