charite.christo.strap.extensions
Class Hydrophobicity

java.lang.Object
  charite.christo.protein.AbstractValueOfResidue
      charite.christo.strap.extensions.Hydrophobicity

All Implemented Interfaces:

Colored, HasModiCount, HasSharedControlPanel, NeedsSharedInstance, HasProtein, ValueOfResidue, java.awt.event.ActionListener, java.util.EventListener

public class Hydrophobicity
extends AbstractValueOfResidue
implements HasSharedControlPanel, java.awt.event.ActionListener

HELP This was translated from HydrophobicityProfiler.pl into java at http://gchelpdesk.ualberta.ca/servers/HydrophobicityProfiler/HydrophobicityProfiler.php
See MOL_TOOLKIT:hydropathy
Related links: Description of hydrophobicity scales: http://www.clcbio.com/index.php?id=43

Field Summary

float[]	_lastScale
float[]	_scale
static float[]	CORNETTE
static float[]	EISENBERG
static float[]	ENGELMAN
static float[]	HOPP_WOODS
static float[]	JANIN
static float[]	KYTE_DOOLITTLE
static float[]	ROSE
static java.lang.String[]	SCALE_NAMES

Constructor Summary

Hydrophobicity()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
javax.swing.JComponent	getSharedControlPanel()
double[]	getValues() Plugin that returns a numeric value for each amino acid of the protein or null.
void	setScale(java.lang.String sScale)
void	setWindowSize(int wSize)

Methods inherited from class charite.christo.protein.AbstractValueOfResidue

getColor, getProtein, getSharedInstance, modificationCount, setColor, setProtein, setSharedInstance

Methods inherited from class java.lang.Object

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

Methods inherited from interface charite.christo.NeedsSharedInstance

getSharedInstance, setSharedInstance

Field Detail

_scale

public float[] _scale

_lastScale

public float[] _lastScale

SCALE_NAMES

public static final java.lang.String[] SCALE_NAMES

KYTE_DOOLITTLE

public static final float[] KYTE_DOOLITTLE

HOPP_WOODS

public static final float[] HOPP_WOODS

JANIN

public static final float[] JANIN

ROSE

public static final float[] ROSE

EISENBERG

public static final float[] EISENBERG

ENGELMAN

public static final float[] ENGELMAN

CORNETTE

public static final float[] CORNETTE

Constructor Detail

Hydrophobicity

public Hydrophobicity()

Method Detail

getValues

public double[] getValues()

Description copied from interface: ValueOfResidue

Plugin that returns a numeric value for each amino acid of the protein or null. These are plotted in the alignment pane. It should notify changes by dispatching a JAVADOC:StrapEvent of type JAVADOC:StrapEvent#VALUE_OF_RESIDUE_CHANGED

Specified by:

getValues in interface ValueOfResidue

getSharedControlPanel

public javax.swing.JComponent getSharedControlPanel()

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

actionPerformed

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

Specified by:

actionPerformed in interface java.awt.event.ActionListener

setWindowSize

public void setWindowSize(int wSize)

setScale

public void setScale(java.lang.String sScale)