uk.ac.man.bioinf.sequence.alignment
Interface SequenceAlignment

All Superinterfaces:

AlignmentEventProvider, EventListener, Identifiable, SequenceEventProvider, SequenceListener, VetoableSequenceListener

All Known Implementing Classes:

AbstractSequenceAlignment, EmptySequenceAlignment, GroupSequenceAlignment

public interface SequenceAlignment

extends SequenceEventProvider, VetoableSequenceListener, AlignmentEventProvider, Identifiable

SequenceAlignment.java This interface is designed to mimic a biological sequence alignment. As a consequence, the sequences contained within should be GappedSequence.

Version:

$Id: SequenceAlignment.java,v 1.17 2001/04/11 17:04:43 lord Exp $

Author:

J Selley

See Also:

Created: Tue Feb 15 16:24:23 2000

Method Summary

void	addSequence(GappedSequence seq, int inset) Adds a sequence to the current alignment.
int	getInset(int seqIndex) 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 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 startPos, int length, int startSeq, int numSeqs) Returns a sub-alignment, given the exact location in this alignment.
SequenceAlignment	getSubAlignment(SequenceAlignmentRectangle rect)
GappedSequence	removeSequence(int seqIndex) Removes a sequence from the alignment.
void	setInset(int seqIndex, int size) Sets the inset of a sequence within the alignment.

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

addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener

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

vetoableChangeOccurred

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

changeOccurred

Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider

addAlignmentListener, addVetoableAlignmentListener, removeAlignmentListener, removeVetoableAlignmentListener

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

getIdentifier

Method Detail

getSubAlignment

public SequenceAlignment getSubAlignment(int startPos,
                                         int length,
                                         int startSeq,
                                         int numSeqs)

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

Parameters:

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

length - 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)

addSequence

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

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).

Parameters:

seq - the sequence to be added

inset - the sequence inset

Throws:

veto - to the addition

AlignmentVetoException

removeSequence

public GappedSequence removeSequence(int seqIndex)
                              throws AlignmentVetoException

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

Parameters:

seqIndex - the index of the sequence

Returns:

the sequence

Throws:

veto - to the removal

AlignmentVetoException

setInset

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

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).

Parameters:

seqIndex - the index of the sequence

size - the size of the inset

Throws:

veto - to setting

AlignmentVetoException

getInset

public int getInset(int seqIndex)

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

Parameters:

seqIndex - the sequence index

Returns:

the inset or preceeding number of gaps

getSequenceType

public SequenceType getSequenceType()

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

Returns:

the sequence type

getSequenceAt

public GappedSequence getSequenceAt(int index)
                             throws NoSuchSequenceException

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

Parameters:

index - the index of the target sequence

Returns:

the sequence of interest

Throws:

if - index < 1 or index > getNumberSequences()

NoSuchSequenceException

getSequenceIndex

public int getSequenceIndex(GappedSequence seq)

Returns the index in the alignment of a provided sequence.

Parameters:

seq - the query sequence

Returns:

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

getNumberSequences

public int getNumberSequences()

Returns the total number of sequences in the alignment.

Returns:

the number of sequences

getLength

public int getLength()

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

Returns:

length of alignment