uk.ac.man.bioinf.sequence.complex
Interface ComplexSequence
- All Superinterfaces:
- Identifiable, Sequence
- All Known Subinterfaces:
- ComplexEditableGappedSequence, GappedComplexSequence
- All Known Implementing Classes:
- AbstractComplexSequence, DefaultGappedComplexSequence
- public interface ComplexSequence
- extends Sequence
ComplexSequence.java
Created: Wed Nov 22 17:56:08 2000
- Version:
- $Id: ComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
- Author:
- Phillip Lord
addModificationAt
public ComplexElement addModificationAt(Modification mod,
int index)
throws NoSuchSequenceElementException,
SequenceVetoException
NoSuchSequenceElementException
SequenceVetoException
removeModificationAt
public ComplexElement removeModificationAt(Modification mod,
int index)
throws NoSuchSequenceElementException,
SequenceVetoException,
NoSuchModificationException
NoSuchSequenceElementException
SequenceVetoException
NoSuchModificationException
getComplexElementAt
public ComplexElement getComplexElementAt(int index)
getComplexElementAtAsChar
public char[] getComplexElementAtAsChar(int index)
- Representing a ComplexElement as a char is not a simple task. An
Element can have any number of Modifications each of which comes
with its own char representation. The following approach is
used. Each Element is represented first by its own char
representation, and then by its all of its modifications, and
then finally by an underscore _, which acts as a standard
terminator. Counting the number of underscores should show how
many Elements there are.
This is not meant to be a particular wonderfully parse-able
format.
- Parameters:
index
-
- Returns:
- a
char[]
value
getComplexSequenceAsChars
public char[] getComplexSequenceAsChars()