org.biojava.nbio.core.sequence.edits

Class Edit.Delete<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C>

org.biojava.nbio.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.biojava.nbio.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

Constructors

Constructor and Description
Delete(int position)
Delete(int start, int end)

Method Summary

Modifier and Type	Method and Description
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.biojava.nbio.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

Delete

public Delete(int position)

Delete

public 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>