uk.ac.man.bioinf.analysis.misc
Class PercentageIDCalculator

java.lang.Object
  |
  +--uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
All Implemented Interfaces:
AlignmentListener, EventListener, SequenceListener

public class PercentageIDCalculator
extends Object
implements AlignmentListener, SequenceListener

PercentageIDCalculator.java This class performs a variance calculation on the given sequence alignment. The calculation is done by calling the calculateAlignment method, and the results got from the getVariance, and getConsensus methods. Both calculations are done by a simple Percentage ID calculation. Created: Fri Jun 16 18:38:00 2000

Version:
$Id: PercentageIDCalculator.java,v 1.6 2001/04/11 17:04:41 lord Exp $
Author:
Phillip Lord

Constructor Summary
PercentageIDCalculator(SequenceAlignment alignment)
           
 
Method Summary
 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
 SequenceAlignment getAlignment()
           
 int getCheckSum()
          Returns a checksum value.
 Element[] getConsensus()
           
 double[] getVariance()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PercentageIDCalculator

public PercentageIDCalculator(SequenceAlignment alignment)
Method Detail

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

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 -

getCheckSum

public int getCheckSum()
Returns a checksum value. If this value has changed there consensus sequence may well have changed.

Returns:
a value of type 'int'

getVariance

public double[] getVariance()

getConsensus

public Element[] getConsensus()

getAlignment

public SequenceAlignment getAlignment()