Class DrawHistogram

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

All Implemented Interfaces:

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

class DrawHistogram

extends java.awt.Canvas

implements java.awt.event.MouseListener

Class to draw an intensity histogram in popup frame. It is updated by 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: 2002/10/14 20:46:12 $ $Revision: $

Author:

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

See Also:

MAExplorer Home, ShowPlotPopup, 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

(package private) int	activeBin active bin idx [0:MAXBINS-1] else -1
private float[]	binDataValue [0:MAXBINS] bins actual value @start of bin for display
private int[]	binFreq [0:MAXBINS] bins frequency for display
private int	cvPrecision precision in intensity data report
private float	deltaBin value of hist[] bin in [minX:maxX]
private boolean	drawIntoImageFlag set if draw plot to GIF file
private int[]	hist freq hist[0:nHist-1].
private java.lang.String	horizCaption horizontal caption
private java.lang.String	horizVariableCaption horizontal variable caption
private int	iHeight working canvas height
private int	intensL idx lower intensity range binDataValue[] space
private int	intensU idx upper intensity range binDataValue[] space
private int	iWidth working canvas width
private boolean	logScalingFlag Linear(false)/Log(true)
private MAExplorer	mae link to global MAExplorer instance
(package private) static int	MAXBINS Break histogram into bins
private int	maxBinX ARG: maximum possible value range set by scrollers
private int	maxFreq maximum range of values found in binFreq[]
private float	maxX ARG: maximum possible value range set by scrollers
private int	meanBin mean bin intensity value for medianFreq
private int	meanFreq mean binFreq[]
private float	meanValue mean binFreq of weighted binFreq[]
private int	medianBin median bin intensity value for medianFreq
private int	medianFreq median binFreq[]
private float	medianH set from ms hist[] statistics
private float	medianValue median binFreq of binDataValue[]
(package private) static int	MIN_CANVAS_HEIGHT default canvas height
(package private) static int	MIN_CANVAS_WIDTH default canvas width
private int	minBinX ARG: minimum possible value range set by scrollers
private int	minFreq minimum range of values found in binFreq[]
private float	minX ARG: minimum possible value range set by scrollers
private float	modeH set from ms hist[] statistics
private MaHybridSample	ms link to global MaHybridSample instance
private java.lang.String	mTitle ARG: opt.
private java.lang.String	ncStr Info on genes in the current bin
(package private) int	nHist hist[0:nHist-1] of raw data.
private java.lang.String	oGifFileName full Gif file path name
private boolean	outsideRangeFlag for testing range
private int	plotMode ARG: plot mode
private int	pointType point type: DRAW _PLUS, _CIRCLE, _BOX
int	preferredHeight preferred canvas height
int	preferredWidth preferred canvas width
private java.awt.Font	smallFont font used for lableing
private ShowPlotPopup	spp ARG: parent window
(package private) static int	TARGET_SIZE target Size for selecting a line
private java.lang.String	title title
private java.lang.String	vertCaption vertical caption
private int[]	x1 x1 [0:MAXBINS-1] for clicking on point in list
private int[]	x2 x2 [0:MAXBINS-1] for clicking on point in list

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)

DrawHistogram(MAExplorer mae, ShowPlotPopup spp, java.lang.String mTitle, java.lang.String horizVariableCaption, int plotMode) DrawHistogram() - constructor to create an intensity histogram.

Method Summary

(package private) boolean	drawGifFile(java.lang.String oGifFileName) drawGifFile() - draw plot into Gif image file if in stand-alone mode.
(package private) void	drawHistogram(java.awt.Graphics g) drawHistogram() - draw histogram of hist[].
private static void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign at the specified color.
private void	drawRectangleBin(java.awt.Graphics g, int x, int y, int width, int height, java.awt.Color color, int bIdx, boolean fillIt) drawRectangleBin() - draw histogram bin at the specified color
(package private) void	filterByBin() filterByBin() - filter genes by current activeBin histogram bin(s).
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	mouseHandler(int x, int y) mouseHandler() - interact with current plot if a graphic plot.
void	mouseMoved(java.awt.event.MouseEvent e)
void	mousePressed(java.awt.event.MouseEvent e) mousePressed() - process mouse event
void	mouseReleased(java.awt.event.MouseEvent e)
void	paint(java.awt.Graphics g) paint() - draw the histogram
private void	setHistogramData(java.lang.String vertCaption, java.lang.String horizCaption, java.lang.String title, float minX, float maxX, float deltaBin, float modeH, float medianH, int pointType, int[] hist, int nHist) setHistogramData() - draw histogram of hist[0:nHist-1].
(package private) void	updateHistogramPlot() updateHistogramPlot() - set hist state and do repaint to draw it.
private void	updateSampleBins() updateSampleBins() - map hist[0:nHist-1] to binXXX[0:MAXBINS-1].
(package private) void	updateScaling(boolean logScalingFlag) updateScaling() - set scaling mode in proper sub-object.
(package private) void	updateScrolledRegion(float x1Pos, float x2Pos) 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

private MAExplorer mae

link to global MAExplorer instance

ms

private MaHybridSample ms

link to global MaHybridSample instance

spp

private ShowPlotPopup spp

ARG: parent window

plotMode

private int plotMode

ARG: plot mode

mTitle

private java.lang.String mTitle

ARG: opt. title else generate one

MAXBINS

static final int MAXBINS

Break histogram into bins

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

public int preferredHeight

preferred canvas height

preferredWidth

public int preferredWidth

preferred canvas width

binFreq

private int[] binFreq

[0:MAXBINS] bins frequency for display

binDataValue

private float[] binDataValue

[0:MAXBINS] bins actual value @start of bin for display

x1

private int[] x1

x1 [0:MAXBINS-1] for clicking on point in list

x2

private int[] x2

x2 [0:MAXBINS-1] for clicking on point in list

cvPrecision

private int cvPrecision

precision in intensity data report

iWidth

private int iWidth

working canvas width

iHeight

private int iHeight

working canvas height

oGifFileName

private java.lang.String oGifFileName

full Gif file path name

ncStr

private java.lang.String ncStr

Info on genes in the current bin

vertCaption

private java.lang.String vertCaption

vertical caption

horizCaption

private java.lang.String horizCaption

horizontal caption

horizVariableCaption

private java.lang.String horizVariableCaption

horizontal variable caption

title

private java.lang.String title

title

intensL

private int intensL

idx lower intensity range binDataValue[] space

intensU

private int intensU

idx upper intensity range binDataValue[] space

minFreq

private int minFreq

minimum range of values found in binFreq[]

maxFreq

private int maxFreq

maximum range of values found in binFreq[]

meanFreq

private int meanFreq

mean binFreq[]

medianFreq

private int medianFreq

median binFreq[]

meanBin

private int meanBin

mean bin intensity value for medianFreq

medianBin

private int medianBin

median bin intensity value for medianFreq

minBinX

private int minBinX

ARG: minimum possible value range set by scrollers

maxBinX

private int maxBinX

ARG: maximum possible value range set by scrollers

deltaBin

private float deltaBin

value of hist[] bin in [minX:maxX]

meanValue

private float meanValue

mean binFreq of weighted binFreq[]

medianValue

private float medianValue

median binFreq of binDataValue[]

modeH

private float modeH

set from ms hist[] statistics

medianH

private float medianH

set from ms hist[] statistics

minX

private float minX

ARG: minimum possible value range set by scrollers

maxX

private float maxX

ARG: maximum possible value range set by scrollers

pointType

private int pointType

point type: DRAW _PLUS, _CIRCLE, _BOX

hist

private int[] hist

freq hist[0:nHist-1].

activeBin

int activeBin

active bin idx [0:MAXBINS-1] else -1

nHist

int nHist

hist[0:nHist-1] of raw data. nHist should be MAExplorer.MAX_INTENSITY

drawIntoImageFlag

private boolean drawIntoImageFlag

set if draw plot to GIF file

outsideRangeFlag

private boolean outsideRangeFlag

for testing range

logScalingFlag

private boolean logScalingFlag

Linear(false)/Log(true)

smallFont

private java.awt.Font smallFont

font used for lableing

Constructor Detail

DrawHistogram

DrawHistogram(MAExplorer mae,
              ShowPlotPopup spp,
              java.lang.String mTitle,
              java.lang.String horizVariableCaption,
              int plotMode)

DrawHistogram() - constructor to create an intensity histogram.

Parameters:

mae - is the MAExplorer instance

spp - is the ShowPlotPopup instance

mTitle - is window title

horizVariableCaption - is horizontal caption

plotMode - is the specific plot mode to implement

See Also:

MaHybridSample.calcIntensHist(), updateHistogramPlot()

Method Detail

drawGifFile

boolean drawGifFile(java.lang.String oGifFileName)

drawGifFile() - draw plot into Gif image file if in stand-alone mode. This sets it up and lets paint() to the heavy lifting...

Parameters:

oGifFileName - is the full path GIF output file

Returns:

true if successful

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

updateHistogramPlot

void updateHistogramPlot()

updateHistogramPlot() - set hist state and do repaint to draw it.

See Also:

MaHybridSample.calcIntensHist(), setHistogramData(java.lang.String, java.lang.String, java.lang.String, float, float, float, float, float, int, int[], int)

updateScrolledRegion

void updateScrolledRegion(float x1Pos,
                          float x2Pos)

updateScrolledRegion() - update scrolled region to plot

Parameters:

x1Pos - is x1 position in the range 0.0:1.0

x2Pos - is x2 position in the range 0.0:1.0

See Also:

setHistogramData(java.lang.String, java.lang.String, java.lang.String, float, float, float, float, float, int, int[], int)

setHistogramData

private void setHistogramData(java.lang.String vertCaption,
                              java.lang.String horizCaption,
                              java.lang.String title,
                              float minX,
                              float maxX,
                              float deltaBin,
                              float modeH,
                              float medianH,
                              int pointType,
                              int[] hist,
                              int nHist)

setHistogramData() - draw histogram of hist[0:nHist-1]. Rescale it to 300x400 canvas.

Parameters:

vertCaption - is vertical caption

horizCaption - is horizontal caption

title - for window

minX - is min range to display

maxX - is max range to display

deltaBin - is width of a histogram bin

modeH - the mode computed from histogram

medianH - the median computed from histogram

pointType - (type of symbol)

hist - is the intensity freqency hist[0:MAXINTENS]

nHist - is the number of bins in hist[0:npoints-1]

See Also:

Component.repaint(), updateSampleBins()

updateSampleBins

private void updateSampleBins()

updateSampleBins() - map hist[0:nHist-1] to binXXX[0:MAXBINS-1]. Where binXXX[] is binFreq[], binDataValue[]. Given the data value range [minX:maxX], map hist[0:nHist-1] to binXXX[0:MAXBINS-1]. Also compute minFreq, maxFreq, meanValue, medianValue

paint

public void paint(java.awt.Graphics g)

paint() - draw the histogram

Overrides:

paint in class java.awt.Canvas

Parameters:

g - is graphics context

See Also:

drawHistogram(java.awt.Graphics)

drawPlus

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

drawPlus() - draw plus sign at the specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center 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,
                                    int bIdx,
                                    boolean fillIt)

drawRectangleBin() - draw histogram bin at the 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

fillit - to draw a solid object

drawHistogram

void drawHistogram(java.awt.Graphics g)

drawHistogram() - draw histogram of hist[]. Rescale it to 300x400 size canvas.

Parameters:

g - is graphics context

See Also:

Util.showMsg(java.lang.String), WriteGifEncoder, WriteGifEncoder.writeFile(java.lang.String), drawHistogram(java.awt.Graphics), drawRectangleBin(java.awt.Graphics, int, int, int, int, java.awt.Color, int, boolean), Component.repaint()

filterByBin

void filterByBin()

filterByBin() - filter genes by current activeBin histogram bin(s). Use the spp.histBinRange range to set the desired thresholds. If get a hit, then display data for the gene. If do not get a hit, then clear the filter. Note: because there is only ONE plot so can't get into trouble with multiple plots.

See Also:

Filter.computeWorkingGeneList(), CompositeDatabase.setIntensHistCLfromIntenRange(GeneList, MaHybridSample, float, float, boolean), Component.repaint(), Util.cvf2s(float, int), Util.saveCmdHistory(java.lang.String), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), Component.repaint()

mouseHandler

public void mouseHandler(int x,
                         int y)

mouseHandler() - interact with current plot if a graphic plot. If get a hit, then display data for the gene. Note: because there is only ONE plot so can't get into trouble with multiple plots.

Parameters:

x - mouse position

y - mouse position

See Also:

filterByBin()

mousePressed

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

mousePressed() - process mouse event

Specified by:

mousePressed in interface java.awt.event.MouseListener

Parameters:

e - is mouse pressed event

See Also:

mouseHandler(int, int)

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

mouseMoved

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

mouseDragged

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

updateScaling

void updateScaling(boolean logScalingFlag)

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

Parameters:

logScalingFlag - if using log scaling

See Also:

filterByBin()