org.biojava.nbio.core.sequence.edits

Class Edit.Insert<C extends Compound>

java.lang.Object

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

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

All Implemented Interfaces:

Edit<C>

Enclosing interface:

Edit<C extends Compound>

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

Edit implementation which allows us to insert a base at any position in a Sequence. Specifying 1 base is used to insert at the start and end of a Sequence. If you wish to carry out an in-sequence insertion then you specify the flanking base positions e.g.

   ACTG insert TT @ position 1   : TTACGT
   ACTG insert TT @ position 2,3 : ACTTGT
   ACTG insert A  @ position 4   : ACGTA
 

The code will raise exceptions if you attempt a single base edit with an insertion.

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
Insert(Sequence<C> sequence, int position)
Insert(Sequence<C> sequence, int start, int stop)
Insert(String sequence, int position)
Insert(String sequence, int start, int stop)

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 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

Insert

public Insert(String sequence,
              int position)

Insert

public Insert(Sequence<C> sequence,
              int position)

Insert

public Insert(String sequence,
              int start,
              int stop)

Insert

public Insert(Sequence<C> sequence,
              int start,
              int stop)

Method Detail

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>