charite.christo.metannogen
Class DialogHighlightInPathway

java.lang.Object
  charite.christo.metannogen.DialogHighlightInPathway

All Implemented Interfaces:

ChRunnable, PaintHook, ActionListener, EventListener

public class DialogHighlightInPathway
extends Object
implements ChRunnable, ActionListener, PaintHook

HELP The List contains reaction IDs of the form R02740@cyto. The compartment is optionally. MReactions in the list are highlighted yellow in the pathway views.
Adding reaction: CTRL-left-click a reaction in a path way. Newly included items are highlighted in the text list. Duplicates are avoided. If at least one dataset with a compartment other than "none" exists than the compartment is obtained from these datasets. Otherwise the compartment that is selected in the pathway view is taken. If no compartment is specified either by a datasat or in the pathway view then nothing is added.
Removing a reaction: CTRL+SHIFT-left-click a reaction in a path way

Description of reactions: The full description of the MReaction under the mouse pointer is in the text pane of Metannogen.

Also Ensembl numbers can be entered such as ENSG00000119640. For this purpose some large files will be downloaded. Try on Map glycolysis:

        ENSG00000152556
        ENSG00000067057
        ENSG00000141959
        ENSG00000165140
        ENSG00000130957
        ENSG00000105220
        ENSMUSG00000021196
        ENSMUSG00000020277
        ENSMUSG00000033065
        ENSMUSG00000069805
        ENSMUSG00000021456
        ENSMUSG00000036427

Field Summary

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

DialogHighlightInPathway()

Method Summary

void	actionPerformed(ActionEvent ev)
void	addReaction(String a, String[] ec)
String[]	getReactionIds()
int	getReactionIdsNoCompartment_modificationCount()
boolean	paintHook(JComponent pathwayView, Graphics graphics, boolean after)
void	removeReaction(String a)
Object	run(String id, Object param)

Methods inherited from class java.lang.Object

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

Constructor Detail

DialogHighlightInPathway

public DialogHighlightInPathway()

Method Detail

actionPerformed

public void actionPerformed(ActionEvent ev)

Specified by:

actionPerformed in interface ActionListener

getReactionIdsNoCompartment_modificationCount

public int getReactionIdsNoCompartment_modificationCount()

getReactionIds

public String[] getReactionIds()

run

public Object run(String id,
                  Object param)

Specified by:

run in interface ChRunnable

addReaction

public void addReaction(String a,
                        String[] ec)

removeReaction

public void removeReaction(String a)

paintHook

public boolean paintHook(JComponent pathwayView,
                         Graphics graphics,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent