Class Event

    • Constructor Detail

      • Event

        public Event()
      • Event

        public Event​(int duplications,
                     int speciations,
                     int gene_losses)
      • Event

        public Event​(int duplications,
                     int speciations,
                     int gene_losses,
                     java.lang.String type)
    • Method Detail

      • asText

        public java.lang.StringBuffer asText()
        Specified by:
        asText in interface PhylogenyData
      • copy

        public PhylogenyData copy()
        Description copied from interface: PhylogenyData
        Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.
        Specified by:
        copy in interface PhylogenyData
        Returns:
        a ~deep~ copy of this PhylogenyData
      • getConfidence

        public Confidence getConfidence()
      • getNumberOfDuplications

        public int getNumberOfDuplications()
      • getNumberOfGeneLosses

        public int getNumberOfGeneLosses()
      • getNumberOfSpeciations

        public int getNumberOfSpeciations()
      • isDuplication

        public boolean isDuplication()
        Returns true if this event contains one or more duplications events only
        Returns:
        true if this event contains one or more duplications events only
      • isEqual

        public boolean isEqual​(PhylogenyData event)
        Description copied from interface: PhylogenyData
        Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.
        Specified by:
        isEqual in interface PhylogenyData
        Returns:
        in general, true if and only if all fiels are exactly identical, false otherwise
      • isFusion

        public boolean isFusion()
      • isGeneLoss

        public boolean isGeneLoss()
        Returns true if this event contains one or more gene loss events only
        Returns:
        true if this event contains one or more gene loss events only
      • isOther

        public boolean isOther()
      • isRoot

        public boolean isRoot()
      • isSpeciation

        public boolean isSpeciation()
        Returns true if this event contains one or more speciation events only
        Returns:
        true if this event contains one or more speciation events only
      • isSpeciationOrDuplication

        public boolean isSpeciationOrDuplication()
      • isTransfer

        public boolean isTransfer()
      • isUnassigned

        public boolean isUnassigned()
      • setConfidence

        public void setConfidence​(Confidence confidence)
      • setDuplications

        public void setDuplications​(int duplications)
      • setGeneLosses

        public void setGeneLosses​(int gene_losses)
      • setSpeciations

        public void setSpeciations​(int speciations)
      • toNHX

        public java.lang.StringBuffer toNHX()
        Specified by:
        toNHX in interface PhylogenyData
      • toPhyloXML

        public void toPhyloXML​(java.io.Writer writer,
                               int level,
                               java.lang.String indentation)
                        throws java.io.IOException
        Description copied from interface: PhylogenyData
        Writes a phyloXML representation of this phylogeny data.
        Specified by:
        toPhyloXML in interface PhylogenyData
        Throws:
        java.io.IOException
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • createSingleDuplicationEvent

        public static Event createSingleDuplicationEvent()
      • createSingleSpeciationEvent

        public static Event createSingleSpeciationEvent()
      • createSingleSpeciationOrDuplicationEvent

        public static Event createSingleSpeciationOrDuplicationEvent()