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java.lang.Object | +--uk.ac.man.bioinf.sequence.AbstractSequence | +--uk.ac.man.bioinf.sequence.AbstractMutableSequence | +--uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence | +--uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
DefaultConsensusSequence.java Created: Thu Jun 15 17:00:04 2000
Constructor Summary | |
DefaultConsensusSequence(ConsensusCalculator calculator)
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Method Summary | |
protected void |
calcConsensus()
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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 |
deleteGapAtQuietly(int index)
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void |
destroy()
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protected void |
fireChangeEvent()
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ConsensusCalculator |
getConsensusCalculator()
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Element |
getElementAt(int index)
Returns an element at a given location. |
Element |
getGappedElementAt(int index)
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int |
getGappedLength()
Returns the gapped length of this sequence. |
int |
getGappedPositionOf(int index)
Translate between the gapped index, and the ungapped index |
Element[] |
getGappedSequenceAsElements()
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GappedSequence |
getGappedSubSequence(int start,
int length)
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Identifier |
getIdentifier()
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int |
getLength()
Returns the length of the sequence. |
Element[] |
getSequenceAsElements()
Returns the sequence as an array of elements. |
int |
getUngappedPositionOf(int index)
Translate between the gapped position and the ungapped position. |
void |
insertGapAtQuietly(int index)
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protected void |
installAlignmentListeners(ConsensusCalculator cons)
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protected void |
installVetoListeners()
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void |
setConsensusCalculator(ConsensusCalculator calculator)
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protected void |
uninstallAlignmentListners(ConsensusCalculator cons)
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protected void |
validate()
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Methods inherited from class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence |
checkGappedRange, checkGappedRangeForInsert, deleteGapAt, deleteGapAt, getGappedElementAtAsChar, getGappedSequenceAsChars, getGappedSequenceIndexException, insertGapAt, insertGapAt |
Methods inherited from class uk.ac.man.bioinf.sequence.AbstractMutableSequence |
addSequenceListener, addVetoableSequenceListener, fireSequenceEvent, fireVetoableSequenceEvent, hasListeners, removeSequenceListener, removeVetoableSequenceListener |
Methods inherited from class uk.ac.man.bioinf.sequence.AbstractSequence |
checkRange, checkSequenceType, checkSequenceType, getElementAtAsChar, getSequenceAsChars, getSequenceIndexException, getSequenceType, getSequenceTypeException, getSubSequence |
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.GappedSequence |
deleteGapAt, deleteGapAt, getGappedElementAtAsChar, getGappedSequenceAsChars, insertGapAt, insertGapAt |
Methods inherited from interface uk.ac.man.bioinf.sequence.Sequence |
getElementAtAsChar, getSequenceAsChars, getSequenceType, getSubSequence |
Methods inherited from interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider |
addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener |
Constructor Detail |
public DefaultConsensusSequence(ConsensusCalculator calculator)
Method Detail |
protected void installVetoListeners()
protected void installAlignmentListeners(ConsensusCalculator cons)
protected void uninstallAlignmentListners(ConsensusCalculator cons)
protected void validate()
protected void fireChangeEvent()
protected void calcConsensus()
public void changeOccurred(SequenceEvent event)
SequenceListener
changeOccurred
in interface SequenceListener
event
- public void changeOccurred(AlignmentEvent event)
AlignmentListener
changeOccurred
in interface AlignmentListener
event
- the event typepublic Element getElementAt(int index)
Sequence
getElementAt
in interface Sequence
index
- the location of the target element
public Element getGappedElementAt(int index)
getGappedElementAt
in interface GappedSequence
public int getGappedLength()
GappedSequence
getGappedLength
in interface GappedSequence
public int getGappedPositionOf(int index)
GappedSequence
getGappedPositionOf
in interface GappedSequence
index
- the ungapped position
public Element[] getGappedSequenceAsElements()
getGappedSequenceAsElements
in interface GappedSequence
public GappedSequence getGappedSubSequence(int start, int length)
getGappedSubSequence
in interface GappedSequence
public int getUngappedPositionOf(int index)
GappedSequence
getUngappedPositionOf
in interface GappedSequence
index
-
public int getLength()
Sequence
getLength
in interface Sequence
public Element[] getSequenceAsElements()
Sequence
getSequenceAsElements
in interface Sequence
public Identifier getIdentifier()
getIdentifier
in interface Identifiable
public void setConsensusCalculator(ConsensusCalculator calculator)
setConsensusCalculator
in interface ConsensusSequence
public ConsensusCalculator getConsensusCalculator()
getConsensusCalculator
in interface ConsensusSequence
public void deleteGapAtQuietly(int index)
deleteGapAtQuietly
in class AbstractGappedSequence
public void insertGapAtQuietly(int index)
insertGapAtQuietly
in class AbstractGappedSequence
public void destroy()
destroy
in interface ConsensusSequence
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