ij.plugin
Class GelAnalyzer

java.lang.Object
  ij.plugin.GelAnalyzer

All Implemented Interfaces:

PlugIn

public class GelAnalyzer
extends java.lang.Object
implements PlugIn

This plugin generates gel profile plots that can be analyzed using the wand tool. It is similar to the "Gel Plotting Macros" in NIH Image.

Field Summary

(package private) java.awt.Font	f
(package private) static java.awt.Rectangle	firstRect
(package private) static ImagePlus	gel
(package private) static java.lang.String	GEL
(package private) ImagePlus	imp
(package private) static int	INVERT
(package private) boolean	invertedLut
(package private) static boolean	invertPeaks
(package private) static ImageProcessor	ipLanes
(package private) static boolean	isVertical
(package private) static boolean	labelWithPercentages
(package private) static int	MAX_LANES
(package private) static int	nLanes
(package private) static int	OD
(package private) double	odMax
(package private) double	odMin
(package private) static int	options
(package private) static int	OUTLINE
(package private) static boolean	outlineLanes
(package private) static int	PERCENT
(package private) static int	plotHeight
(package private) static PlotsCanvas	plotsCanvas
(package private) static java.util.Vector	roiList
(package private) static int	saveID
(package private) static int	saveNLanes
(package private) static boolean	uncalibratedOD
(package private) static int[]	x

Constructor Summary

GelAnalyzer()

Method Summary

(package private) double[]	od(double[] profile)
(package private) void	outlineLanes()
(package private) void	plotLanes(ImagePlus imp, boolean replot)
void	run(java.lang.String arg) This method is called when the plugin is loaded.
static void	savePreferences(java.util.Properties prefs) Called once when ImageJ quits.
(package private) void	selectFirstLane(java.awt.Rectangle rect)
(package private) void	selectNextLane(java.awt.Rectangle rect)
(package private) void	setCustomLut(ImageProcessor ip)
(package private) void	show(java.lang.String msg)
(package private) void	showDialog()
(package private) void	updateRoiList(java.awt.Rectangle rect)

Methods inherited from class java.lang.Object

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

Field Detail

GEL

static final java.lang.String GEL

See Also:

Constant Field Values

OD

static final int OD

See Also:

Constant Field Values

PERCENT

static final int PERCENT

See Also:

Constant Field Values

OUTLINE

static final int OUTLINE

See Also:

Constant Field Values

INVERT

static final int INVERT

See Also:

Constant Field Values

saveID

static int saveID

nLanes

static int nLanes

saveNLanes

static int saveNLanes

firstRect

static java.awt.Rectangle firstRect

MAX_LANES

static final int MAX_LANES

See Also:

Constant Field Values

x

static int[] x

plotsCanvas

static PlotsCanvas plotsCanvas

ipLanes

static ImageProcessor ipLanes

gel

static ImagePlus gel

plotHeight

static int plotHeight

options

static int options

uncalibratedOD

static boolean uncalibratedOD

labelWithPercentages

static boolean labelWithPercentages

outlineLanes

static boolean outlineLanes

invertPeaks

static boolean invertPeaks

roiList

static java.util.Vector roiList

invertedLut

boolean invertedLut

imp

ImagePlus imp

f

java.awt.Font f

odMin

double odMin

odMax

double odMax

isVertical

static boolean isVertical

Constructor Detail

GelAnalyzer

public GelAnalyzer()

Method Detail

run

public void run(java.lang.String arg)

Description copied from interface: PlugIn

This method is called when the plugin is loaded. 'arg', which may be blank, is the argument specified for this plugin in IJ_Props.txt.

Specified by:

run in interface PlugIn

showDialog

void showDialog()

selectFirstLane

void selectFirstLane(java.awt.Rectangle rect)

selectNextLane

void selectNextLane(java.awt.Rectangle rect)

updateRoiList

void updateRoiList(java.awt.Rectangle rect)

plotLanes

void plotLanes(ImagePlus imp,
               boolean replot)

od

double[] od(double[] profile)

outlineLanes

void outlineLanes()

setCustomLut

void setCustomLut(ImageProcessor ip)

show

void show(java.lang.String msg)

savePreferences

public static void savePreferences(java.util.Properties prefs)

Called once when ImageJ quits.