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java.lang.Object | +--uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
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
Constructor Summary | |
AbstractSequenceAlignment()
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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)
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protected void |
fireVetoableAlignmentEvent(VetoableAlignmentEvent event)
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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 |
public AbstractSequenceAlignment()
Method Detail |
protected abstract void setLengthQuietly(int length)
protected abstract void addSequenceQuietly(GappedSequence sequence, int inset)
sequence
- the sequenceinset
- the inset of the sequencepublic SequenceAlignment getSubAlignment(SequenceAlignmentRectangle rect)
getSubAlignment
in interface SequenceAlignment
public void addSequence(GappedSequence seq, int inset) throws AlignmentVetoException
addSequence
in interface SequenceAlignment
seq
- the sequenceinset
- the sequence inset
AlignmentVetoException
- veto to the additionpublic void addSequence(SequenceAlignment align) throws AlignmentVetoException
align
- the alignment of sequences to be added
AlignmentVetoException
- veto to the addition - this can
be sequence based as well as alignment basedprotected abstract GappedSequence removeSequenceQuietly(int seqIndex)
seqIndex
- the sequence index
public GappedSequence removeSequence(int seqIndex) throws AlignmentVetoException
removeSequence
in interface SequenceAlignment
seqIndex
- the sequence index
AlignmentVetoException
- veto to the removalprotected abstract void setInsetQuietly(int seqIndex, int inset)
seqIndex
- the sequence indexinset
- the inset or preceeding number of gapspublic void setInset(int seqIndex, int inset) throws AlignmentVetoException
setInset
in interface SequenceAlignment
seqIndex
- the sequence indexinset
- the inset or preceeding number of gaps
AlignmentVetoException
protected void fireAlignmentEvent(AlignmentEvent event)
protected void fireVetoableAlignmentEvent(VetoableAlignmentEvent event) throws AlignmentVetoException
AlignmentVetoException
public void addAlignmentListener(AlignmentListener listener)
addAlignmentListener
in interface AlignmentEventProvider
listener
- a MS listenerpublic void removeAlignmentListener(AlignmentListener listener)
removeAlignmentListener
in interface AlignmentEventProvider
listener
- the MS listener to be removedpublic void addVetoableAlignmentListener(VetoableAlignmentListener listener)
addVetoableAlignmentListener
in interface AlignmentEventProvider
listener
- a vetoable MS listener to be addedpublic void removeVetoableAlignmentListener(VetoableAlignmentListener listener)
removeVetoableAlignmentListener
in interface AlignmentEventProvider
listener
- the vetoable MS listener to be removedpublic void addSequenceListener(SequenceListener listener)
SequenceEventProvider
addSequenceListener
in interface SequenceEventProvider
listener
- the sequence listenerpublic void addVetoableSequenceListener(VetoableSequenceListener listener)
SequenceEventProvider
addVetoableSequenceListener
in interface SequenceEventProvider
listener
- the vetoable sequence listenerpublic void removeSequenceListener(SequenceListener listener)
SequenceEventProvider
removeSequenceListener
in interface SequenceEventProvider
listener
- the sequence listenerpublic void removeVetoableSequenceListener(VetoableSequenceListener listener)
SequenceEventProvider
removeVetoableSequenceListener
in interface SequenceEventProvider
listener
- the vetoable sequence listenerpublic void vetoableChangeOccurred(VetoableSequenceEvent event) throws SequenceVetoException
VetoableSequenceListener
vetoableChangeOccurred
in interface VetoableSequenceListener
event
- the event
SequenceVetoException
- if the listener does not wish
the event to occur.public void changeOccurred(SequenceEvent event)
SequenceListener
changeOccurred
in interface SequenceListener
event
-
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