Class Edit.AbstractEdit<C extends Compound>

  • All Implemented Interfaces:
    Direct Known Subclasses:
    Edit.Delete, Edit.Insert, Edit.Substitute
    Enclosing interface:
    Edit<C extends Compound>

    public abstract static class Edit.AbstractEdit<C extends Compound>
    extends Object
    implements Edit<C>
    Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence. These ends can be of 0 length but conceptionally they can still exist.
    • Method Detail

      • getFivePrime

        protected abstract Sequence<CgetFivePrime​(Sequence<C> editingSequence)
        Should return the 5-prime end of the given Sequence according to the edit. An empty Sequence is valid.
      • getThreePrime

        protected abstract Sequence<CgetThreePrime​(Sequence<C> editingSequence)
        Should return the 3-prime end of the given Sequence according to the edit. An empty Sequence is valid.
      • getTargetSequence

        public Sequence<CgetTargetSequence​(Sequence<C> editingSequence)
        Returns the Sequence which is our edit.
        editingSequence - Asked for in-case we need to do String to Sequence conversion so we need a CompoundSet which is given by the Sequence we are editing
        The Sequence object we wish to insert
      • getEmptySequence

        protected Sequence<CgetEmptySequence​(Sequence<C> editingSequence)
        Returns an empty sequence with the given compound set of the editing sequence
      • getEnd

        public int getEnd()