charite.christo.metannogen
Class FluxData

java.lang.Object
  charite.christo.metannogen.FluxData

All Implemented Interfaces:

ChRunnable, PaintHook, TooltipProvider, ActionListener, EventListener

public class FluxData
extends Object
implements ChRunnable, ActionListener, PaintHook, TooltipProvider

HELP With this dialog numeric values can be highlighted in graphical pathway maps. The dialog is initialized with the URL of a directory containing data files. The data files must have the ending ".txt".

File-format Each line of the file contains a reaction or dataset identifier in the first column and a float number in the second column. The columns are separated by Tab. Only the first two columns are regarded. Lines starting with "#" or not having a tab-character are ignored. Example:

...
HR00115 40      15019.8 PPi@GolErMi + H2O@GolErMi --> 2 Pi@GolErMi   R00004@GolErMi PP@GolErMi
HR00115 1833.69 15019.8 PPi@cyto + H2O@cyto --> 2 Pi@cyto    R00004@cyto PP@cyto
HR00149 53.9141 (1)     NADH@cyto + 2 Ferricytochrome@b5@cyto <=> NAD+@cyto + 2 Ferrocytochrome@b5@cyto   R00100@cyto CYB5R3@cyto
HR00158 1533.69 2.43034 ATP@mito + AMP@mito <=> 2 ADP@mito        R00127@mito AK1@mito
HR00164 34      159086  2 ATP@mito + CO2@mito + H2O@mito + NH3@mito <=> 2 ADP@mito + Pi@mito + Carbamoyl-P@mito   R00149@mito CPS1@mito
...

The identifiers may have a compartment suffix starting with an @ sign. Example:

...
HR00164 34      159086  2 ATP@mito + CO2@mito + H2O@mito + NH3@mito <=> 2 ADP@mito + Pi@mito + Carbamoyl-P@mito   R00149@mito CPS1@mito
...

More than one experiment can be contained in one file. In this case, header lines should start with at least three "#"-signs. Example:

############################################# HDL:

...

############################################# VLDL:
...

What values are not mapped? If an identifier is not found in the graphical pathway map then the line is ignored. All ignored identifiers are highlighted in the text.

Field Summary

Map<String,Color>

mapCompartmentColor

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Method Summary

void	actionPerformed(ActionEvent ev)
static Customize	customizeColors()
String[]	getCompartments()
String	getToolTipText(JComponent pathwayView, MouseEvent ev)
static void	main(String[] argv)
Map<String,Color>	mapCompartmentColor()
static FluxData	newInstance(String url0, String title)
boolean	paintHook(JComponent pathwayView, Graphics graphics, boolean after)
Object	run(String id, Object arg)
void	show(String title)

Methods inherited from class java.lang.Object

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

Field Detail

mapCompartmentColor

public Map<String,Color> mapCompartmentColor

Method Detail

newInstance

public static FluxData newInstance(String url0,
                                   String title)

show

public void show(String title)

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

actionPerformed

public void actionPerformed(ActionEvent ev)

Specified by:

actionPerformed in interface ActionListener

getCompartments

public String[] getCompartments()

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

customizeColors

public static Customize customizeColors()

mapCompartmentColor

public Map<String,Color> mapCompartmentColor()

getToolTipText

public String getToolTipText(JComponent pathwayView,
                             MouseEvent ev)

Specified by:

getToolTipText in interface TooltipProvider

main

public static void main(String[] argv)
                 throws Exception

Throws:

Exception