Constructor Detail

• Sequence

  public Sequence()

• Sequence

  public Sequence(MolecularSequence mol_seq)

Method Detail

• addAnnotation

  public void addAnnotation(Annotation annotation)

• addCrossReference

  public void addCrossReference(Accession cross_reference)

• addSequenceRelation

  public void addSequenceRelation(SequenceRelation sr)

• addUri

  public void addUri(Uri uri)

  Specified by:

  addUri in interface MultipleUris

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• asText

  public java.lang.StringBuffer asText()

  Specified by:

  asText in interface PhylogenyData

• compareTo

  public int compareTo(Sequence o)

  Specified by:

  compareTo in interface java.lang.Comparable<Sequence>

• copy

  public PhylogenyData copy()

  Not a deep copy.

  Specified by:

  copy in interface PhylogenyData

  Returns:

  a ~deep~ copy of this PhylogenyData

• equals

  public boolean equals(java.lang.Object o)

  Overrides:

  equals in class java.lang.Object

• getAccession

  public Accession getAccession()

• getAnnotation

  public Annotation getAnnotation(int i)

• getAnnotations

  public java.util.SortedSet<Annotation> getAnnotations()

• getCrossReferences

  public java.util.SortedSet<Accession> getCrossReferences()

• getDomainArchitecture

  public DomainArchitecture getDomainArchitecture()

• getGeneName

  public java.lang.String getGeneName()

• getLocation

  public java.lang.String getLocation()

• getMolecularSequence

  public java.lang.String getMolecularSequence()

• getName

  public java.lang.String getName()

• getSequenceRelations

  public java.util.List<SequenceRelation> getSequenceRelations()

• getSourceId

  public java.lang.String getSourceId()

• getSymbol

  public java.lang.String getSymbol()

• getType

  public java.lang.String getType()

• getUri

  public Uri getUri(int index)

  Specified by:

  getUri in interface MultipleUris

• getUris

  public java.util.List<Uri> getUris()

  Specified by:

  getUris in interface MultipleUris

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class java.lang.Object

• hasSequenceRelations

  public boolean hasSequenceRelations()

• init

  public void init()

• isEmpty

  public boolean isEmpty()

• 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

• isMolecularSequenceAligned

  public boolean isMolecularSequenceAligned()

• setAccession

  public void setAccession(Accession accession)

• setDomainArchitecture

  public void setDomainArchitecture(DomainArchitecture ds)

• setGeneName

  public void setGeneName(java.lang.String gene_name)

• setLocation

  public void setLocation(java.lang.String description)

• setMolecularSequence

  public void setMolecularSequence(java.lang.String mol_sequence)

• setMolecularSequenceAligned

  public void setMolecularSequenceAligned(boolean aligned)

• setName

  public void setName(java.lang.String name)

• setSourceId

  public void setSourceId(java.lang.String source_id)

• setSymbol

  public void setSymbol(java.lang.String symbol)
                 throws PhyloXmlDataFormatException

  Throws:

  PhyloXmlDataFormatException

• setType

  public void setType(java.lang.String type)
               throws PhyloXmlDataFormatException

  Throws:

  PhyloXmlDataFormatException

• setUris

  public void setUris(java.util.List<Uri> uris)

  Specified by:

  setUris in interface MultipleUris

• 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