Class Draw2Dplot

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Canvas
              |
              +--Draw2Dplot

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:

DrawScatterPlot

class Draw2Dplot

extends java.awt.Canvas

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

This is a base class used for drawing 2D graphics plots. It contains code to draw axes, titles, captions, scale the data, overlay graphics, point event handlers, etc. In particular DrawScatterPlot, ExprProfileOverlay extend this class.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. 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. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/07/07 21:42:38 $ $Revision: 1.12 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home, DrawScatterPlot, ExprProfileOverlay, 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

private java.lang.String	aText ARGS:
private java.lang.String	aTextOrig copy of original aText disp below title3
(package private) CompositeDatabase	cdb link to global CompositeDatabase instance
(package private) int	cvPrecision fraction precision reporting data
(package private) float	cx1 clipped x1 for clipping divider
(package private) float	cx2 clipped x2 for clipping divider
(package private) float	cy1 clipped y1 for clipping divider
(package private) float	cy2 clipped y2for clipping divider
(package private) GeneList	dispCL associated GeneList if not null
private boolean	draw180lineFlag flag: draw 180 degree line
private boolean	draw45lineFlag flag: draw 45 degree line
(package private) boolean	drawIntoImageFlag flag: set if draw plot to GIF file
(package private) ExprProfileOverlay	epov if ExprProfileOverlay is the parent, else null
(package private) GeneList	eventHandlerCL set to gene list being used
(package private) Filter	fc link to global Filter instance
private java.awt.Font	fontReg regular font
(package private) java.awt.Graphics	gScatterPlot Graphics context used with displayPlot
private java.lang.String	horizCaption ARGS: horizontal caption
private int	iFontHdrSize
private int	iFontSize integer regular font size
private int	iHeight working canvas height
private java.lang.String	info1 ARGS:
private java.lang.String	info2 ARGS:
private java.lang.String	info3 ARGS:
private java.lang.String	info4 ARGS:
private int	iWidth working canvas width
private boolean[]	jGrpList group # for EP [0:maxGenes-1]
private boolean	logScalingFlag flag: Linear(false)/Log(true)
(package private) MAExplorer	mae link to global instance
private int[]	mapPntToMid map point # in [0:nGroup*maxGenes] to [0:maxGenes]
(package private) int	maxLineList max allowed # of EGL genes
(package private) double	maxX max X range set in initial call
(package private) double	maxXscroll max X range set by ShowPlotPopup scrollers
(package private) double	maxY max X range set in initial call
(package private) double	maxYscroll max Y range set by ShowPlotPopup scrollers
(package private) static int	MIN_CANVAS_HEIGHT default canvas height
(package private) static int	MIN_CANVAS_WIDTH default canvas width
(package private) double	minX min X range set in initial call
(package private) double	minXscroll min X range set by ShowPlotPopup scrollers
(package private) double	minY min Y range set in initial call
(package private) double	minYscroll min Y range set by ShowPlotPopup scrollers
(package private) MaHybridSample	ms link to global MaHybridSample instance
(package private) int	nLineGroup # sequential points to connect group with line for use with EP 2D plot # of lines/line-group
(package private) int	nList # elements in x(y)(p)List[0:nList-1]
(package private) int	nPointsPlotted # points plotted.
(package private) java.lang.String	oGifFileName full Gif file path name
(package private) OverlayMap	olmap link to scatterplot named overlay maps instance
(package private) int	plotMode2D plot mode for spp
(package private) int	preferredHeight preferred canvas height
(package private) int	preferredWidth preferred canvas width
private int[]	propList property of data to draw
(package private) double	scaleX scale factor X-axis
(package private) double	scaleY scale factor X-axis
(package private) boolean	showNonFilteredGenesFlag show grayed out non-filtered genes
(package private) ShowPlotPopup	spp if ShowPlotPopup is the parent, else null
(package private) static int	TARGET_SIZE target Size for selecting a line
private java.lang.String	title ARGS: horizontal caption
private java.lang.String	title1 ARGS:
private java.lang.String	title2 ARGS:
private java.lang.String	title3 ARGS:
private java.lang.String	topTitle ARGS:
private boolean	useXaxisIntNbrFlag flag: label all vert lines w/int #
private java.lang.String	vertCaption ARGS: vertical caption
(package private) float	vx1 viewport x1 for clipping divider
(package private) float	vx2 viewport x2 for clipping divider
(package private) float	vy1 viewport y1 for clipping divider
(package private) float	vy2 viewport y2 for clipping divider
private float	xBase baseline for xxList to xPnt
(package private) float[]	xDataScatterPlot x Data for computing ratios when clicking
private int[][]	xLineList X values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
(package private) float[]	xList ALL of actual X data points to draw [0:nList-1]
(package private) int[]	xPlotted x plot coordinate for clicking on point in list
private int	xPnt xList[] data mapped to int
private float	xScale slope for xList to xPnt
private int	xText --
private float	yBase baseline for yList to xyPnt
(package private) float[]	yDataScatterPlot y Data for computing ratios when clicking
private int[][]	yLineList Y values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
(package private) float[]	yList ALL of actual Y data points to draw [0:nList-1]
(package private) int[]	yPlotted y plot coordinate for clicking on point in list
private int	yPnt yList[] data mapped to int
private float	yScale slope for yList to yPnt
private int	yText --

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)

Draw2Dplot(MAExplorer mae, int plotMode, ShowPlotPopup spp, ExprProfileOverlay epov, java.lang.String title, int nPoints, int nLineGroup, boolean useXaxisIntNbrFlag) Draw2Dplot() - constructor

Method Summary

private int	clipCodeViewport(float x, float y) clip_code_viewport(x,y) - Return the clipping code of where (x,y) is w.r.t.
(package private) boolean	clipViewport(float x1, float x2, float y1, float y2) clipViewport(x1,x2,y1,y2) - Compute if (x1,x2,y1,y2) is inside of Viewport window.
(package private) void	draw2Dplot(java.awt.Graphics g) draw2Dplot() - draw a plot in the current graphics context.
private void	drawCircle(java.awt.Graphics g, int xC, int yC, int radius, java.awt.Color color) drawCircle() - draw a circle as overlay graphic in specified 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 grayvalue
private void	drawNamedOverlayMaps(java.awt.Graphics g, float scaleXplot, float scaleYplot, double minXscroll, double minYscroll, int xOffset, int yOffset) drawNamedOverlayMaps() try to draw overlay maps if there are any and they are enabled
private void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign as overlay graphic in specified color.
private void	drawRectangleBin(java.awt.Graphics g, int x, int y, int width, int height, java.awt.Color color) drawRectangleBin() - draw rectangle (histogram) bin as overlay graphic in specified color.
private void	drawSquare(java.awt.Graphics g, int xC, int yC, int radius, java.awt.Color color) drawSquare() - draw a square as overlay graphic in specified color.
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
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 gene.
void	mouseReleased(java.awt.event.MouseEvent e)
void	paint(java.awt.Graphics g) paint() - draw the 2D plot.
(package private) void	set2DplotSubtitles(java.lang.String info1, java.lang.String info2, java.lang.String info3, java.lang.String info4) set2DplotSubtitles() - set info1,2,3,4 subtitles for plot.
(package private) void	setDataToClip(float x1, float x2, float y1, float y2) setDataToClip() - set (cx1,cx2,cy1,cy2) data to clip from((x1,x2,y1,y2)
private void	setFontsFromState() setFontsFromState() - set the regular fonts from the state variables
(package private) void	setViewport(float vx1, float vx2, float vy1, float vy2) setViewport() - set the viewport (vx1,vx2,vy1,vy2) between two points.
(package private) void	update2Dplot(java.lang.String vertCaption, java.lang.String horizCaption, java.lang.String title, java.lang.String topTitle, java.lang.String title1, java.lang.String title2, java.lang.String title3, java.lang.String aText, int xText, int yText, double scaleX, double scaleY, double minX, double maxX, double minY, double maxY, boolean draw45lineFlag, boolean draw180lineFlag, float[] xList, float[] yList, int[] propList, GeneList dispCL, int nList, int[] mapPntToMid) update2Dplot() - set data for plot and then update the plot.
(package private) void	updateScaling(boolean logScalingFlag, boolean showNonFilteredGenesFlag) updateScaling() - set scaling mode in proper sub-object.
(package private) void	updateScrolledRegion(float x1Pos, float x2Pos, float y1Pos, float y2Pos) updateScrolledRegion() - update scrolled region to plot.

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

mae

MAExplorer mae

link to global instance

ms

MaHybridSample ms

link to global MaHybridSample instance

fc

Filter fc

link to global Filter instance

cdb

CompositeDatabase cdb

link to global CompositeDatabase instance

epov

ExprProfileOverlay epov

if ExprProfileOverlay is the parent, else null

spp

ShowPlotPopup spp

if ShowPlotPopup is the parent, else null

olmap

OverlayMap olmap

link to scatterplot named overlay maps instance

plotMode2D

int plotMode2D

plot mode for spp

MIN_CANVAS_WIDTH

static final int MIN_CANVAS_WIDTH

default canvas width

MIN_CANVAS_HEIGHT

static final int MIN_CANVAS_HEIGHT

default canvas height

TARGET_SIZE

static final int TARGET_SIZE

target Size for selecting a line

preferredHeight

int preferredHeight

preferred canvas height

preferredWidth

int preferredWidth

preferred canvas width

iWidth

private int iWidth

working canvas width

iHeight

private int iHeight

working canvas height

xDataScatterPlot

float[] xDataScatterPlot

x Data for computing ratios when clicking

yDataScatterPlot

float[] yDataScatterPlot

y Data for computing ratios when clicking

xPlotted

int[] xPlotted

x plot coordinate for clicking on point in list

yPlotted

int[] yPlotted

y plot coordinate for clicking on point in list

vx1

float vx1

viewport x1 for clipping divider

vx2

float vx2

viewport x2 for clipping divider

vy1

float vy1

viewport y1 for clipping divider

vy2

float vy2

viewport y2 for clipping divider

cx1

float cx1

clipped x1 for clipping divider

cx2

float cx2

clipped x2 for clipping divider

cy1

float cy1

clipped y1 for clipping divider

cy2

float cy2

clipped y2for clipping divider

cvPrecision

int cvPrecision

fraction precision reporting data

nPointsPlotted

int nPointsPlotted

# points plotted. # points= #genes X #samples

eventHandlerCL

GeneList eventHandlerCL

set to gene list being used

gScatterPlot

java.awt.Graphics gScatterPlot

Graphics context used with displayPlot

drawIntoImageFlag

boolean drawIntoImageFlag

flag: set if draw plot to GIF file

oGifFileName

java.lang.String oGifFileName

full Gif file path name

vertCaption

private java.lang.String vertCaption

ARGS: vertical caption

horizCaption

private java.lang.String horizCaption

ARGS: horizontal caption

title

private java.lang.String title

ARGS: horizontal caption

topTitle

private java.lang.String topTitle

ARGS:

title1

private java.lang.String title1

ARGS:

title2

private java.lang.String title2

ARGS:

title3

private java.lang.String title3

ARGS:

info1

private java.lang.String info1

ARGS:

info2

private java.lang.String info2

ARGS:

info3

private java.lang.String info3

ARGS:

info4

private java.lang.String info4

ARGS:

aText

private java.lang.String aText

ARGS:

aTextOrig

private java.lang.String aTextOrig

copy of original aText disp below title3

iFontSize

private int iFontSize

integer regular font size

iFontHdrSize

private int iFontHdrSize

fontReg

private java.awt.Font fontReg

regular font

xText

private int xText

--

yText

private int yText

--

scaleX

double scaleX

scale factor X-axis

scaleY

double scaleY

scale factor X-axis

minX

double minX

min X range set in initial call

maxX

double maxX

max X range set in initial call

minY

double minY

min Y range set in initial call

maxY

double maxY

max X range set in initial call

minXscroll

double minXscroll

min X range set by ShowPlotPopup scrollers

minYscroll

double minYscroll

min Y range set by ShowPlotPopup scrollers

maxXscroll

double maxXscroll

max X range set by ShowPlotPopup scrollers

maxYscroll

double maxYscroll

max Y range set by ShowPlotPopup scrollers

showNonFilteredGenesFlag

boolean showNonFilteredGenesFlag

show grayed out non-filtered genes

logScalingFlag

private boolean logScalingFlag

flag: Linear(false)/Log(true)

draw45lineFlag

private boolean draw45lineFlag

flag: draw 45 degree line

draw180lineFlag

private boolean draw180lineFlag

flag: draw 180 degree line

useXaxisIntNbrFlag

private boolean useXaxisIntNbrFlag

flag: label all vert lines w/int #

xScale

private float xScale

slope for xList to xPnt

yScale

private float yScale

slope for yList to yPnt

xBase

private float xBase

baseline for xxList to xPnt

yBase

private float yBase

baseline for yList to xyPnt

xList

float[] xList

ALL of actual X data points to draw [0:nList-1]

yList

float[] yList

ALL of actual Y data points to draw [0:nList-1]

xLineList

private int[][] xLineList

X values for only EGL gene points [0:nGroup-1][0:maxGenes-1]

yLineList

private int[][] yLineList

Y values for only EGL gene points [0:nGroup-1][0:maxGenes-1]

mapPntToMid

private int[] mapPntToMid

map point # in [0:nGroup*maxGenes] to [0:maxGenes]

jGrpList

private boolean[] jGrpList

group # for EP [0:maxGenes-1]

xPnt

private int xPnt

xList[] data mapped to int

yPnt

private int yPnt

yList[] data mapped to int

propList

private int[] propList

property of data to draw

dispCL

GeneList dispCL

associated GeneList if not null

maxLineList

int maxLineList

max allowed # of EGL genes

nList

int nList

# elements in x(y)(p)List[0:nList-1]

nLineGroup

int nLineGroup

# sequential points to connect group with line for use with EP 2D plot # of lines/line-group

Constructor Detail

Draw2Dplot

Draw2Dplot(MAExplorer mae,
           int plotMode,
           ShowPlotPopup spp,
           ExprProfileOverlay epov,
           java.lang.String title,
           int nPoints,
           int nLineGroup,
           boolean useXaxisIntNbrFlag)

Draw2Dplot() - constructor

Parameters:

mae - is the MAExplorer instance

plotMode - is the 2D plot mode

spp - is the ShowPlotPopup instance

epov - is ExprProfileOverlay instance if not null

title - is window title

nPoints - is the # points= #genes X #samples

nLineGroup - # of lines/line-group. 1 for scatter plot

useXaxisIntNbrFlag - to label all vert lines w/int #

Method Detail

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Component

Returns:

window size

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Overrides:

getMinimumSize in class java.awt.Component

Returns:

window size

setViewport

void setViewport(float vx1,
                 float vx2,
                 float vy1,
                 float vy2)

setViewport() - set the viewport (vx1,vx2,vy1,vy2) between two points.

Parameters:

vx1 - is viewport x1 coordinate

vx2 - is viewport x2 coordinate

vy1 - is viewport y1 coordinate

vy2 - is viewport y2 coordinate

setDataToClip

void setDataToClip(float x1,
                   float x2,
                   float y1,
                   float y2)

setDataToClip() - set (cx1,cx2,cy1,cy2) data to clip from((x1,x2,y1,y2)

Parameters:

x1 - is coordinate

x2 - is coordinate

y1 - is coordinate

y2 - is coordinate

clipCodeViewport

private int clipCodeViewport(float x,
                             float y)

clip_code_viewport(x,y) - Return the clipping code of where (x,y) is w.r.t. the DPORT Viewport clipping window. See Newman & Sproull (1979) pp 65-68 for discussion of algorithm.

Parameters:

x - is coordinate

y - is coordinate

Returns:

clipping code

clipViewport

boolean clipViewport(float x1,
                     float x2,
                     float y1,
                     float y2)

clipViewport(x1,x2,y1,y2) - Compute if (x1,x2,y1,y2) is inside of Viewport window. Copy initial data to (x1,x2,y1,y2) to (cx1,cx2,cy1,cy2). If not recompute (cx1,cx2, cy1, cy2) such that it is. If both points are outside of the window, then it can not be divided so return false else true. See Newman & Sproull (1979) pp 65-68 for discussion of algorithm.

Parameters:

x1 - is coordinate

x2 - is coordinate

y1 - is coordinate

y2 - is coordinate

Returns:

true if clipped and data is in (cx1,cx2,cy1,cy2).

See Also:

setDataToClip(float, float, float, float), clipCodeViewport(float, float)

paint

public void paint(java.awt.Graphics g)

paint() - draw the 2D plot.

Overrides:

paint in class java.awt.Canvas

Parameters:

g - is graphics context

See Also:

draw2Dplot(java.awt.Graphics)

drawPlus

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

drawPlus() - draw plus sign as overlay graphic in specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

color - is color to draw

drawCircle

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

drawCircle() - draw a circle as overlay graphic in specified color. The color is optional and if null it draws it in green (blue). if mae.useDichromasyFlag then use blue.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

radius - of object

color - is color to draw

drawSquare

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

drawSquare() - draw a square as overlay graphic in specified color. 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 center of object

y - is center of object

radius - of object

color - is color to draw

drawRectangleBin

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

drawRectangleBin() - draw rectangle (histogram) bin as overlay graphic in specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

width - of object

height - of object

color - is color to draw

drawFilledGrayCircle

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

drawFilledGrayCircle() - draw filled circle of specified grayvalue

Parameters:

g - is graphics context

x - is center of object

y - is center of object

radius - of object

grayvalue - is gray value color to draw

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 center of object

y - is center of object

radius - of object

red - is red component of color

green - is green component of color

blue - is blue component of color

update2Dplot

void update2Dplot(java.lang.String vertCaption,
                  java.lang.String horizCaption,
                  java.lang.String title,
                  java.lang.String topTitle,
                  java.lang.String title1,
                  java.lang.String title2,
                  java.lang.String title3,
                  java.lang.String aText,
                  int xText,
                  int yText,
                  double scaleX,
                  double scaleY,
                  double minX,
                  double maxX,
                  double minY,
                  double maxY,
                  boolean draw45lineFlag,
                  boolean draw180lineFlag,
                  float[] xList,
                  float[] yList,
                  int[] propList,
                  GeneList dispCL,
                  int nList,
                  int[] mapPntToMid)

update2Dplot() - set data for plot and then update the plot. This is generally called through the PopupRegistry through the parent class.

Parameters:

vertCaption - vertical caption

horizCaption - is horizontal caption

title - is window titloe

topTitle - is top title in plot

title1 - is next top title in plot

title2 - is next top title in plot

title3 - is next top title in plot

aText - is bottom title in plot

xText - is bottom title in plot

yText - is bottom title in plot

scaleX - is global scaling

scaleY - is global scaling

minX - is min possible X

maxX - is max possible X range

minY - is min possible Y

maxY - is max possible Y range

draw45lineFlag -

draw180lineFlag -

xList[] - is list of X axis data points

yList - is list of Y axis data points

propList - is gene property list fo points (optional)

dispCL - is the display GeneList if not null

nList - is the # entries in List[]'s

mapPntToMid - is the expression profile overlay nHP*nGenes MIDs mapping

See Also:

paint(java.awt.Graphics), Component.repaint()

updateScrolledRegion

void updateScrolledRegion(float x1Pos,
                          float x2Pos,
                          float y1Pos,
                          float y2Pos)

updateScrolledRegion() - update scrolled region to plot.

Parameters:

x1Pos - in range 0.0:1.0

x2Pos - in range 0.0:1.0

y1Pos - in range 0.0:1.0

y2Pos - in range 0.0:1.0

See Also:

paint(java.awt.Graphics)

set2DplotSubtitles

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

set2DplotSubtitles() - set info1,2,3,4 subtitles for plot. Do not repaint.

Parameters:

info1 - is extra subtitles

info2 - is extra subtitles

info3 - is extra subtitles

info4 - is extra subtitles

setFontsFromState

private void setFontsFromState()

setFontsFromState() - set the regular fonts from the state variables

drawNamedOverlayMaps

private void drawNamedOverlayMaps(java.awt.Graphics g,
                                  float scaleXplot,
                                  float scaleYplot,
                                  double minXscroll,
                                  double minYscroll,
                                  int xOffset,
                                  int yOffset)

drawNamedOverlayMaps() try to draw overlay maps if there are any and they are enabled

Parameters:

g - is graphics context

draw2Dplot

void draw2Dplot(java.awt.Graphics g)

draw2Dplot() - draw a plot in the current graphics context.

Parameters:

g - is graphics context

See Also:

GeneList.isMIDinGeneList(int), Util.cvd2s(double, int), WriteGifEncoder, WriteGifEncoder.writeFile(java.lang.String), draw2Dplot(java.awt.Graphics), drawCircle(java.awt.Graphics, int, int, int, java.awt.Color), drawPlus(java.awt.Graphics, int, int, java.awt.Color), drawSquare(java.awt.Graphics, int, int, int, java.awt.Color), Component.repaint()

updateScaling

void updateScaling(boolean logScalingFlag,
                   boolean showNonFilteredGenesFlag)

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

Parameters:

logScalingFlag - to do log scaling if set

showNonFilteredGenesFlag - if set

See Also:

Component.repaint()

mousePressed

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

mousePressed() - process mouse event, change current gene.

Specified by:

mousePressed in interface java.awt.event.MouseListener

Parameters:

e - is mouse pressed event

See Also:

DrawScatterPlot.mouseHandler(int, int, int, boolean), ExprProfileOverlay.mouseHandler(int, int, int, boolean)

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 mouse moved event

See Also:

DrawScatterPlot.mouseHandler(int, int, int, boolean), ExprProfileOverlay.mouseHandler(int, int, int, boolean)

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