Class DrawRatioHistogram

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

All Implemented Interfaces:

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

class DrawRatioHistogram

extends java.awt.Canvas

implements java.awt.event.MouseListener

This class draws a ratio histogram on an extended Canvas. 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: 2003/02/18 18:02:26 $ $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

private int	activeBin active bin # [0:nHist] else -1
private int[]	binIndex corresponding hist bin index
private CompositeDatabase	cdb link to global instance
private int	curXbinIdx index of X axis for data arrays
private boolean	drawIntoImageFlag set if draw plot to GIF file
private int[]	histRatio freq bin hist[0:nHist-1].
private double[]	histValue value bin hist[0:nHist-1].
private java.lang.String	horizCaption horizontal caption
private java.lang.String	horizVariableCaption horizontal variable caption
private int	iHeight
private int	iWidth
private boolean	logScalingFlag Linear(false)/Log(true)
private MAExplorer	mae link to global instance
private double	maxX ARG: maximum possible value range set by scrollers
private double	maxXfound min value of range of values found
(package private) static int	MIN_CANVAS_HEIGHT
(package private) static int	MIN_CANVAS_WIDTH
private double	minX ARG: minimum possible value range set by scrollers
private double	minXfound min value of range of values found
private java.lang.String	ncStr Info on genes in the current bin
private int	nHist hist[0:npoints-1]
private java.lang.String	oGifFileName full Gif file path name
private boolean	outsideRangeFlag for testing range
private java.awt.Canvas	pCanvas canvas used to draw ratio histogram
private int	plotMode plot mode
private int	pointType point type: DRAW _PLUS, _CIRCLE, _BOX
int	preferredHeight
int	preferredWidth
private float	ratioLower lower range of histogram values
private float	ratioUpper upper range of histogram values
private java.awt.Font	smallFont font used for lableing
private ShowPlotPopup	spp link to global instance
(package private) static int	TARGET_SIZE target Size for selecting a line
private java.lang.String	title title
private java.lang.String	titleX X title
private java.lang.String	titleY Y title
private java.lang.String	vertCaption vertical caption
private int[]	x1 X2 [1:nHist] for clicking on point in list
private int[]	x2 X2 [1:nHist] 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)

DrawRatioHistogram(MAExplorer mae, ShowPlotPopup spp, int plotMode) DrawRatioHistogram() - constructor to draw ratio 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	drawHistogramRatios(java.awt.Graphics g) drawHistogramRatios() - draw histogram of rg.ratioHist[].
(package private) static void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign in the specified color.
(package private) void	drawRectangleBin(java.awt.Graphics g, int x, int y, int width, int height, java.awt.Color color, int binIdx, boolean fillIt) drawRectangleBin() - draw histogram bin
(package private) void	filterByBin() filterByBin() - filter genes by current activeBin histogram bin.
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
(package private) void	setHistogramRatiosData(java.lang.String vertCaption, java.lang.String horizCaption, java.lang.String title, java.lang.String titleX, java.lang.String titleY, double minX, double maxX, int pointType, int[] histRatio, double[] histValue, int nHist) setHistogramRatiosData() - draw histogram of rg.ratioHist[].
(package private) void	updateRatioHistogramPlot() updateRatioHistogramPlot() - set ratioHist state & do repaint to draw it.
(package private) void	updateScaling(boolean logScalingFlag) updateScaling() - set scaling mode in proper sub-object.

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 instance

cdb

private CompositeDatabase cdb

link to global instance

spp

private ShowPlotPopup spp

link to global instance

plotMode

private int plotMode

plot mode

pCanvas

private java.awt.Canvas pCanvas

canvas used to draw ratio histogram

MIN_CANVAS_WIDTH

static final int MIN_CANVAS_WIDTH

MIN_CANVAS_HEIGHT

static final int MIN_CANVAS_HEIGHT

TARGET_SIZE

static final int TARGET_SIZE

target Size for selecting a line

preferredHeight

public int preferredHeight

preferredWidth

public int preferredWidth

x1

private int[] x1

X2 [1:nHist] for clicking on point in list

x2

private int[] x2

X2 [1:nHist] for clicking on point in list

binIndex

private int[] binIndex

corresponding hist bin index

iWidth

private int iWidth

iHeight

private int iHeight

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

titleX

private java.lang.String titleX

X title

titleY

private java.lang.String titleY

Y title

minXfound

private double minXfound

min value of range of values found

maxXfound

private double maxXfound

min value of range of values found

minX

private double minX

ARG: minimum possible value range set by scrollers

maxX

private double maxX

ARG: maximum possible value range set by scrollers

pointType

private int pointType

point type: DRAW _PLUS, _CIRCLE, _BOX

histRatio

private int[] histRatio

freq bin hist[0:nHist-1].

histValue

private double[] histValue

value bin hist[0:nHist-1].

curXbinIdx

private int curXbinIdx

index of X axis for data arrays

activeBin

private int activeBin

active bin # [0:nHist] else -1

nHist

private int nHist

hist[0:npoints-1]

ratioLower

private float ratioLower

lower range of histogram values

ratioUpper

private float ratioUpper

upper range of histogram values

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

DrawRatioHistogram

DrawRatioHistogram(MAExplorer mae,
                   ShowPlotPopup spp,
                   int plotMode)

DrawRatioHistogram() - constructor to draw ratio histogram

Parameters:

mae - is the MAExplorer instance

spp - is the ShowPlotPopup instance

plotMode - is the specific plot mode to implement

See Also:

updateRatioHistogramPlot()

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

See Also:

Component.repaint()

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

updateRatioHistogramPlot

void updateRatioHistogramPlot()

updateRatioHistogramPlot() - set ratioHist state & do repaint to draw it. Does {PLOT_HIST_F1F2_RATIO, PLOT_HIST_HP_XY_RATIO, PLOT_HIST_HP_XY_SETS_RATIO }. [CHECK] compute hist of SETS of X and Y microarray samples.

See Also:

CompositeDatabase.calcHistOfF1F2Ratios(GeneList, MaHybridSample), CompositeDatabase.calcHistOfHP_XYratios(GeneList, boolean), setHistogramRatiosData(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, double, double, int, int[], double[], int)

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:

drawHistogramRatios(java.awt.Graphics)

drawPlus

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

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

Parameters:

g - is graphics context

x - is center of object

y - is center of object

color - is color to draw

drawRectangleBin

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

drawRectangleBin() - draw histogram bin

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

setHistogramRatiosData

void setHistogramRatiosData(java.lang.String vertCaption,
                            java.lang.String horizCaption,
                            java.lang.String title,
                            java.lang.String titleX,
                            java.lang.String titleY,
                            double minX,
                            double maxX,
                            int pointType,
                            int[] histRatio,
                            double[] histValue,
                            int nHist)

setHistogramRatiosData() - draw histogram of rg.ratioHist[]. Rescale it to 300x400 canvas.

Parameters:

vertCaption - is the vertical caption

horizCaption -

title - is the window title

titleX - is the X axis title

titleY - is the Y axis title

minX - is lowest X axis value

maxX - is highest X axis value

pointType - is either DRAW _PLUS, _CIRCLE, _BOX

histRatio - is the ratios of the ratio histogram

histValue - is the bin values frequencies of the ratio histogram

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

See Also:

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

drawHistogramRatios

void drawHistogramRatios(java.awt.Graphics g)

drawHistogramRatios() - draw histogram of rg.ratioHist[]. Rescale it to 300x400 canvas.

Parameters:

g - is graphics context

See Also:

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

filterByBin

void filterByBin()

filterByBin() - filter genes by current activeBin histogram bin. Use the spp.histBinRange range to set the desired thresholds. Both nHist>0 and activeBin>=0 to do filtering. If get a hit, then display data for the gene.

See Also:

CompositeDatabase.setRatioHistCLfromF1F2Ratios(GeneList, MaHybridSample, float, float, boolean), CompositeDatabase.setRatioHistCLfromHP_XYratios(GeneList, MaHybridSample, MaHybridSample, float, float, boolean), CompositeDatabase.setRatioHistCLfromHP_XYsetRatios(GeneList, float, float, boolean), Filter.computeWorkingGeneList(), 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.

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) [DEPRICATED]

Parameters:

logScalingFlag - if using log scaling

See Also:

filterByBin()