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.

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	Description
AbstractEdit(int start)
AbstractEdit(int start, int end)

Method Summary

Modifier and Type	Method	Description
Sequence<C>	edit(Sequence<C> editingSequence)
protected Sequence<C>	getEmptySequence(Sequence<C> editingSequence)	Returns an empty sequence with the given compound set of the editing sequence
int	getEnd()
protected abstract Sequence<C>	getFivePrime(Sequence<C> editingSequence)	Should return the 5-prime end of the given Sequence according to the edit.
int	getStart()
Sequence<C>	getTargetSequence(Sequence<C> editingSequence)	Returns the Sequence which is our edit.
protected abstract Sequence<C>	getThreePrime(Sequence<C> editingSequence)	Should return the 3-prime end of the given Sequence according to the edit.
protected void	setSequence(Sequence<C> sequence)
protected void	setStringSequence(String stringSequence)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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.

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()