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SequenceAlignment.java This interface is designed to mimic a biological sequence alignment. As a consequence, the sequences contained within should be GappedSequence.
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)
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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 |
public SequenceAlignment getSubAlignment(int startPos, int length, int startSeq, int numSeqs)
startPos
- the start position for the sub-alignment (i.e: x1)length
- the length of the sub alignmentstartSeq
- the first sequence in the current alignment to be
included in the sub-alignment (i.e: y1)
public SequenceAlignment getSubAlignment(SequenceAlignmentRectangle rect)
public void addSequence(GappedSequence seq, int inset) throws AlignmentVetoException
seq
- the sequence to be addedinset
- the sequence inset
veto
- to the addition
AlignmentVetoException
public GappedSequence removeSequence(int seqIndex) throws AlignmentVetoException
seqIndex
- the index of the sequence
veto
- to the removal
AlignmentVetoException
public void setInset(int seqIndex, int size) throws AlignmentVetoException
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).
seqIndex
- the index of the sequencesize
- the size of the inset
veto
- to setting
AlignmentVetoException
public int getInset(int seqIndex)
seqIndex
- the sequence index
public SequenceType getSequenceType()
public GappedSequence getSequenceAt(int index) throws NoSuchSequenceException
index
- the index of the target sequence
if
- index < 1 or index > getNumberSequences()
NoSuchSequenceException
public int getSequenceIndex(GappedSequence seq)
seq
- the query sequence
public int getNumberSequences()
public int getLength()
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