Rev Language Reference

AbstractHomologousDiscreteCharacterData

Methods

  • [](Natural index)
  • addMissingTaxa(String taxon)
  • applyMissingSitesMask(AbstractHomologousDiscreteCharacterData ref)
  • chartype()
  • computeMultinomialProfileLikelihood()
  • computeSiteFrequencySpectrum(Bool folded, String ambiguityTreatment)
  • computeStateFrequencies()
  • excludeAll()
  • excludeCharacter(Natural pos)
  • excludeCharacter(Natural[] ...)
  • excludeTaxa(String taxon)
  • excludeTaxa(String[] taxa)
  • expandCharacters(Natural factor)
  • filename()
  • getEmpiricalBaseFrequencies()
  • getIncludedCharacterIndices()
  • getNumInvariantSites(Bool excludeAmbiguous)
  • getNumStatesVector()
  • getPairwiseDifference(Bool excludeAmbiguous)
  • getStateDescriptions()
  • includeAll()
  • includeCharacter(Natural ...)
  • includeCharacter(Natural[] ...)
  • includeTaxa(String name)
  • includeTaxa(String[] names)
  • isHomologous()
  • isResolved(Natural taxonIndex, Natural charIndex)
  • isSequenceMissing(String name)
  • maxGcContent(Bool excludeAmbiguous)
  • maxInvariableBlockLength(Bool excludeAmbiguous)
  • maxPairwiseDifference(Bool excludeAmbiguous)
  • maxStates()
  • maxVariableBlockLength(Bool excludeAmbiguous)
  • meanGcContent(Bool excludeAmbiguous)
  • meanGcContentByCodonPosition(Natural index, Bool excludeAmbiguous)
  • minGcContent(Bool excludeAmbiguous)
  • minPairwiseDifference(Bool excludeAmbiguous)
  • names()
  • nchar()
  • ntaxa()
  • numInvariableBlocks(Bool excludeAmbiguous)
  • numTaxaMissingSequence(Probability x)
  • percentageMissing(String name)
  • removeRandomSites(Probability fraction)
  • removeTaxa(String name)
  • removeTaxa(String[] names)
  • setCodonPartition(Natural ...)
  • setCodonPartition(Natural[] ...)
  • setHomeologPhase(String data_name, String tip_name)
  • setNumStatesPartition(Natural ...)
  • setTaxonName(String current, String new)
  • setTaxonObject(String current, Taxon new)
  • show()
  • size()
  • taxa()
  • taxonIndex(String name)
  • translateCharacters(String type)
  • varGcContent(Bool excludeAmbiguous)
  • varGcContentByCodonPosition(Natural index, Bool excludeAmbiguous)

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