org.biojava3.core.sequence.edits
Class Edit.Delete<C extends Compound>

java.lang.Object
  extended by org.biojava3.core.sequence.edits.Edit.AbstractEdit<C>
      extended by org.biojava3.core.sequence.edits.Edit.Delete<C>
All Implemented Interfaces:
Edit<C>
Enclosing interface:
Edit<C extends Compound>

public static class Edit.Delete<C extends Compound>
extends Edit.AbstractEdit<C>

Implementation which allows for the deletion of bases from a Sequence


Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.core.sequence.edits.Edit
Edit.AbstractEdit<C extends Compound>, Edit.Delete<C extends Compound>, Edit.Insert<C extends Compound>, Edit.Substitute<C extends Compound>
 
Constructor Summary
Edit.Delete(int position)
           
Edit.Delete(int start, int end)
           
 
Method Summary
protected  Sequence<C> getFivePrime(Sequence<C> editingSequence)
          Should return the 5-prime end of the given Sequence according to the edit.
protected  int getRealEnd()
           
protected  int getRealStart()
           
protected  Sequence<C> getThreePrime(Sequence<C> editingSequence)
          Should return the 3-prime end of the given Sequence according to the edit.
 
Methods inherited from class org.biojava3.core.sequence.edits.Edit.AbstractEdit
edit, getEmptySequence, getEnd, getStart, getTargetSequence, setSequence, setStringSequence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Edit.Delete

public Edit.Delete(int position)

Edit.Delete

public Edit.Delete(int start,
                   int end)
Method Detail

getRealStart

protected int getRealStart()

getRealEnd

protected int getRealEnd()

getFivePrime

protected Sequence<C> getFivePrime(Sequence<C> editingSequence)
Description copied from class: Edit.AbstractEdit
Should return the 5-prime end of the given Sequence according to the edit. An empty Sequence is valid.

Specified by:
getFivePrime in class Edit.AbstractEdit<C extends Compound>

getThreePrime

protected Sequence<C> getThreePrime(Sequence<C> editingSequence)
Description copied from class: Edit.AbstractEdit
Should return the 3-prime end of the given Sequence according to the edit. An empty Sequence is valid.

Specified by:
getThreePrime in class Edit.AbstractEdit<C extends Compound>