charite.christo.strap.extensions
Class AlignmentEntropy

java.lang.Object
  charite.christo.strap.extensions.AlignmentEntropy

All Implemented Interfaces:

HasModiCount, HasSharedControlPanel, NeedsSharedInstance, StrapListener, ValueOfAlignPosition, java.awt.event.ActionListener, java.util.EventListener

public class AlignmentEntropy
extends java.lang.Object
implements ValueOfAlignPosition, StrapListener, HasSharedControlPanel, java.awt.event.ActionListener, HasModiCount

HELP A profile of the sequence variability of the multiple sequence alignment is displayed. The variability is calculated with the formula by Shannon. Gaps are treated as a 21th amino acid.

Field Summary

static int	GAP_IS_21TH_AMINO_ACID
static int	GAP_IS_A_DIFFERENT_AMINO_ACID
static int	SKIP_GAPS

Constructor Summary

AlignmentEntropy()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
Protein[]	getProteins()
javax.swing.JComponent	getSharedControlPanel()
java.lang.Object	getSharedInstance()
double[]	getValues()
double[]	getValues(int mode)
void	handleEvent(StrapEvent ev)
int	modificationCount() Avoid calculating by caching the value;
void	setProteins(Protein... proteins)
void	setSharedInstance(java.lang.Object shared)

Methods inherited from class java.lang.Object

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

Field Detail

SKIP_GAPS

public static final int SKIP_GAPS

See Also:

Constant Field Values

GAP_IS_21TH_AMINO_ACID

public static final int GAP_IS_21TH_AMINO_ACID

See Also:

Constant Field Values

GAP_IS_A_DIFFERENT_AMINO_ACID

public static final int GAP_IS_A_DIFFERENT_AMINO_ACID

See Also:

Constant Field Values

Constructor Detail

AlignmentEntropy

public AlignmentEntropy()

Method Detail

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

setProteins

public void setProteins(Protein... proteins)

Specified by:

setProteins in interface ValueOfAlignPosition

getProteins

public Protein[] getProteins()

Specified by:

getProteins in interface ValueOfAlignPosition

handleEvent

public void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener

modificationCount

public int modificationCount()

Avoid calculating by caching the value;

Specified by:

modificationCount in interface HasModiCount

getValues

public double[] getValues()

Specified by:

getValues in interface ValueOfAlignPosition

getValues

public double[] getValues(int mode)

getSharedControlPanel

public javax.swing.JComponent getSharedControlPanel()

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

setSharedInstance

public void setSharedInstance(java.lang.Object shared)

Specified by:

setSharedInstance in interface NeedsSharedInstance

getSharedInstance

public java.lang.Object getSharedInstance()

Specified by:

getSharedInstance in interface NeedsSharedInstance