Package org.forester.phylogeny.data

Class Event

java.lang.Object
org.forester.phylogeny.data.Event
All Implemented Interfaces:
PhylogenyData
public class Event extends Object implements PhylogenyData

  • Field Details

  • Constructor Details

    • Event

      public Event()

    • Event

      public Event(Event.EventType type)

    • Event

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

    • Event

      public Event(int duplications, int speciations, int gene_losses, String type)

    • Event

      public Event(String nhx) throws NHXFormatException
      Throws:
      NHXFormatException

  • Method Details

    • asSimpleText

      public StringBuffer asSimpleText()
      Specified by:
      asSimpleText in interface PhylogenyData

    • asText

      public 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()

    • getEventType

      public Event.EventType getEventType()

    • 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 StringBuffer toNHX()
      Specified by:
      toNHX in interface PhylogenyData

    • toPhyloXML

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

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • createSingleDuplicationEvent

      public static Event createSingleDuplicationEvent()

    • createSingleSpeciationEvent

      public static Event createSingleSpeciationEvent()

    • createSingleSpeciationOrDuplicationEvent

      public static Event createSingleSpeciationOrDuplicationEvent()