Package org.biojava.nbio.core.sequence.edits

Class Edit.AbstractEdit<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C>
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 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 Details

    • AbstractEdit

      public AbstractEdit(int start)

    • AbstractEdit

      public AbstractEdit(int start, int end)

  • Method Details

    • 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.

    • edit

      public Sequence<C> edit(Sequence<C> editingSequence)
      Specified by:
      edit in interface Edit<C extends Compound>

    • setStringSequence

      protected void setStringSequence(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()