Class Draw2DprotPlot

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Canvas
              |
              +--Draw2DprotPlot

All Implemented Interfaces:

javax.accessibility.Accessible, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.io.Serializable

Direct Known Subclasses:

DrawProtScatterPlot

public class Draw2DprotPlot

extends java.awt.Canvas

implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener

Class Draw2DPlot.java - draw 2D graphics protein scatterplot. This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick). As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file.

Version:

$Date: 2002/10/14 20:17:17 $ $Revision: $

Author:

P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD

See Also:

ProtPlot Home

This work was derived from MAExplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://maexplorer.sourceforge.org/, Serialized Form

Inner classes inherited from class java.awt.Canvas

java.awt.Canvas.AccessibleAWTCanvas

Inner classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock

Field Summary

java.lang.String	aText
private java.awt.Color	curProteinColor
int	cvPrecision
static int	dbugCnt debugging counter
private boolean	drawIntoImageFlag set if draw clustergram to GIF file
(package private) float	eDiff
(package private) float	eDiffBest
Filter	fil instance of Filter
java.lang.String	horizCaption
(package private) int	iBest Best index of spot closest to where clicked with mouse
private int	iCurMPid
private int	iHeight
private java.awt.Image	img [TODO] buffered spot image.
java.lang.String	info1
java.lang.String	info2
java.lang.String	info3
java.lang.String	info4
java.lang.String	info5
java.lang.String	info6
private int	iWidth
private int	leftTextX
static double	ln10 log(x)= ln10*ln(x)
static double	log10e ln(x)= log10e*log(x)
private float	logScaleX
private float	logScaleY
private boolean	logScalingFlag Linear(false)/Log(true)
java.lang.String	lowerTitle1
java.lang.String	lowerTitle2
double	maxX range set in initial call
double	maxXscroll range set by ShowPlotPopup scrollers
double	maxY range set in initial call
double	maxYscroll range set by ShowPlotPopup scrollers
(package private) static int	MIN_CANVAS_HEIGHT
(package private) static int	MIN_CANVAS_WIDTH
double	minX range set in initial call
double	minXscroll range set by ShowPlotPopup scrollers
double	minY range set in initial call
double	minYscroll range set by ShowPlotPopup scrollers
(package private) java.awt.Font	normFont The normal font
private java.awt.Color	notOkColor
int	nPointsMax maximum drawing list size.
int	nPointsPlotted # points plotted after data is filtered
private java.lang.String	oGifFileName GIF output file if used
private java.awt.Color	okColor
private java.awt.Color	pointColor
int	preferredHeight target Size for selecting a line
int	preferredWidth target Size for selecting a line
ProtPlot	prp instance of ProtPlot
private int	radius
(package private) static int	RADIUS
ReadPRP	rd instance of ReadPRP
private int	scale
(package private) static int	SCALE_DEF
double	scaleX
private float	scaleXplot
double	scaleY
private float	scaleYplot
private java.lang.String	sMaxX
private java.lang.String	sMaxY
private java.lang.String	sMinX
private java.lang.String	sMinY
ShowScatterPlotPopup	spp instance of ShowScatterPlotPopup if the parent, else null
(package private) static int	TARGET_SIZE
java.lang.String	title
(package private) java.awt.Font	titleFont The title font
java.lang.String	topTitle1
java.lang.String	topTitle2
java.lang.String	topTitle3
java.lang.String	topTitle4
private UtilPRP	util instance of UtilPRP
java.lang.String	vertCaption
private float	xBase baseline for xList to xPnt
private int	xcurProtein current protein if defined
float[]	xDataScatterPlot X Coords [0:nPointsMax-1] used for computing ratios when clicking
private int	xLeft
private int	xOffset
(package private) static int	XOFFSET_DEF
int[]	xPlotted X Coord [0:nPointsMax-1] for clicking on point in list
private int	xPnt xList[0:prp.nMpidSamples-1] data mapped to int
private float	xRange
(package private) static int	XRANGE_DEF
private int	xRight
private float	xScale slope for xList to xPnt
private int	xText
private float	yBase baseline for yList to yPnt
private int	ycurProtein current protein if defined
float[]	yDataScatterPlot Y Coord [0:nPointsMax-1] used for computing ratios when clicking
private int	yOffset
(package private) static int	YOFFSET_DEF
int[]	yPlotted Y Coord [0:nPointsMax-1] for clicking on point in list
private int	yPnt yList[0:prp.nMpidSamples-1] data mapped to int
private float	yRange
(package private) static int	YRANGE_DEF
private float	yScale slope for yList to yPnt
private int	yText
private int	yTop

Fields inherited from class java.awt.Canvas

base, nameCounter, serialVersionUID

Fields inherited from class java.awt.Component

accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dbg, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

(package private)

Draw2DprotPlot(ProtPlot prp, ShowScatterPlotPopup spp, java.lang.String title) Draw2Dplot() - constructor

Method Summary

static double	alog10(double x) alog10() - compute alog(x) base 10.
void	calcBaseImage() calcBaseImage() - calculate base image for plot into img.
private void	draw2Dplot(java.awt.Graphics g) draw2Dplot() - draw a plot in the current graphics context This is the main plot drawing method generally called by paint().
private void	drawCircle(java.awt.Graphics g, int xC, int yC, int radius, java.awt.Color color) drawCircle() - draw a circle The color is optional and if null it draws it in green (blue).
private void	drawCmapRatioScaleMap(java.awt.Graphics gi, int yTop, int xRight, float maxValue, float minValue) drawCmapRatioScaleMap() - draw Cmap ratio scale factor color map on the right side of the canvas.
private void	drawFilledColoredCircle(java.awt.Graphics g, int x, int y, int radius, java.awt.Color color) drawFilledColoredCircle() - draw filled circle of specified RGB color
private void	drawFilledColoredCircle(java.awt.Graphics g, int x, int y, int radius, int red, int green, int blue) drawFilledColoredCircle() - draw filled circle of specified RGB color
private void	drawFilledGrayCircle(java.awt.Graphics g, int x, int y, int radius, int grayValue) drawFilledGrayCircle() - draw filled circle of specified gray value
private void	drawFilterStatusText(java.awt.Graphics g) drawFilterStatusText() - draw additional text on Filter status if required
boolean	drawGifFile(java.lang.String oGifFileName) drawGifFile() - draw clustergram into Gif image file.
private void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign
private boolean	drawProtein(java.awt.Graphics g, int idx, int mPid) drawProteinSpot() - draw protein mPid if passes the data filter
private void	drawRedPlusGreenRatioScaleMap(java.awt.Graphics gi, int yTop, int xRight, float maxValue, float minValue) drawRedPlusGreenRatioScaleMap() - draw (Red+Green)=(X+Y) scale factor color map on right side of the canvas
private void	drawScaleMap(java.awt.Graphics gi, int yTop, int xRight, float maxValue, float minValue) drawScaleMap() - draw scale factor color map on right side of the canvas
private void	drawScatterPlotScaleAndLabels(java.awt.Graphics g) drawScatterPlotScaleAndLabels() - draw scatterplot scale lines and labels
private void	drawSquare(java.awt.Graphics g, int xC, int yC, int radius, java.awt.Color color) drawSquare() - draw a square The color is optional and if null it draws it in green (blue).
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
static double	log10(double x) log10() - compute log(x) base 10.
static double	logZero(double x) logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
void	mouseClicked(java.awt.event.MouseEvent e)
void	mouseDragged(java.awt.event.MouseEvent e)
void	mouseEntered(java.awt.event.MouseEvent e)
void	mouseExited(java.awt.event.MouseEvent e)
void	mouseMoved(java.awt.event.MouseEvent e) mouseMoved() - process mouse event - update MouseOver
void	mousePressed(java.awt.event.MouseEvent e) mousePressed() - process mouse event, change current clone
void	mouseReleased(java.awt.event.MouseEvent e)
void	paint(java.awt.Graphics g) paint() - draw the expression profile
void	set2DplotSubtitles(java.lang.String info1, java.lang.String info2, java.lang.String info3, java.lang.String info4, java.lang.String info5, java.lang.String info6) set2DplotSubtitles() - set info1,2,3,4,5,6 subtitles for plot
void	setupArrays(int nPointsToPlot) setupArrays() - setup the arrays.
void	update2Dplot(java.lang.String vertCaption, java.lang.String horizCaption, java.lang.String title, java.lang.String topTitle1, java.lang.String topTitle2, java.lang.String topTitle3, java.lang.String topTitle4, java.lang.String lowerTitle1, java.lang.String lowerTitle2, java.lang.String aText, int xText, int yText, double scaleX, double scaleY, double minX, double maxX, double minY, double maxY) update2Dplot() - set data for plot.
void	updateScaling(boolean logScalingFlag) updateScaling() - set scaling mode in proper sub-object.
void	updateScrolledRegion(float xLB, float xUB, float yLB, float yUB) updateScrolledRegion() - update scrolled region to plot [(x1,y1):(x2,y2)].

Methods inherited from class java.awt.Canvas

, addNotify, constructComponentName, getAccessibleContext, postsOldMouseEvents

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkGD, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createChildHierarchyEvents, createHierarchyEvents, createImage, createImage, deliverEvent, disable, disableEvents, dispatchEvent, dispatchEventImpl, doLayout, enable, enable, enableEvents, enableInputMethods, eventEnabled, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getAlignmentX, getAlignmentY, getBackground, getBounds, getBounds, getColorModel, getComponentAt, getComponentAt, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getListeners, getLocale, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getMaximumSize, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkit, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, initIDs, inside, invalidate, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, layout, lightweightPaint, lightweightPrint, list, list, list, list, list, locate, location, lostFocus, minimumSize, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, numListening, paintAll, paintHeavyweightComponents, paramString, postEvent, preferredSize, prepareImage, prepareImage, print, printAll, printHeavyweightComponents, processComponentEvent, processEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, readObject, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, resetGC, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFont, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, show, size, toString, transferFocus, update, validate, writeObject

Methods inherited from class java.lang.Object

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

Field Detail

prp

public ProtPlot prp

instance of ProtPlot

rd

public ReadPRP rd

instance of ReadPRP

fil

public Filter fil

instance of Filter

spp

public ShowScatterPlotPopup spp

instance of ShowScatterPlotPopup if the parent, else null

util

private UtilPRP util

instance of UtilPRP

dbugCnt

public static int dbugCnt

debugging counter

ln10

public static final double ln10

log(x)= ln10*ln(x)

log10e

public static final double log10e

ln(x)= log10e*log(x)

RADIUS

static final int RADIUS

MIN_CANVAS_WIDTH

static final int MIN_CANVAS_WIDTH

MIN_CANVAS_HEIGHT

static final int MIN_CANVAS_HEIGHT

XRANGE_DEF

static final int XRANGE_DEF

YRANGE_DEF

static final int YRANGE_DEF

XOFFSET_DEF

static final int XOFFSET_DEF

YOFFSET_DEF

static final int YOFFSET_DEF

SCALE_DEF

static final int SCALE_DEF

TARGET_SIZE

static final int TARGET_SIZE

preferredHeight

public int preferredHeight

target Size for selecting a line

preferredWidth

public int preferredWidth

target Size for selecting a line

iWidth

private int iWidth

iHeight

private int iHeight

normFont

java.awt.Font normFont

The normal font

titleFont

java.awt.Font titleFont

The title font

nPointsMax

public int nPointsMax

maximum drawing list size. Set when going to draw

xDataScatterPlot

public float[] xDataScatterPlot

X Coords [0:nPointsMax-1] used for computing ratios when clicking

yDataScatterPlot

public float[] yDataScatterPlot

Y Coord [0:nPointsMax-1] used for computing ratios when clicking

xPlotted

public int[] xPlotted

X Coord [0:nPointsMax-1] for clicking on point in list

yPlotted

public int[] yPlotted

Y Coord [0:nPointsMax-1] for clicking on point in list

nPointsPlotted

public int nPointsPlotted

# points plotted after data is filtered

cvPrecision

public int cvPrecision

vertCaption

public java.lang.String vertCaption

horizCaption

public java.lang.String horizCaption

title

public java.lang.String title

topTitle1

public java.lang.String topTitle1

topTitle2

public java.lang.String topTitle2

topTitle3

public java.lang.String topTitle3

topTitle4

public java.lang.String topTitle4

lowerTitle1

public java.lang.String lowerTitle1

lowerTitle2

public java.lang.String lowerTitle2

info1

public java.lang.String info1

info2

public java.lang.String info2

info3

public java.lang.String info3

info4

public java.lang.String info4

info5

public java.lang.String info5

info6

public java.lang.String info6

aText

public java.lang.String aText

xText

private int xText

yText

private int yText

scaleX

public double scaleX

scaleY

public double scaleY

minX

public double minX

range set in initial call

maxX

public double maxX

range set in initial call

minY

public double minY

range set in initial call

maxY

public double maxY

range set in initial call

minXscroll

public double minXscroll

range set by ShowPlotPopup scrollers

minYscroll

public double minYscroll

range set by ShowPlotPopup scrollers

maxXscroll

public double maxXscroll

range set by ShowPlotPopup scrollers

maxYscroll

public double maxYscroll

range set by ShowPlotPopup scrollers

logScalingFlag

private boolean logScalingFlag

Linear(false)/Log(true)

xScale

private float xScale

slope for xList to xPnt

yScale

private float yScale

slope for yList to yPnt

xBase

private float xBase

baseline for xList to xPnt

yBase

private float yBase

baseline for yList to yPnt

xOffset

private int xOffset

yOffset

private int yOffset

xRange

private float xRange

yRange

private float yRange

xLeft

private int xLeft

xRight

private int xRight

scaleXplot

private float scaleXplot

scaleYplot

private float scaleYplot

logScaleY

private float logScaleY

logScaleX

private float logScaleX

scale

private int scale

radius

private int radius

leftTextX

private int leftTextX

yTop

private int yTop

iCurMPid

private int iCurMPid

xcurProtein

private int xcurProtein

current protein if defined

ycurProtein

private int ycurProtein

current protein if defined

sMinX

private java.lang.String sMinX

sMaxX

private java.lang.String sMaxX

sMinY

private java.lang.String sMinY

sMaxY

private java.lang.String sMaxY

curProteinColor

private java.awt.Color curProteinColor

okColor

private java.awt.Color okColor

notOkColor

private java.awt.Color notOkColor

pointColor

private java.awt.Color pointColor

xPnt

private int xPnt

xList[0:prp.nMpidSamples-1] data mapped to int

yPnt

private int yPnt

yList[0:prp.nMpidSamples-1] data mapped to int

iBest

int iBest

Best index of spot closest to where clicked with mouse

eDiff

float eDiff

eDiffBest

float eDiffBest

img

private java.awt.Image img

[TODO] buffered spot image. This gets updated 1. if useFilterFlag, useExprFlag changes 2. if filtering and the Filter or tissue bits change.

drawIntoImageFlag

private boolean drawIntoImageFlag

set if draw clustergram to GIF file

oGifFileName

private java.lang.String oGifFileName

GIF output file if used

Constructor Detail

Draw2DprotPlot

Draw2DprotPlot(ProtPlot prp,
               ShowScatterPlotPopup spp,
               java.lang.String title)

Draw2Dplot() - constructor

Parameters:

prp - is instance of ProtPlot

spp - is instance of ShowScatterPlotPopup if it is parent, else null

title - for the display

Method Detail

setupArrays

public void setupArrays(int nPointsToPlot)

setupArrays() - setup the arrays. If the # of points to plot increases then realloc the arrays.

Parameters:

nPointsToPlot - is max # of points to plot

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Component

Returns:

the preferred size

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the preferred size

Overrides:

getMinimumSize in class java.awt.Component

Returns:

the minimum preferred size

drawGifFile

public boolean drawGifFile(java.lang.String oGifFileName)

drawGifFile() - draw clustergram into Gif image file. This sets it up and lets paint() to the heavy lifting...

Parameters:

oGifFileName - is the name of the GIF output file.

See Also:

Component.repaint()

paint

public void paint(java.awt.Graphics g)

paint() - draw the expression profile

Overrides:

paint in class java.awt.Canvas

Parameters:

g - is graphics context

drawPlus

private final void drawPlus(java.awt.Graphics g,
                            int x,
                            int y,
                            java.awt.Color color)

drawPlus() - draw plus sign

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

color - to draw the plus sign

drawCircle

private final void drawCircle(java.awt.Graphics g,
                              int xC,
                              int yC,
                              int radius,
                              java.awt.Color color)

drawCircle() - draw a circle The color is optional and if null it draws it in green (blue). if prp.useDichromasyFlag then use blue.

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

radius - is size of circle to draw

color - to draw the circle

drawSquare

private final void drawSquare(java.awt.Graphics g,
                              int xC,
                              int yC,
                              int radius,
                              java.awt.Color color)

drawSquare() - draw a square The color is optional and if null it draws it in green (blue). if useDichomasyFlag then use blue.

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

radius - is size of circle to draw

color - to draw the circle

drawFilledGrayCircle

private final void drawFilledGrayCircle(java.awt.Graphics g,
                                        int x,
                                        int y,
                                        int radius,
                                        int grayValue)

drawFilledGrayCircle() - draw filled circle of specified gray value

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

radius - is size of circle to draw

grayValue - to draw the circle

drawFilledColoredCircle

private final void drawFilledColoredCircle(java.awt.Graphics g,
                                           int x,
                                           int y,
                                           int radius,
                                           int red,
                                           int green,
                                           int blue)

drawFilledColoredCircle() - draw filled circle of specified RGB color

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

radius - is size of circle to draw

red - to component of color to draw

green - to component of color to draw

blue - to component of color to draw

drawFilledColoredCircle

private final void drawFilledColoredCircle(java.awt.Graphics g,
                                           int x,
                                           int y,
                                           int radius,
                                           java.awt.Color color)

drawFilledColoredCircle() - draw filled circle of specified RGB color

Parameters:

g - is graphics context

x - is x coordinate to plot

y - is y coordinate to plot

red - to component of color to draw

green - to component of color to draw

blue - to component of color to draw

update2Dplot

public void update2Dplot(java.lang.String vertCaption,
                         java.lang.String horizCaption,
                         java.lang.String title,
                         java.lang.String topTitle1,
                         java.lang.String topTitle2,
                         java.lang.String topTitle3,
                         java.lang.String topTitle4,
                         java.lang.String lowerTitle1,
                         java.lang.String lowerTitle2,
                         java.lang.String aText,
                         int xText,
                         int yText,
                         double scaleX,
                         double scaleY,
                         double minX,
                         double maxX,
                         double minY,
                         double maxY)

update2Dplot() - set data for plot. The list of mPids is in global list prp.mPidSamples[0:prp.nMpidSamples-1].

Parameters:

vertCaption - vertical caption

horizCaption - horizontal caption

title - title of the display

topTitle1 - is the upper LHC data

topTitle2 -

topTitle3 -

topTitle4 -

lowerTitle1 - is the data for below X axis

lowerTitle2 -

aText -

xText -

yText -

scaleX - is the global scaling (1.0 fixed)

scaleY - is the global scaling (1.0 fixed)

minX - is the min possible range of X of current set of samples

maxX - is the max possible range of X

minY - is the min possible range of Y

maxY - is the max possible range of Y

updateScrolledRegion

public void updateScrolledRegion(float xLB,
                                 float xUB,
                                 float yLB,
                                 float yUB)

updateScrolledRegion() - update scrolled region to plot [(x1,y1):(x2,y2)].

Parameters:

xLB - range 0.0:1.0

xUB - in range 0.0:1.0

yLB - in range 0.0:1.0

yUB - in range 0.0:1.0

set2DplotSubtitles

public void set2DplotSubtitles(java.lang.String info1,
                               java.lang.String info2,
                               java.lang.String info3,
                               java.lang.String info4,
                               java.lang.String info5,
                               java.lang.String info6)

set2DplotSubtitles() - set info1,2,3,4,5,6 subtitles for plot

Parameters:

info1 - is the data for the 1st info line

info2 - is the data for the 2nd info line

info3 - is the data for the 3rd info line

info4 - is the data for the 4th info line

info5 - is the data for the 5th info line

info6 - is the data for the 5th info line

calcBaseImage

public void calcBaseImage()

calcBaseImage() - calculate base image for plot into img. This gets updated 1. if useFilterFlag, useExprFlag changes 2. if filtering and the Filter or tissue bits change.

drawRedPlusGreenRatioScaleMap

private void drawRedPlusGreenRatioScaleMap(java.awt.Graphics gi,
                                           int yTop,
                                           int xRight,
                                           float maxValue,
                                           float minValue)

drawRedPlusGreenRatioScaleMap() - draw (Red+Green)=(X+Y) scale factor color map on right side of the canvas

 It makes a color grid
             Max-ratio         Min-ratio
  Max-expr  RED (X=1.0) . . . GREEN (Y=1.0)  full colors
                        . . .
  Min-expr  RED (X=0.0) . . . GREEN (Y=0.0)  (black)

 So at each point it makes a color (R,G,B)= (255*X*r,255*Y*r',0).
 where r 

Parameters:

gi - is graphics context

yTop - position of the scale map

xRight - position of the scale map

maxValue - correspoding to top of scale map

minValue - correspoding to bottom of scale map

drawCmapRatioScaleMap

private void drawCmapRatioScaleMap(java.awt.Graphics gi,
                                   int yTop,
                                   int xRight,
                                   float maxValue,
                                   float minValue)

drawCmapRatioScaleMap() - draw Cmap ratio scale factor color map on the right side of the canvas. Ratio values range from -10.0 through 1.0 through +10.0. Ratio Values beyond [-10.0 : +10.0] are mapped to [-10.0 : +10.0]. The spp.eCMapRatios[0:8] contains the ratio values The spp.eCMapRatios[0:8] contains the colors values

 Color points are:
   +10.0  brightest red (255,0,0)     eCmapColor[0]
   + 5.0  bright red (200,0,0)        eCmapColor[1]
   + 2.0  medium red (170,0,0)        eCmapColor[2]
   + 1.5  dim red (128,0,0)           eCmapColor[3]
   + 1.0  black (0,0,0)               eCmapColor[4]
   -1/1.5   dim green (0,128,0)       eCmapColor[5]
   -1/2.0   medium green (0,170,0)    eCmapColor[6]
   -1/5.0   bright green (0,200,0)    eCmapColor[7]
   -1/10.0  brightest green (0,255,0) eCmapColor[8]

Parameters:

gi - is graphics context

yTop - position of the scale map

xRight - position of the scale map

maxValue - correspoding to top of scale map

minValue - correspoding to bottom of scale map

drawScaleMap

private void drawScaleMap(java.awt.Graphics gi,
                          int yTop,
                          int xRight,
                          float maxValue,
                          float minValue)

drawScaleMap() - draw scale factor color map on right side of the canvas

Parameters:

gi - is graphics context

yTop - position of the scale map

xRight - position of the scale map

maxValue - correspoding to top of scale map

minValue - correspoding to bottom of scale map

drawFilterStatusText

private void drawFilterStatusText(java.awt.Graphics g)

drawFilterStatusText() - draw additional text on Filter status if required

Parameters:

g - is graphics context

drawScatterPlotScaleAndLabels

private void drawScatterPlotScaleAndLabels(java.awt.Graphics g)

drawScatterPlotScaleAndLabels() - draw scatterplot scale lines and labels

drawProtein

private boolean drawProtein(java.awt.Graphics g,
                            int idx,
                            int mPid)

drawProteinSpot() - draw protein mPid if passes the data filter

Parameters:

g - is Graphics context

idx - is the idx'th index that corresponds to the mPid

mPid - is protein to draw

Returns:

true if drew the spot

draw2Dplot

private void draw2Dplot(java.awt.Graphics g)

draw2Dplot() - draw a plot in the current graphics context This is the main plot drawing method generally called by paint().

Parameters:

g - is graphics context

updateScaling

public void updateScaling(boolean logScalingFlag)

updateScaling() - set scaling mode in proper sub-object. Linear(false)/Log(true)

Parameters:

logScalingFlag - to enable log scaling

logZero

public static double logZero(double x)

logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).

Parameters:

x - is value to use

Returns:

log10(x) with zero detection

log10

public static double log10(double x)

log10() - compute log(x) base 10. Since log(x)= ln(10)*ln(x).

Parameters:

x - is value to use

Returns:

log10(x)

alog10

public static double alog10(double x)

alog10() - compute alog(x) base 10. Since ln(x)= log10(e)*log(x).

Parameters:

x - is value to use

Returns:

alog10(x)

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

mousePressed() - process mouse event, change current clone

Specified by:

mousePressed in interface java.awt.event.MouseListener

Parameters:

e - is MouseEvent

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)

mouseMoved() - process mouse event - update MouseOver

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

Parameters:

e - is MouseEvent

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)

Specified by:

mouseExited in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

Specified by:

mouseReleased in interface java.awt.event.MouseListener

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener