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java.lang.Object | +--uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
EmptySequenceAlignment.java Created: Wed Apr 19 17:23:30 2000
Method Summary | |
void |
addAlignmentListener(AlignmentListener listener)
Add a listener specifically interested in events connected with the MSA. |
void |
addSequence(GappedSequence seq,
int inset)
Adds a sequence to the current alignment. |
void |
addSequenceListener(SequenceListener listener)
Adds the specified sequence listener. |
void |
addVetoableAlignmentListener(VetoableAlignmentListener listener)
Adds a listener interested in vetoing multiple sequence alignment specific events. |
void |
addVetoableSequenceListener(VetoableSequenceListener listener)
Adds the specified vetoable sequence listener. |
void |
changeOccurred(SequenceEvent event)
Method called when a change occurs |
Identifier |
getIdentifier()
|
int |
getInset(int index)
Returns the inset of sequence within the alignment. |
static EmptySequenceAlignment |
getInstance()
|
int |
getLength()
Returns the length of the alignment (i.e: the longest sequence). |
int |
getNumberSequences()
Returns the total number of sequences in the alignment. |
GappedSequence |
getSequenceAt(int index)
Provides the sequence at a particular location in the alignment. |
int |
getSequenceIndex(GappedSequence seq)
Returns the index in the alignment of a provided sequence. |
SequenceType |
getSequenceType()
Returns the sequence type of the alignment (e.g: protein sequences). |
SequenceAlignment |
getSubAlignment(int a,
int b,
int c,
int d)
Returns a sub-alignment, given the exact location in this alignment. |
SequenceAlignment |
getSubAlignment(SequenceAlignmentRectangle rect)
|
void |
removeAlignmentListener(AlignmentListener listener)
Removes a multiple sequence alignment listener. |
GappedSequence |
removeSequence(int seqIndex)
Removes a sequence from the alignment. |
void |
removeSequenceListener(SequenceListener listener)
Removes the specified sequence listener. |
void |
removeVetoableAlignmentListener(VetoableAlignmentListener listener)
Removes a vetoable multiple sequence alignment listener. |
void |
removeVetoableSequenceListener(VetoableSequenceListener listener)
Removes the specified vetoable sequence listener. |
void |
setInset(int seqIndex,
int size)
Sets the inset of a sequence within the alignment. |
void |
setInsetQuietly(int seqIndex,
int inset)
|
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 |
Method Detail |
public static EmptySequenceAlignment getInstance()
public int getInset(int index)
SequenceAlignment
getInset
in interface SequenceAlignment
index
- the sequence index
public int getLength()
SequenceAlignment
getLength
in interface SequenceAlignment
public int getNumberSequences()
SequenceAlignment
getNumberSequences
in interface SequenceAlignment
public GappedSequence getSequenceAt(int index)
SequenceAlignment
getSequenceAt
in interface SequenceAlignment
index
- the index of the target sequence
public int getSequenceIndex(GappedSequence seq)
SequenceAlignment
getSequenceIndex
in interface SequenceAlignment
seq
- the query sequence
public SequenceType getSequenceType()
SequenceAlignment
getSequenceType
in interface SequenceAlignment
public SequenceAlignment getSubAlignment(int a, int b, int c, int d)
SequenceAlignment
getSubAlignment
in interface SequenceAlignment
a
- the start position for the sub-alignment (i.e: x1)b
- the length of the sub alignmentc
- the first sequence in the current alignment to be
included in the sub-alignment (i.e: y1)
public SequenceAlignment getSubAlignment(SequenceAlignmentRectangle rect)
getSubAlignment
in interface SequenceAlignment
public void setInset(int seqIndex, int size)
SequenceAlignment
Special N.B.: This was put into the interface because it was felt that there would not be any instances when you would not wish to do this (apart from a read-only alignment, in which case there are ways and means).
setInset
in interface SequenceAlignment
seqIndex
- the index of the sequencesize
- the size of the insetpublic void setInsetQuietly(int seqIndex, int inset)
public void addSequence(GappedSequence seq, int inset)
SequenceAlignment
addSequence
in interface SequenceAlignment
seq
- the sequence to be addedinset
- the sequence insetpublic GappedSequence removeSequence(int seqIndex)
SequenceAlignment
removeSequence
in interface SequenceAlignment
seqIndex
- the index of the sequence
public void setLengthQuietly(int length)
public void addAlignmentListener(AlignmentListener listener)
AlignmentEventProvider
addAlignmentListener
in interface AlignmentEventProvider
listener
- a multiple sequence alignment listenerpublic void removeAlignmentListener(AlignmentListener listener)
AlignmentEventProvider
removeAlignmentListener
in interface AlignmentEventProvider
listener
- the listener to be removedpublic void addVetoableAlignmentListener(VetoableAlignmentListener listener)
AlignmentEventProvider
addVetoableAlignmentListener
in interface AlignmentEventProvider
listener
- a vetoable multiple sequence alignment listenerpublic void removeVetoableAlignmentListener(VetoableAlignmentListener listener)
AlignmentEventProvider
removeVetoableAlignmentListener
in interface AlignmentEventProvider
listener
- the listener to be removedpublic void vetoableChangeOccurred(VetoableSequenceEvent event)
VetoableSequenceListener
vetoableChangeOccurred
in interface VetoableSequenceListener
event
- the eventpublic void changeOccurred(SequenceEvent event)
SequenceListener
changeOccurred
in interface SequenceListener
event
- public 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 Identifier getIdentifier()
getIdentifier
in interface Identifiable
|
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