Class Sequence

    • Constructor Detail

      • Sequence

        public Sequence()
    • Method Detail

      • addAnnotation

        public void addAnnotation​(Annotation annotation)
      • addCrossReference

        public void addCrossReference​(Accession cross_reference)
      • addSequenceRelation

        public void addSequenceRelation​(SequenceRelation sr)
      • 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>
      • 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()
      • 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()
      • 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)
      • 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)
      • 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