org.biojava.nbio.core.sequence.edits

Interface Edit<C extends Compound>

Type Parameters:

C - The type of compound to edit

All Known Implementing Classes:

Edit.AbstractEdit, Edit.Delete, Edit.Insert, Edit.Substitute

public interface Edit<C extends Compound>

Interface for carrying out edit operations on a Sequence. The 3 major methods of Editing are supported

• Insertion
• Deletion
• Substitution

The interface is provided so end users can use our implementations, which are implementations which attempts to create views of Sequences in an editted form not a full-realised editted Sequence, or their own.

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Edit.AbstractEdit<C extends Compound> 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.
static class	Edit.Delete<C extends Compound> Implementation which allows for the deletion of bases from a Sequence
static class	Edit.Insert<C extends Compound> Edit implementation which allows us to insert a base at any position in a Sequence.
static class	Edit.Substitute<C extends Compound> Allows for the substitution of bases into an existing Sequence.

Method Summary

Modifier and Type	Method and Description
Sequence<C>	edit(Sequence<C> sequence)

Method Detail

edit

Sequence<C> edit(Sequence<C> sequence)