Field Detail

• typesToNames

  public static final java.util.Map<SequenceRelation.SEQUENCE_RELATION_TYPE,​java.lang.String> typesToNames

• SEQUENCE_RELATION_TYPE_ORTHOLOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_ORTHOLOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_PARALOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_PARALOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_XENOLOGY

  public static final java.lang.String SEQUENCE_RELATION_TYPE_XENOLOGY

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_UNKNOWN

  public static final java.lang.String SEQUENCE_RELATION_TYPE_UNKNOWN

  See Also:

  Constant Field Values

• SEQUENCE_RELATION_TYPE_OTHER

  public static final java.lang.String SEQUENCE_RELATION_TYPE_OTHER

  See Also:

  Constant Field Values

Constructor Detail

• SequenceRelation

  public SequenceRelation()

Method Detail

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• 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()

• getDistance

  public java.lang.Double getDistance()

• getRef0

  public Sequence getRef0()

• getRef1

  public Sequence getRef1()

• getType

  public SequenceRelation.SEQUENCE_RELATION_TYPE getType()

• isEqual

  public boolean isEqual​(PhylogenyData data)

  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

• setConfidence

  public void setConfidence​(Confidence confidence)

• setDistance

  public void setDistance​(java.lang.Double distance)

• setRef0

  public void setRef0​(Sequence ref0)

• setRef1

  public void setRef1​(Sequence ref1)

• setType

  public void setType​(SequenceRelation.SEQUENCE_RELATION_TYPE type)

• 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

• getPrintableNameByType

  public static java.lang.String getPrintableNameByType​(SequenceRelation.SEQUENCE_RELATION_TYPE type)