uk.ac.man.bioinf.sequence.alignment
Class AbstractSequenceAlignment

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment

All Implemented Interfaces:

AlignmentEventProvider, EventListener, Identifiable, SequenceAlignment, SequenceEventProvider, SequenceListener, VetoableSequenceListener

Direct Known Subclasses:

DefaultSequenceAlignment

public abstract class AbstractSequenceAlignment

extends Object

implements SequenceAlignment, VetoableSequenceListener

AbstractSequenceAlignment.java An abstract class to extend for the basic definition of a multiple sequence alignment. This class basically ensures listener handling. Created: Mon Feb 21 13:02:10 2000

Version:

$Id: AbstractSequenceAlignment.java,v 1.13 2001/04/11 17:04:43 lord Exp $

Author:

J Selley

Constructor Summary

AbstractSequenceAlignment()

Method Summary

void	addAlignmentListener(AlignmentListener listener) Delegates to the AlignmentListenerSupport object, the addition of a Multiple Sequence (MS) listener.
void	addSequence(GappedSequence seq, int inset) Adds a sequence to the alignment.
void	addSequence(SequenceAlignment align) Calls addSequence on every sequence in the supplied alignment.
void	addSequenceListener(SequenceListener listener) Adds the specified sequence listener.
protected abstract void	addSequenceQuietly(GappedSequence sequence, int inset) Adds a sequence to the alignment, quietly, without notifying listeners.
void	addVetoableAlignmentListener(VetoableAlignmentListener listener) Delegates to the AlignmentListenerSupport the addition of a vetoable MS listener.
void	addVetoableSequenceListener(VetoableSequenceListener listener) Adds the specified vetoable sequence listener.
void	changeOccurred(SequenceEvent event) Method called when a change occurs
protected void	fireAlignmentEvent(AlignmentEvent event)
protected void	fireVetoableAlignmentEvent(VetoableAlignmentEvent event)
SequenceAlignment	getSubAlignment(SequenceAlignmentRectangle rect)
void	removeAlignmentListener(AlignmentListener listener) Delegates to the AlignmentListenerSupport the removal of the MS listener.
GappedSequence	removeSequence(int seqIndex) Removes a sequence from the alignment.
void	removeSequenceListener(SequenceListener listener) Removes the specified sequence listener.
protected abstract GappedSequence	removeSequenceQuietly(int seqIndex) Remove a sequence from the alignment, quietly, without notifying listeners.
void	removeVetoableAlignmentListener(VetoableAlignmentListener listener) Delegates to the AlignmentListenerSupport the removal of the vetoable MS listener.
void	removeVetoableSequenceListener(VetoableSequenceListener listener) Removes the specified vetoable sequence listener.
void	setInset(int seqIndex, int inset) Set the inset (or number of preceeding gaps) in a sequence.
protected abstract void	setInsetQuietly(int seqIndex, int inset) Set the inset (or number of preceeding gaps) in a sequence, quietly without notifying listeners.
protected abstract void	setLengthQuietly(int length)
void	vetoableChangeOccurred(VetoableSequenceEvent event) Method signalled before a prospective change occurs

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.SequenceAlignment

getInset, getLength, getNumberSequences, getSequenceAt, getSequenceIndex, getSequenceType, getSubAlignment

Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.Identifiable

getIdentifier

Constructor Detail

AbstractSequenceAlignment

public AbstractSequenceAlignment()

Method Detail

setLengthQuietly

protected abstract void setLengthQuietly(int length)

addSequenceQuietly

protected abstract void addSequenceQuietly(GappedSequence sequence,
                                           int inset)

Adds a sequence to the alignment, quietly, without notifying listeners.

Parameters:

sequence - the sequence

inset - the inset of the sequence

getSubAlignment

public SequenceAlignment getSubAlignment(SequenceAlignmentRectangle rect)

Specified by:

getSubAlignment in interface SequenceAlignment

addSequence

public void addSequence(GappedSequence seq,
                        int inset)
                 throws AlignmentVetoException

Adds a sequence to the alignment. This action can be vetoed by a listener.

Specified by:

addSequence in interface SequenceAlignment

Parameters:

seq - the sequence

inset - the sequence inset

Throws:

AlignmentVetoException - veto to the addition

addSequence

public void addSequence(SequenceAlignment align)
                 throws AlignmentVetoException

Calls addSequence on every sequence in the supplied alignment. This basically provides a simple shortcut method.

Parameters:

align - the alignment of sequences to be added

Throws:

AlignmentVetoException - veto to the addition - this can be sequence based as well as alignment based

removeSequenceQuietly

protected abstract GappedSequence removeSequenceQuietly(int seqIndex)

Remove a sequence from the alignment, quietly, without notifying listeners.

Parameters:

seqIndex - the sequence index

Returns:

the sequence

removeSequence

public GappedSequence removeSequence(int seqIndex)
                              throws AlignmentVetoException

Removes a sequence from the alignment. This action can be veetoed by a listener.

Specified by:

removeSequence in interface SequenceAlignment

Parameters:

seqIndex - the sequence index

Returns:

the sequence

Throws:

AlignmentVetoException - veto to the removal

setInsetQuietly

protected abstract void setInsetQuietly(int seqIndex,
                                        int inset)

Set the inset (or number of preceeding gaps) in a sequence, quietly without notifying listeners.

Parameters:

seqIndex - the sequence index

inset - the inset or preceeding number of gaps

setInset

public void setInset(int seqIndex,
                     int inset)
              throws AlignmentVetoException

Set the inset (or number of preceeding gaps) in a sequence.

Specified by:

setInset in interface SequenceAlignment

Parameters:

seqIndex - the sequence index

inset - the inset or preceeding number of gaps

AlignmentVetoException

fireAlignmentEvent

protected void fireAlignmentEvent(AlignmentEvent event)

fireVetoableAlignmentEvent

protected void fireVetoableAlignmentEvent(VetoableAlignmentEvent event)
                                   throws AlignmentVetoException

AlignmentVetoException

addAlignmentListener

public void addAlignmentListener(AlignmentListener listener)

Delegates to the AlignmentListenerSupport object, the addition of a Multiple Sequence (MS) listener.

Specified by:

addAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - a MS listener

removeAlignmentListener

public void removeAlignmentListener(AlignmentListener listener)

Delegates to the AlignmentListenerSupport the removal of the MS listener.

Specified by:

removeAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - the MS listener to be removed

addVetoableAlignmentListener

public void addVetoableAlignmentListener(VetoableAlignmentListener listener)

Delegates to the AlignmentListenerSupport the addition of a vetoable MS listener.

Specified by:

addVetoableAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - a vetoable MS listener to be added

removeVetoableAlignmentListener

public void removeVetoableAlignmentListener(VetoableAlignmentListener listener)

Delegates to the AlignmentListenerSupport the removal of the vetoable MS listener.

Specified by:

removeVetoableAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - the vetoable MS listener to be removed

addSequenceListener

public void addSequenceListener(SequenceListener listener)

Description copied from interface: SequenceEventProvider

Adds the specified sequence listener.

Specified by:

addSequenceListener in interface SequenceEventProvider

Parameters:

listener - the sequence listener

addVetoableSequenceListener

public void addVetoableSequenceListener(VetoableSequenceListener listener)

Description copied from interface: SequenceEventProvider

Adds the specified vetoable sequence listener.

Specified by:

addVetoableSequenceListener in interface SequenceEventProvider

Parameters:

listener - the vetoable sequence listener

removeSequenceListener

public void removeSequenceListener(SequenceListener listener)

Description copied from interface: SequenceEventProvider

Removes the specified sequence listener.

Specified by:

removeSequenceListener in interface SequenceEventProvider

Parameters:

listener - the sequence listener

removeVetoableSequenceListener

public void removeVetoableSequenceListener(VetoableSequenceListener listener)

Description copied from interface: SequenceEventProvider

Removes the specified vetoable sequence listener.

Specified by:

removeVetoableSequenceListener in interface SequenceEventProvider

Parameters:

listener - the vetoable sequence listener

vetoableChangeOccurred

public void vetoableChangeOccurred(VetoableSequenceEvent event)
                            throws SequenceVetoException

Description copied from interface: VetoableSequenceListener

Method signalled before a prospective change occurs

Specified by:

vetoableChangeOccurred in interface VetoableSequenceListener

Parameters:

event - the event

Throws:

SequenceVetoException - if the listener does not wish the event to occur.

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 -