uk.ac.man.bioinf.analysis.consensus
Class DefaultConsensusSequence

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.AbstractSequence
        |
        +--uk.ac.man.bioinf.sequence.AbstractMutableSequence
              |
              +--uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
                    |
                    +--uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence

All Implemented Interfaces:

AlignmentListener, ConsensusSequence, EventListener, GappedSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider, SequenceListener

Direct Known Subclasses:

ThreadedConsensusSequence

public class DefaultConsensusSequence

extends AbstractGappedSequence

implements ConsensusSequence, AlignmentListener, SequenceListener

DefaultConsensusSequence.java Created: Thu Jun 15 17:00:04 2000

Version:

$Id: DefaultConsensusSequence.java,v 1.8 2001/04/11 17:04:41 lord Exp $

Author:

Phillip Lord

Constructor Summary

DefaultConsensusSequence(ConsensusCalculator calculator)

Method Summary

protected void	calcConsensus()
void	changeOccurred(AlignmentEvent event) method signalled after a change has occured to a multiple alignment
void	changeOccurred(SequenceEvent event) Method called when a change occurs
void	deleteGapAtQuietly(int index)
void	destroy()
protected void	fireChangeEvent()
ConsensusCalculator	getConsensusCalculator()
Element	getElementAt(int index) Returns an element at a given location.
Element	getGappedElementAt(int index)
int	getGappedLength() Returns the gapped length of this sequence.
int	getGappedPositionOf(int index) Translate between the gapped index, and the ungapped index
Element[]	getGappedSequenceAsElements()
GappedSequence	getGappedSubSequence(int start, int length)
Identifier	getIdentifier()
int	getLength() Returns the length of the sequence.
Element[]	getSequenceAsElements() Returns the sequence as an array of elements.
int	getUngappedPositionOf(int index) Translate between the gapped position and the ungapped position.
void	insertGapAtQuietly(int index)
protected void	installAlignmentListeners(ConsensusCalculator cons)
protected void	installVetoListeners()
void	setConsensusCalculator(ConsensusCalculator calculator)
protected void	uninstallAlignmentListners(ConsensusCalculator cons)
protected void	validate()

Methods inherited from class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence

checkGappedRange, checkGappedRangeForInsert, deleteGapAt, deleteGapAt, getGappedElementAtAsChar, getGappedSequenceAsChars, getGappedSequenceIndexException, insertGapAt, insertGapAt

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractMutableSequence

addSequenceListener, addVetoableSequenceListener, fireSequenceEvent, fireVetoableSequenceEvent, hasListeners, removeSequenceListener, removeVetoableSequenceListener

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractSequence

checkRange, checkSequenceType, checkSequenceType, getElementAtAsChar, getSequenceAsChars, getSequenceIndexException, getSequenceType, getSequenceTypeException, getSubSequence

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.GappedSequence

deleteGapAt, deleteGapAt, getGappedElementAtAsChar, getGappedSequenceAsChars, insertGapAt, insertGapAt

Methods inherited from interface uk.ac.man.bioinf.sequence.Sequence

getElementAtAsChar, getSequenceAsChars, getSequenceType, getSubSequence

Methods inherited from interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider

addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener

Constructor Detail

DefaultConsensusSequence

public DefaultConsensusSequence(ConsensusCalculator calculator)

Method Detail

installVetoListeners

protected void installVetoListeners()

installAlignmentListeners

protected void installAlignmentListeners(ConsensusCalculator cons)

uninstallAlignmentListners

protected void uninstallAlignmentListners(ConsensusCalculator cons)

validate

protected void validate()

fireChangeEvent

protected void fireChangeEvent()

calcConsensus

protected void calcConsensus()

changeOccurred

public void changeOccurred(SequenceEvent event)

Description copied from interface: SequenceListener

Method called when a change occurs

Specified by:

changeOccurred in interface SequenceListener

Parameters:

event -

changeOccurred

public void changeOccurred(AlignmentEvent event)

Description copied from interface: AlignmentListener

method signalled after a change has occured to a multiple alignment

Specified by:

changeOccurred in interface AlignmentListener

Parameters:

event - the event type

getElementAt

public Element getElementAt(int index)

Description copied from interface: Sequence

Returns an element at a given location.

Specified by:

getElementAt in interface Sequence

Parameters:

index - the location of the target element

Returns:

the element

getGappedElementAt

public Element getGappedElementAt(int index)

Specified by:

getGappedElementAt in interface GappedSequence

getGappedLength

public int getGappedLength()

Description copied from interface: GappedSequence

Returns the gapped length of this sequence. That is the length of the sequence including its gaps. Conversely this means that the getLength method of the Sequence interface returns the length of the sequence ignoring the gaps.

Specified by:

getGappedLength in interface GappedSequence

Returns:

the length

getGappedPositionOf

public int getGappedPositionOf(int index)

Description copied from interface: GappedSequence

Translate between the gapped index, and the ungapped index

Specified by:

getGappedPositionOf in interface GappedSequence

Parameters:

index - the ungapped position

Returns:

the gapped position of the equivalent element

getGappedSequenceAsElements

public Element[] getGappedSequenceAsElements()

Specified by:

getGappedSequenceAsElements in interface GappedSequence

getGappedSubSequence

public GappedSequence getGappedSubSequence(int start,
                                           int length)

Specified by:

getGappedSubSequence in interface GappedSequence

getUngappedPositionOf

public int getUngappedPositionOf(int index)

Description copied from interface: GappedSequence

Translate between the gapped position and the ungapped position. I havent quite decided what to do at the moment if the index refers to a gap. One idea is to throw a NoSuchSequenceElementException which makes a certain amount of sense but isnt really that useful. Perhaps a better idea is to run -(insertion-point) where the insertion point is the nearest element before the current requested position which is not a gap. That way a value less than 0 would indicate a gap and would also return a useful value

Specified by:

getUngappedPositionOf in interface GappedSequence

Parameters:

index -

Returns:

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the sequence.

Specified by:

getLength in interface Sequence

Returns:

the length of the sequence

getSequenceAsElements

public Element[] getSequenceAsElements()

Description copied from interface: Sequence

Returns the sequence as an array of elements.

Specified by:

getSequenceAsElements in interface Sequence

Returns:

the sequence

getIdentifier

public Identifier getIdentifier()

Specified by:

getIdentifier in interface Identifiable

setConsensusCalculator

public void setConsensusCalculator(ConsensusCalculator calculator)

Specified by:

setConsensusCalculator in interface ConsensusSequence

getConsensusCalculator

public ConsensusCalculator getConsensusCalculator()

Specified by:

getConsensusCalculator in interface ConsensusSequence

deleteGapAtQuietly

public void deleteGapAtQuietly(int index)

Specified by:

deleteGapAtQuietly in class AbstractGappedSequence

insertGapAtQuietly

public void insertGapAtQuietly(int index)

Specified by:

insertGapAtQuietly in class AbstractGappedSequence

destroy

public void destroy()

Specified by:

destroy in interface ConsensusSequence