Class SimpleHomology

    • Constructor Detail

      • SimpleHomology

        public SimpleHomology()
        Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder.
    • Method Detail

      • getFeatures

        public FeatureHolder getFeatures()
        getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
        Specified by:
        getFeatures in interface Homology
        Returns:
        a FeatureHolder.
      • getAlignment

        public Alignment getAlignment()
        getAlignment returns the alignment, which uses the HomologyFeatures as keys.
        Specified by:
        getAlignment in interface Homology
        Returns:
        an Alignment.
      • setAlignment

        public void setAlignment​(Alignment alignment)
                          throws BioException,
                                 ChangeVetoException
        setAlignment sets the alignment which describes the homology. The alignment, should use the HomologyFeatures as keys. A suitable FeatureHolder is automatically created.
        Parameters:
        alignment - an Alignment.
        Throws:
        BioException - if an error occurs.
        ChangeVetoException - if the SimpleHomology is locked.
      • toString

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