uk.ac.man.bioinf.sequence.group
Class GroupSequenceAlignment

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup
        |
        +--uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment

All Implemented Interfaces:

AlignmentEventProvider, AlignmentListener, EventListener, GappedSequenceGroup, Identifiable, SequenceAlignment, SequenceEventProvider, SequenceGroup, SequenceListener, VetoableSequenceListener

Direct Known Subclasses:

CinemaGroup

public class GroupSequenceAlignment

extends AbstractGappedSequenceGroup

implements SequenceAlignment, AlignmentListener

GroupSequenceAlignment.java This is a sequence group which also reflects a sequence alignment. The sequences will be given out in the same order, as they are in the SequenceAlignment. A given group is linked specifically to a single SequenceAlignment. If sequences are removed from the SequenceAlignment then they are automatically removed from this class. Created: Thu Jun 1 23:20:37 2000

Version:

$Id: GroupSequenceAlignment.java,v 1.9 2001/04/11 17:04:43 lord Exp $

Author:

Phillip Lord

Constructor Summary

GroupSequenceAlignment(SequenceAlignment alignment)
Start an empty sequence group associated with the given sequence alignment.

GroupSequenceAlignment(SequenceAlignment alignment, IntArrayList seqArray)
Starts an Sequence group with the sequences given in the IntArrayList

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	addSequenceToGroup(Sequence sequence) Adds a sequence to this group.
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(AlignmentEvent event) method signalled after a change has occured to a multiple alignment
void	changeOccurred(SequenceEvent event) Method called when a change occurs
void	clearSequences() Empty the group of sequences
boolean	containsSequence(Sequence sequence) Does this group contain the sequence
Identifier	getIdentifier()
int	getInset(int index) Returns the inset of sequence within the alignment.
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 sequence) Returns the index in the alignment of a provided sequence.
Sequence[]	getSequences() Get all the sequences in this group.
SequenceType	getSequenceType() Returns the sequence type of the alignment (e.g: protein sequences).
SequenceAlignment	getSubAlignment(int startPos, int endPos, int startSeq, int endSeq) Returns a sub-alignment, given the exact location in this alignment.
SequenceAlignment	getSubAlignment(SequenceAlignmentRectangle rect)
Iterator	iterator() Returns an iterator of all the sequences.
void	removeAlignmentListener(AlignmentListener listener) Removes a multiple sequence alignment listener.
GappedSequence	removeSequence(int seqIndex) Removes a sequence from the alignment.
void	removeSequenceFromGroup(Sequence sequence) Removes a sequence from this group
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	vetoableChangeOccurred(VetoableAlignmentEvent event)
void	vetoableChangeOccurred(VetoableSequenceEvent event) Method signalled before a prospective change occurs

Methods inherited from class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup

getGappedSequences

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupSequenceAlignment

public GroupSequenceAlignment(SequenceAlignment alignment)

Start an empty sequence group associated with the given sequence alignment.

Parameters:

alignment - the alignment

GroupSequenceAlignment

public GroupSequenceAlignment(SequenceAlignment alignment,
                              IntArrayList seqArray)

Starts an Sequence group with the sequences given in the IntArrayList

Parameters:

alignment -

seqArray -

Method Detail

getSequences

public Sequence[] getSequences()

Description copied from interface: SequenceGroup

Get all the sequences in this group.

Specified by:

getSequences in interface SequenceGroup

Returns:

addSequenceToGroup

public void addSequenceToGroup(Sequence sequence)

Adds a sequence to this group.

Specified by:

addSequenceToGroup in interface SequenceGroup

Parameters:

sequence - the sequence

Throws:

IllegalArgumentException - if this sequence is not part of the associated SequenceAlignment

addSequence

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

Description copied from interface: SequenceAlignment

Adds a sequence to the current alignment. If listeners are listening to the alignment, they will be able to veto the add (thats the idea atleast).

Specified by:

addSequence in interface SequenceAlignment

Parameters:

seq - the sequence to be added

inset - the sequence inset

AlignmentVetoException

getLength

public int getLength()

Description copied from interface: SequenceAlignment

Returns the length of the alignment (i.e: the longest sequence).

Specified by:

getLength in interface SequenceAlignment

Returns:

length of alignment

removeSequenceFromGroup

public void removeSequenceFromGroup(Sequence sequence)

Description copied from interface: SequenceGroup

Removes a sequence from this group

Specified by:

removeSequenceFromGroup in interface SequenceGroup

Parameters:

sequence - the sequence

removeSequence

public GappedSequence removeSequence(int seqIndex)
                              throws AlignmentVetoException

Description copied from interface: SequenceAlignment

Removes a sequence from the alignment. It requires the knowledge of the sequence location in the alignment.

Specified by:

removeSequence in interface SequenceAlignment

Parameters:

seqIndex - the index of the sequence

Returns:

the sequence

AlignmentVetoException

setInset

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

Description copied from interface: SequenceAlignment

Sets the inset of a sequence within the alignment. An inset of zero will mean that the first element starts at the left most position of the alignment.

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).

Specified by:

setInset in interface SequenceAlignment

Parameters:

seqIndex - the index of the sequence

size - the size of the inset

AlignmentVetoException

clearSequences

public void clearSequences()

Description copied from interface: SequenceGroup

Empty the group of sequences

Specified by:

clearSequences in interface SequenceGroup

getNumberSequences

public int getNumberSequences()

Description copied from interface: SequenceAlignment

Returns the total number of sequences in the alignment.

Specified by:

getNumberSequences in interface SequenceAlignment

Returns:

the number of sequences

containsSequence

public boolean containsSequence(Sequence sequence)

Description copied from interface: SequenceGroup

Does this group contain the sequence

Specified by:

containsSequence in interface SequenceGroup

Parameters:

sequence - the sequence

Returns:

true if containined

iterator

public Iterator iterator()

Description copied from interface: SequenceGroup

Returns an iterator of all the sequences. This should be fail fast if the group is modified whilst the iterator is being used.

Specified by:

iterator in interface SequenceGroup

Returns:

getSequenceAt

public GappedSequence getSequenceAt(int index)

Description copied from interface: SequenceAlignment

Provides the sequence at a particular location in the alignment. The indexing STARTS AT 1, and not 0.

Specified by:

getSequenceAt in interface SequenceAlignment

Parameters:

index - the index of the target sequence

Returns:

the sequence of interest

getSubAlignment

public SequenceAlignment getSubAlignment(int startPos,
                                         int endPos,
                                         int startSeq,
                                         int endSeq)

Description copied from interface: SequenceAlignment

Returns a sub-alignment, given the exact location in this alignment.

Specified by:

getSubAlignment in interface SequenceAlignment

Parameters:

startPos - the start position for the sub-alignment (i.e: x1)

endPos - the length of the sub alignment

startSeq - the first sequence in the current alignment to be included in the sub-alignment (i.e: y1)

Returns:

the sub-alignment

getSubAlignment

public SequenceAlignment getSubAlignment(SequenceAlignmentRectangle rect)

Specified by:

getSubAlignment in interface SequenceAlignment

getSequenceType

public SequenceType getSequenceType()

Description copied from interface: SequenceAlignment

Returns the sequence type of the alignment (e.g: protein sequences).

Specified by:

getSequenceType in interface SequenceAlignment

Returns:

the sequence type

getInset

public int getInset(int index)

Description copied from interface: SequenceAlignment

Returns the inset of sequence within the alignment. A inset of 0 means that the first element means that the Sequence starts at the left most position of the alignment

Specified by:

getInset in interface SequenceAlignment

Parameters:

index - the sequence index

Returns:

the inset or preceeding number of gaps

getSequenceIndex

public int getSequenceIndex(GappedSequence sequence)

Description copied from interface: SequenceAlignment

Returns the index in the alignment of a provided sequence.

Specified by:

getSequenceIndex in interface SequenceAlignment

Parameters:

sequence - the query sequence

Returns:

the index of the sequence, or -1 if not found

removeAlignmentListener

public void removeAlignmentListener(AlignmentListener listener)

Description copied from interface: AlignmentEventProvider

Removes a multiple sequence alignment listener.

Specified by:

removeAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - the listener to be removed

addAlignmentListener

public void addAlignmentListener(AlignmentListener listener)

Description copied from interface: AlignmentEventProvider

Add a listener specifically interested in events connected with the MSA.

Specified by:

addAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - a multiple sequence alignment listener

removeVetoableAlignmentListener

public void removeVetoableAlignmentListener(VetoableAlignmentListener listener)

Description copied from interface: AlignmentEventProvider

Removes a vetoable multiple sequence alignment listener.

Specified by:

removeVetoableAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - the listener to be removed

addVetoableAlignmentListener

public void addVetoableAlignmentListener(VetoableAlignmentListener listener)

Description copied from interface: AlignmentEventProvider

Adds a listener interested in vetoing multiple sequence alignment specific events.

Specified by:

addVetoableAlignmentListener in interface AlignmentEventProvider

Parameters:

listener - a vetoable multiple sequence alignment listener

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 -

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(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

vetoableChangeOccurred

public void vetoableChangeOccurred(VetoableAlignmentEvent event)
                            throws AlignmentVetoException

AlignmentVetoException

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

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

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

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

getIdentifier

public Identifier getIdentifier()

Specified by:

getIdentifier in interface Identifiable