Class DrawPseudoImage

java.lang.Object
  |
  +--DrawPseudoImage

class DrawPseudoImage

extends java.lang.Object

Class to draw microarray data (ratio, intensity, p-value, etc) as a pseudoarray image. The image is eventually displayed using ScrollableImageCanvas. Note the Pseudoarray image size is fixed and is mae.(pWidth,pHeight). The pseudoarray image is updated when mae.updatePseudoImgFlag is set by many different processes including the PopupRegistry when the normalization, Filter.workingCL, or other state values change.

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: 2003/04/03 21:01:38 $ / $Revision: 1.13 $

Author:

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

See Also:

MAExplorer Home

Field Summary

private java.awt.Font	font regular font
private java.awt.Font	fontHdr Header font
private int	guardRegion # pixels in target image on each edge
(package private) java.awt.Point[]	hpXYpseudoImgList list of HP names [mae.hps.nHP+1]
private int	iFontHdrSize integer header font size is 2+ regular size unless the latter is 12pt in which case the header font size is also 12 pt.
private int	iFontSize integer regular font size
private MAExplorer	mae link to global MAExplorer instance
(package private) static int	MAX_COLORS [Dark green:dark red] - MUST BE ODD #!!!
private int	maxLeftLabelPixelsWidth max # pixels in left labels
(package private) float	rangeInc PseudoArray image color range increment
(package private) java.awt.Color[]	ratioColor color table used for PseudoArray image color mapping
(package private) float[]	ratioRange ratio range for values used in PseudoArray image color mapping
(package private) boolean	setHPXflag set HP-X (HP-Y) if click on sample name
(package private) java.awt.Color[]	spectrumColor color table used for PseudoArray image color spectrum color mapping
(package private) float[]	spectrumRange range of values for values used in PseudoArray image color spectrum mapping
private boolean	useRYGcolorsFlag flag: color for ratio data.
private int	xSpotOffset add to orig data coords x_textQ[]
private int	ySpotOffset add to orig data coords y_textQ[]

Constructor Summary

(package private)

DrawPseudoImage(MAExplorer mae) DrawPseudoImage() - constructor

Method Summary

(package private) java.lang.String	clipStrToWidth(java.lang.String str, int maxPixelWidth, int maxSubStrLen, java.awt.Graphics g, java.awt.Font font) clipStrToWidth() - clip string to maxPixelWidth and font char width.
private void	drawFilledColoredCircle(java.awt.Graphics g, int x, int y, int radius, java.awt.Color color) drawFilledColoredCircle() - draw filled circle of 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 color Clip colors to [0:255].
private void	drawFilledGrayCircle(java.awt.Graphics g, int x, int y, int radius, int grayValue) drawFilledGrayCircle() - draw filled circle of specified grayvalue [0:255].
private void	drawGridLabelsInImage(MaHybridSample ms, java.awt.Graphics g, boolean isRatioPlot, boolean isDualPseudoImageFlag) drawGridLabelsInImage() - draw ms.textQ[] in the image at (x,y)[] locations.
private void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign using specified color.
(package private) void	drawPseudoImage(java.awt.Graphics gi, int piWidth, int piHeight, int plotMode, MaHybridSample ms) drawPseudoImage() - draw pseudoarray image of filled grayscale circles using the totC[] density values.
private void	drawScaleMap(java.awt.Graphics gi, boolean isRatioPlot, boolean useRYGcolorsFlag, float minI, float maxI) drawScaleMap() - draw color scale map on the left of the canvas
private void	setFontsFromState() setFontsFromState() - set the regular and header fonts from the state variables
private void	setPseudoColorRange() setPseudoColorRange() - set isZscoreLog flag and pseudocolor range.

Methods inherited from class java.lang.Object

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

Field Detail

mae

private MAExplorer mae

link to global MAExplorer instance

MAX_COLORS

static final int MAX_COLORS

[Dark green:dark red] - MUST BE ODD #!!!

useRYGcolorsFlag

private boolean useRYGcolorsFlag

flag: color for ratio data. use continuous Red-Yellow-Green color range from [min:max] else use discrete Red-Black-Green.

ratioColor

java.awt.Color[] ratioColor

color table used for PseudoArray image color mapping

rangeInc

float rangeInc

PseudoArray image color range increment

ratioRange

float[] ratioRange

ratio range for values used in PseudoArray image color mapping

spectrumColor

java.awt.Color[] spectrumColor

color table used for PseudoArray image color spectrum color mapping

spectrumRange

float[] spectrumRange

range of values for values used in PseudoArray image color spectrum mapping

maxLeftLabelPixelsWidth

private int maxLeftLabelPixelsWidth

max # pixels in left labels

xSpotOffset

private int xSpotOffset

add to orig data coords x_textQ[]

ySpotOffset

private int ySpotOffset

add to orig data coords y_textQ[]

guardRegion

private int guardRegion

# pixels in target image on each edge

iFontSize

private int iFontSize

integer regular font size

iFontHdrSize

private int iFontHdrSize

integer header font size is 2+ regular size unless the latter is 12pt in which case the header font size is also 12 pt.

font

private java.awt.Font font

regular font

fontHdr

private java.awt.Font fontHdr

Header font

setHPXflag

boolean setHPXflag

set HP-X (HP-Y) if click on sample name

hpXYpseudoImgList

java.awt.Point[] hpXYpseudoImgList

list of HP names [mae.hps.nHP+1]

Constructor Detail

DrawPseudoImage

DrawPseudoImage(MAExplorer mae)

DrawPseudoImage() - constructor

Parameters:

mae - is the MAExplorer instance

See Also:

setPseudoColorRange()

Method Detail

setPseudoColorRange

private void setPseudoColorRange()

setPseudoColorRange() - set isZscoreLog flag and pseudocolor range.

See Also:

Util.setupColorRatioRange(float, java.awt.Color[], float[], int, boolean), Util.setupColorSpectrumRange(java.awt.Color[], float[], int, boolean)

drawPlus

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

drawPlus() - draw plus sign using specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

color - is color to draw

drawFilledGrayCircle

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

drawFilledGrayCircle() - draw filled circle of specified grayvalue [0:255].

Parameters:

g - is graphics context

x - is center of object

y - is center of object

radius - of object

grayValue - is the gray value color to draw

drawFilledColoredCircle

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 color Clip colors to [0:255].

Parameters:

g - is graphics context

x - is center of object

y - is center of object

radius - of object

red - is the red color component

green - is the green color component

blue - is the blue color component

drawFilledColoredCircle

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

drawFilledColoredCircle() - draw filled circle of specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

radius - of object

color - is the color to draw

clipStrToWidth

java.lang.String clipStrToWidth(java.lang.String str,
                                int maxPixelWidth,
                                int maxSubStrLen,
                                java.awt.Graphics g,
                                java.awt.Font font)

clipStrToWidth() - clip string to maxPixelWidth and font char width. If the string will not fit in the maxPixelWidth, then remove characters that exceed that length.

Parameters:

str - is the string to possibly clip

maxPixelWidth - is the maximum pixel width

maxSubStrLen - is the max substring length

g - is graphics context

font - is the current font being used

Returns:

possibly clipped string

setFontsFromState

private void setFontsFromState()

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

drawScaleMap

private void drawScaleMap(java.awt.Graphics gi,
                          boolean isRatioPlot,
                          boolean useRYGcolorsFlag,
                          float minI,
                          float maxI)

drawScaleMap() - draw color scale map on the left of the canvas

Parameters:

gi - is graphics context

isRatioPlot - indicates doing a ratio rather than intensity plot

useRYGcolorsFlag - using additive colors rather than lookup map

minI - minimum intensity

maxI - maximum intensity

See Also:

clipStrToWidth(java.lang.String, int, int, java.awt.Graphics, java.awt.Font)

drawGridLabelsInImage

private void drawGridLabelsInImage(MaHybridSample ms,
                                   java.awt.Graphics g,
                                   boolean isRatioPlot,
                                   boolean isDualPseudoImageFlag)

drawGridLabelsInImage() - draw ms.textQ[] in the image at (x,y)[] locations. NOTE: the data is setup in the Sample object ms.

Parameters:

ms - is sample being used

g - is graphics context

isRatioPlot - is ratio plot rather than intensity plot

isDualPseudoImageFlag - shows two arrays side by side

See Also:

SampleSets.setHPxyModStrings()

drawPseudoImage

void drawPseudoImage(java.awt.Graphics gi,
                     int piWidth,
                     int piHeight,
                     int plotMode,
                     MaHybridSample ms)

drawPseudoImage() - draw pseudoarray image of filled grayscale circles using the totC[] density values. Depending on the value of plotModePseudImage, it implements:

   PLOT_PSEUDOIMG                  -  gray value white to black
   PLOT_PSEUDO_HP_XY_P_VALUE_IMG   -  pValue[0.0:1.0] spectrum value white to black
   PLOT_PSEUDO_HP_EP_CV_VALUE_IMG  -  pValue[0.0:1.0] spectrum value white to black
   PLOT_PSEUDOCOLOR_HP_XY_RYG_IMG  -  sum Red(X)+Green(Y) is Red,yellow,green
   PLOT_PSEUDO_F1F2_RYG_IMG        -  sum Red(F2)+Green(F1) is Red,yellow,green
   PLOT_PSEUDOCOLOR_HP_XY_IMG      -  ratio X/Y is Red,black,green
   PLOT_PSEUDOCOLOR_F1F2_IMG       -  ratio F1/F2 is Red,black,green

NOTE: currently it maps data to either RGB or 0:255 grayscale.

Parameters:

gi - is graphics context

piWidth - is width of image

piHeight - is height of image

plotMode - is type of image

ms - is sample being plotted

See Also:

HPxyData.updateDataAndStat(int), MaHybridSample.computeMinMaxF1F2Data(boolean, boolean), MaHybridSample.getDataByGID(int, boolean, int), MaHybridSample.getSpotDataStatic(int, boolean), MaHybridSample.getSpotData12Static(int, int, boolean), Statistics.calcTandPvalues(int, int, double, double, double, double), Util.setRatioColor(float, java.awt.Color[], float[], int), drawFilledColoredCircle(java.awt.Graphics, int, int, int, int, int, int), drawGridLabelsInImage(MaHybridSample, java.awt.Graphics, boolean, boolean), drawScaleMap(java.awt.Graphics, boolean, boolean, float, float), setPseudoColorRange()