uk.ac.man.bioinf.sequence.alignment
Class AbstractGappedSequence
java.lang.Object
|
+--uk.ac.man.bioinf.sequence.AbstractSequence
|
+--uk.ac.man.bioinf.sequence.AbstractMutableSequence
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+--uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
- All Implemented Interfaces:
- GappedSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider
- Direct Known Subclasses:
- DefaultConsensusSequence, DefaultGappedSequence
- public abstract class AbstractGappedSequence
- extends AbstractMutableSequence
- implements GappedSequence
AbstractGappedSequence.java
Created: Sat Mar 4 12:17:02 2000
- Version:
- $Id: AbstractGappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
- Author:
- Phillip Lord
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AbstractGappedSequence
public AbstractGappedSequence(SequenceType type)
insertGapAtQuietly
protected abstract void insertGapAtQuietly(int index)
insertGapAt
public void insertGapAt(int index)
throws SequenceVetoException
- Specified by:
insertGapAt
in interface GappedSequence
SequenceVetoException
insertGapAt
public void insertGapAt(int index,
int length)
throws SequenceVetoException
- Description copied from interface:
GappedSequence
- Inserts the elements at this position. If the index is one longer
than the length of the sequence the sequence will be extended.
- Specified by:
insertGapAt
in interface GappedSequence
- Parameters:
index
- the index at which to insert
SequenceVetoException
deleteGapAtQuietly
protected abstract void deleteGapAtQuietly(int index)
deleteGapAt
public void deleteGapAt(int index)
throws SequenceVetoException
- Description copied from interface:
GappedSequence
- Delete the element at index.
- Specified by:
deleteGapAt
in interface GappedSequence
- Parameters:
index
- the index to delete
- Returns:
- the element which has just been deleted
SequenceVetoException
deleteGapAt
public void deleteGapAt(int index,
int length)
throws SequenceVetoException
- Description copied from interface:
GappedSequence
- Delete the elements starting at index for the specified length
- Specified by:
deleteGapAt
in interface GappedSequence
- Parameters:
index
- the index to start atlength
- the length to delete
- Returns:
- the elements just deleted
SequenceVetoException
getGappedElementAtAsChar
public char getGappedElementAtAsChar(int index)
- Specified by:
getGappedElementAtAsChar
in interface GappedSequence
getGappedSequenceAsChars
public char[] getGappedSequenceAsChars()
- Specified by:
getGappedSequenceAsChars
in interface GappedSequence
checkGappedRange
protected void checkGappedRange(int index)
checkGappedRangeForInsert
protected void checkGappedRangeForInsert(int index)
getGappedSequenceIndexException
protected NoSuchSequenceElementException getGappedSequenceIndexException(int index)