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