charite.christo.strap.extensions
Class ResidueValues_from_textfile

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

All Implemented Interfaces:

Disposable, HasControlPanel, HasModiCount, HasProtein, ValueOfResidue, java.awt.event.ActionListener, java.lang.Runnable, java.util.EventListener

public final class ResidueValues_from_textfile
extends java.lang.Object
implements ValueOfResidue, HasControlPanel, Disposable, java.awt.event.ActionListener, java.lang.Runnable, HasModiCount

HELP The purpose of this class is to assign numeric values to residues in proteins. STRAP expects a plain text file containing the data. These data file can be typed by hand using a text program or may be generated by other programs or scripts. When the contents of the data file[s] is changed the plot is updated automatically. The numbers in the file must be separated by space (space, line break, tab) or colon. The decimal point is a dot and not a colon. Undefined values should be coded as NaN ("Not A Number"). The file name is specified in the control panel.

Field Summary

Fields inherited from interface charite.christo.Disposable

NONE

Constructor Summary

ResidueValues_from_textfile()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
void	dispose()
javax.swing.JComponent	getControlPanel(boolean real)
Protein	getProtein()
double[]	getValues() Plugin that returns a numeric value for each amino acid of the protein or null.
int	modificationCount()
void	run()
void	setProtein(Protein p)

Methods inherited from class java.lang.Object

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

Constructor Detail

ResidueValues_from_textfile

public ResidueValues_from_textfile()

Method Detail

dispose

public void dispose()

Specified by:

dispose in interface Disposable

setProtein

public void setProtein(Protein p)

Specified by:

setProtein in interface ValueOfResidue

getProtein

public Protein getProtein()

Specified by:

getProtein in interface HasProtein

actionPerformed

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

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

modificationCount

public int modificationCount()

Specified by:

modificationCount in interface HasModiCount

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

run

public void run()

Specified by:

run in interface java.lang.Runnable