Class DrawProtScatterPlot

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

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

public class DrawProtScatterPlot

extends Draw2DprotPlot

Class DrawProtScatterPlot.java - draw scatterplot using Draw2Dplot base class. 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

private int	maxPoints max # points allocated for drawing arrays
private int	prevBestMPID previus best mPid of protein selected by mouse motion or clicking
private ProtPlot	prp instance of ProtPlot
private ReadPRP	rd instance of ReadPRP of current sample
private ReadPRP	rdX instance of ReadPRP of ratio sample X
private ReadPRP	rdY instance of ReadPRP of ratio sample Y
private boolean	showAssocWebPageFlag flag to allow popup web access to associated protein database
private ShowScatterPlotPopup	spp instance of ShowScatterPlotPopup
private UtilPRP	util instance of UtilPRP

Fields inherited from class Draw2DprotPlot

aText, curProteinColor, cvPrecision, dbugCnt, drawIntoImageFlag, eDiff, eDiffBest, fil, horizCaption, iBest, iCurMPid, iHeight, img, info1, info2, info3, info4, info5, info6, iWidth, leftTextX, ln10, log10e, logScaleX, logScaleY, logScalingFlag, lowerTitle1, lowerTitle2, maxX, maxXscroll, maxY, maxYscroll, MIN_CANVAS_HEIGHT, MIN_CANVAS_WIDTH, minX, minXscroll, minY, minYscroll, normFont, notOkColor, nPointsMax, nPointsPlotted, oGifFileName, okColor, pointColor, preferredHeight, preferredWidth, radius, RADIUS, scale, SCALE_DEF, scaleX, scaleXplot, scaleY, scaleYplot, sMaxX, sMaxY, sMinX, sMinY, TARGET_SIZE, title, titleFont, topTitle1, topTitle2, topTitle3, topTitle4, vertCaption, xBase, xcurProtein, xDataScatterPlot, xLeft, xOffset, XOFFSET_DEF, xPlotted, xPnt, xRange, XRANGE_DEF, xRight, xScale, xText, yBase, ycurProtein, yDataScatterPlot, yOffset, YOFFSET_DEF, yPlotted, yPnt, yRange, YRANGE_DEF, yScale, yText, 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)

DrawProtScatterPlot(ProtPlot prp, ShowScatterPlotPopup spp) DrawProtScatterPlot() - constructor

Method Summary

private void	draw_MWvsPI_scatterPlot() draw_MWvsPI_scatterPlot() - draw (Mw vs pI) scatterplot (repeatedly) of Filter data.
private boolean	draw_XvsY_scatterPlot() draw_XvsY_scatterPlot() - draw (X vs Y) scatterplot (repeatedly) of Filter data.
private void	drawScatterPlot() drawScatterPlot() - draw scatterplot (repeatedly) of Filter data This generates the data lists that are passed to the drawing engine.
void	mouseHandler(int x, int y, int mouseKeyMods, boolean updateCurProtFlag) mouseHandler() - interact with current plot if a graphic plot.
void	setCurProtein(int mPid, boolean updateCurProtFlag) setCurProtein() - set current protein spot to mPid if it exists (not -1).
void	setNewDraw2DprotPlot() setNewDraw2DprotPlot() - reset data structures for new sample
void	showProteinOfInterest(int mPid, int mouseKeyMods, boolean updateCurProtFlag) showProteinOfInterest() - show quant&NCBI data if click on a point in plot
void	updateScatterPlot() updateScatterPlot() - refresh scatterplot data and redraw the canvas

Methods inherited from class Draw2DprotPlot

alog10, calcBaseImage, draw2Dplot, drawCircle, drawCmapRatioScaleMap, drawFilledColoredCircle, drawFilledColoredCircle, drawFilledGrayCircle, drawFilterStatusText, drawGifFile, drawPlus, drawProtein, drawRedPlusGreenRatioScaleMap, drawScaleMap, drawScatterPlotScaleAndLabels, drawSquare, getMinimumSize, getPreferredSize, log10, logZero, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, paint, set2DplotSubtitles, setupArrays, update2Dplot, updateScaling, updateScrolledRegion

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

private ProtPlot prp

instance of ProtPlot

rd

private ReadPRP rd

instance of ReadPRP of current sample

rdX

private ReadPRP rdX

instance of ReadPRP of ratio sample X

rdY

private ReadPRP rdY

instance of ReadPRP of ratio sample Y

spp

private ShowScatterPlotPopup spp

instance of ShowScatterPlotPopup

util

private UtilPRP util

instance of UtilPRP

prevBestMPID

private int prevBestMPID

previus best mPid of protein selected by mouse motion or clicking

showAssocWebPageFlag

private boolean showAssocWebPageFlag

flag to allow popup web access to associated protein database

maxPoints

private int maxPoints

max # points allocated for drawing arrays

Constructor Detail

DrawProtScatterPlot

DrawProtScatterPlot(ProtPlot prp,
                    ShowScatterPlotPopup spp)

DrawProtScatterPlot() - constructor

Parameters:

prp - is instance of ProtPlot

spp - is instance of ShowScatterPlotPopup

Method Detail

setNewDraw2DprotPlot

public void setNewDraw2DprotPlot()

setNewDraw2DprotPlot() - reset data structures for new sample

updateScatterPlot

public void updateScatterPlot()

updateScatterPlot() - refresh scatterplot data and redraw the canvas

drawScatterPlot

private void drawScatterPlot()

drawScatterPlot() - draw scatterplot (repeatedly) of Filter data This generates the data lists that are passed to the drawing engine.

 If the prp.useTotPRPflag switch is set, then include 
 proteins > UNDER_DALTON_LIMIT.
 If prp.useRatioModeFlag is set, then the set  of proteins is the
 union of proteins from the X and Y sets with the ratio set to 0.0
 if it is not in either set.

See Also:

Draw2DprotPlot.update2Dplot(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, int, int, double, double, double, double, double, double)

draw_XvsY_scatterPlot

private boolean draw_XvsY_scatterPlot()

draw_XvsY_scatterPlot() - draw (X vs Y) scatterplot (repeatedly) of Filter data. The prp.useRatioModeFlag must be set. This generates the data lists that are passed to the drawing engine.

See Also:

Draw2DprotPlot.update2Dplot(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, int, int, double, double, double, double, double, double)

draw_MWvsPI_scatterPlot

private void draw_MWvsPI_scatterPlot()

draw_MWvsPI_scatterPlot() - draw (Mw vs pI) scatterplot (repeatedly) of Filter data. This generates the data lists that are passed to the drawing engine.

 If the prp.useTotPRPflag switch is set, then include 
 proteins > UNDER_DALTON_LIMIT.
 If prp.useRatioModeFlag is set, then the set  of proteins is the
 union of proteins from the X and Y sets with the ratio set to 0.0
 if it is not in either set.

See Also:

Draw2DprotPlot.update2Dplot(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, int, int, double, double, double, double, double, double)

setCurProtein

public void setCurProtein(int mPid,
                          boolean updateCurProtFlag)

setCurProtein() - set current protein spot to mPid if it exists (not -1).

Parameters:

mPid - is protein id of current spot (needed for ratio mode)

updateCurProtFlag - it want to also update current protein data

showProteinOfInterest

public void showProteinOfInterest(int mPid,
                                  int mouseKeyMods,
                                  boolean updateCurProtFlag)

showProteinOfInterest() - show quant&NCBI data if click on a point in plot

Parameters:

mouseKeyMods - is keys pressed when click on mouse

updateCurProtFlag - it want to also update current protein data

mouseHandler

public void mouseHandler(int x,
                         int y,
                         int mouseKeyMods,
                         boolean updateCurProtFlag)

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

Parameters:

x - is mouse coordinate

y - is mouse coordinate

mouseKeyMods - is keys pressed when click on mouse

updateCurProtFlag - it want to also update current protein data