Class Edit.AbstractEdit<C extends Compound>

  • All Implemented Interfaces:
    Edit<C>
    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 java.lang.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.
    • Constructor Detail

      • AbstractEdit

        public AbstractEdit​(int start)
      • AbstractEdit

        public AbstractEdit​(int start,
                            int end)
    • Method Detail

      • getFivePrime

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

        protected void setStringSequence​(java.lang.String stringSequence)
      • setSequence

        protected void setSequence​(Sequence<C> sequence)
      • getTargetSequence

        public Sequence<C> getTargetSequence​(Sequence<C> editingSequence)
        Returns the Sequence which is our edit.
        Parameters:
        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
        Returns:
        The Sequence object we wish to insert
      • getEmptySequence

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

        public int getStart()
      • getEnd

        public int getEnd()