org.fhcrc.cpl.toolbox.gui.chart
Class PanelWithRPerspectivePlot

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.fhcrc.cpl.toolbox.gui.chart.PanelWithChart
                      org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart
                          org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPerspectivePlot

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class PanelWithRPerspectivePlot
extends PanelWithBlindImageChart

This class knows how to ask R to plot perspective 3D charts to a file and then display them in a panel

See Also:

Serialized Form

Nested Class Summary

static class

PanelWithRPerspectivePlot.LineVariables

Nested classes/interfaces inherited from class org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart

PanelWithBlindImageChart.PopupListener, PanelWithBlindImageChart.ResizeListener

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.lang.String	backgroundColorString
protected int	chartHeight
protected int	chartWidth
static java.lang.String	DEFAULT_BACKGROUND_COLOR_STRING
static int	DEFAULT_CHART_DIALOG_HEIGHT
static int	DEFAULT_CHART_DIALOG_WIDTH
static int	DEFAULT_CHART_HEIGHT
static int	DEFAULT_CHART_WIDTH
static java.lang.String	DEFAULT_FOREGROUND_COLOR_STRING
static int	DEFAULT_LINE_STYLE
static int	DEFAULT_ROTATION_ANGLE
static double	DEFAULT_SHADE
static int	DEFAULT_TILT_ANGLE
protected java.lang.String	foregroundColorString
static int	LINE_STYLE_DASHED
static int	LINE_STYLE_DOTTED
static int	LINE_STYLE_SOLID
protected java.util.List<java.lang.Integer>	lineStyleList
protected java.util.List<PanelWithRPerspectivePlot.LineVariables>	lineVariableList
protected int	millisToWait
protected java.util.List<java.lang.Integer>	rotationAngles
protected double	shade
protected boolean	showAxisDetails
protected boolean	showBorders
protected boolean	showBox
protected java.util.List<java.lang.Integer>	tiltAngles
protected boolean	useGradientForColor
protected java.lang.String	xAxisName
protected java.lang.String	yAxisName
protected java.lang.String	zAxisName

Fields inherited from class org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart

allImages, image, imagePanel, popupMenu, scrollPane

Fields inherited from class org.fhcrc.cpl.toolbox.gui.chart.PanelWithChart

_chart, _chartPanel, _plot, DEFAULT_HEIGHT_FOR_IMAGE_FILE, DEFAULT_WIDTH_FOR_IMAGE_FILE

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

PanelWithRPerspectivePlot()

Method Summary

void	addLine(double[] xValues, double[] yValues, double[] zValues, java.lang.String color) Draw a solid line
void	addLine(double[] xValues, double[] yValues, double[] zValues, java.lang.String color, int style) Draw a line in the specified style
protected int	calcBin(double val, double globalMin, double binSize)
protected int	countBins(double minValue, double maxValue, double binSize)
protected double[]	enumerateBins(double minValue, double binSize, int numBins)
void	finalize()
java.lang.String	getBackgroundColorString()
int	getChartHeight()
int	getChartWidth()
java.lang.String	getForegroundColorString()
int	getMillisToWait()
java.util.List<java.lang.Integer>	getRotationAngles()
double	getShade()
boolean	getShowAxisDetails()
java.util.List<java.lang.Integer>	getTiltAngles()
boolean	isShowBorders()
boolean	isShowBox()
boolean	isUseGradientForColor()
void	plot(double[] xArray, double[] yArray, double[][] zMatrix)
void	plot(float[] xArray, float[] yArray, double[][] zMatrix)
void	plot(float[] xArray, float[] yArray, float[][] zMatrix)
void	plotPointsSummary(double[] xValues, double[] yValues, double xBinSize, double yBinSize)
void	plotPointsSummary(java.util.List<java.lang.Float> xValuesList, java.util.List<java.lang.Float> yValuesList, double xBinSize, double yBinSize)
void	setAxisRVariableNames(java.lang.String xName, java.lang.String yName, java.lang.String zName)
void	setBackgroundColorString(java.lang.String backgroundColorString)
void	setChartHeight(int chartHeight)
void	setChartWidth(int chartWidth)
void	setForegroundColorString(java.lang.String foregroundColorString)
void	setMillisToWait(int millisToWait)
void	setRotationAngle(int rotationAngle)
void	setRotationAngles(java.util.List<java.lang.Integer> rotationAngles)
void	setShade(double shade)
void	setShowAxisDetails(boolean showAxisDetails)
void	setShowBorders(boolean showBorders)
void	setShowBox(boolean showBox)
void	setTiltAngle(int tiltAngle)
void	setTiltAngles(java.util.List<java.lang.Integer> tiltAngles)
void	setUseGradientForColor(boolean useGradientForColor)

Methods inherited from class org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart

addItemToPopupMenu, addSeparatorToPopupMenu, createImage, cycleImageNext, cycleImagePrevious, displayImage, getImage, initPopupMenu, saveAllImagesToFiles, saveChartDataToFile, saveChartToImageFile, setImage, setImage, setImageFiles, setImages, setPreferredSize

Methods inherited from class org.fhcrc.cpl.toolbox.gui.chart.PanelWithChart

createImage, displayDialog, displayInTab, displayInTab, getChart, getChartPanel, getPlot, getToolTipText, init, init, isShowLegend, saveChartDataToCSV, saveChartDataToTSV, saveChartToImageFile, setShowLegend

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

_log

protected static org.apache.log4j.Logger _log

DEFAULT_CHART_WIDTH

public static final int DEFAULT_CHART_WIDTH

See Also:

Constant Field Values

DEFAULT_CHART_HEIGHT

public static final int DEFAULT_CHART_HEIGHT

See Also:

Constant Field Values

DEFAULT_CHART_DIALOG_WIDTH

public static final int DEFAULT_CHART_DIALOG_WIDTH

See Also:

Constant Field Values

DEFAULT_CHART_DIALOG_HEIGHT

public static final int DEFAULT_CHART_DIALOG_HEIGHT

See Also:

Constant Field Values

DEFAULT_ROTATION_ANGLE

public static final int DEFAULT_ROTATION_ANGLE

See Also:

Constant Field Values

DEFAULT_TILT_ANGLE

public static final int DEFAULT_TILT_ANGLE

See Also:

Constant Field Values

DEFAULT_SHADE

public static final double DEFAULT_SHADE

See Also:

Constant Field Values

useGradientForColor

protected boolean useGradientForColor

showBorders

protected boolean showBorders

showBox

protected boolean showBox

chartWidth

protected int chartWidth

chartHeight

protected int chartHeight

rotationAngles

protected java.util.List<java.lang.Integer> rotationAngles

tiltAngles

protected java.util.List<java.lang.Integer> tiltAngles

shade

protected double shade

LINE_STYLE_SOLID

public static final int LINE_STYLE_SOLID

See Also:

Constant Field Values

LINE_STYLE_DASHED

public static final int LINE_STYLE_DASHED

See Also:

Constant Field Values

LINE_STYLE_DOTTED

public static final int LINE_STYLE_DOTTED

See Also:

Constant Field Values

DEFAULT_LINE_STYLE

public static final int DEFAULT_LINE_STYLE

See Also:

Constant Field Values

DEFAULT_BACKGROUND_COLOR_STRING

public static final java.lang.String DEFAULT_BACKGROUND_COLOR_STRING

See Also:

Constant Field Values

DEFAULT_FOREGROUND_COLOR_STRING

public static final java.lang.String DEFAULT_FOREGROUND_COLOR_STRING

See Also:

Constant Field Values

xAxisName

protected java.lang.String xAxisName

yAxisName

protected java.lang.String yAxisName

zAxisName

protected java.lang.String zAxisName

showAxisDetails

protected boolean showAxisDetails

backgroundColorString

protected java.lang.String backgroundColorString

foregroundColorString

protected java.lang.String foregroundColorString

lineVariableList

protected java.util.List<PanelWithRPerspectivePlot.LineVariables> lineVariableList

lineStyleList

protected java.util.List<java.lang.Integer> lineStyleList

millisToWait

protected int millisToWait

Constructor Detail

PanelWithRPerspectivePlot

public PanelWithRPerspectivePlot()

Method Detail

plotPointsSummary

public void plotPointsSummary(java.util.List<java.lang.Float> xValuesList,
                              java.util.List<java.lang.Float> yValuesList,
                              double xBinSize,
                              double yBinSize)

plotPointsSummary

public void plotPointsSummary(double[] xValues,
                              double[] yValues,
                              double xBinSize,
                              double yBinSize)

calcBin

protected int calcBin(double val,
                      double globalMin,
                      double binSize)

countBins

protected int countBins(double minValue,
                        double maxValue,
                        double binSize)

enumerateBins

protected double[] enumerateBins(double minValue,
                                 double binSize,
                                 int numBins)

plot

public void plot(float[] xArray,
                 float[] yArray,
                 float[][] zMatrix)

plot

public void plot(float[] xArray,
                 float[] yArray,
                 double[][] zMatrix)

addLine

public void addLine(double[] xValues,
                    double[] yValues,
                    double[] zValues,
                    java.lang.String color)

Draw a solid line

Parameters:

xValues -

yValues -

zValues -

color -

addLine

public void addLine(double[] xValues,
                    double[] yValues,
                    double[] zValues,
                    java.lang.String color,
                    int style)

Draw a line in the specified style

Parameters:

xValues -

yValues -

zValues -

color -

style - must be an accepted value of the 'lty' variable to R's 'par'

plot

public void plot(double[] xArray,
                 double[] yArray,
                 double[][] zMatrix)

setAxisRVariableNames

public void setAxisRVariableNames(java.lang.String xName,
                                  java.lang.String yName,
                                  java.lang.String zName)

getRotationAngles

public java.util.List<java.lang.Integer> getRotationAngles()

setRotationAngles

public void setRotationAngles(java.util.List<java.lang.Integer> rotationAngles)

getTiltAngles

public java.util.List<java.lang.Integer> getTiltAngles()

setTiltAngles

public void setTiltAngles(java.util.List<java.lang.Integer> tiltAngles)

setRotationAngle

public void setRotationAngle(int rotationAngle)

setTiltAngle

public void setTiltAngle(int tiltAngle)

getShade

public double getShade()

setShade

public void setShade(double shade)

getChartHeight

public int getChartHeight()

setChartHeight

public void setChartHeight(int chartHeight)

getChartWidth

public int getChartWidth()

setChartWidth

public void setChartWidth(int chartWidth)

getBackgroundColorString

public java.lang.String getBackgroundColorString()

setBackgroundColorString

public void setBackgroundColorString(java.lang.String backgroundColorString)

getForegroundColorString

public java.lang.String getForegroundColorString()

setForegroundColorString

public void setForegroundColorString(java.lang.String foregroundColorString)

getShowAxisDetails

public boolean getShowAxisDetails()

setShowAxisDetails

public void setShowAxisDetails(boolean showAxisDetails)

getMillisToWait

public int getMillisToWait()

setMillisToWait

public void setMillisToWait(int millisToWait)

isUseGradientForColor

public boolean isUseGradientForColor()

setUseGradientForColor

public void setUseGradientForColor(boolean useGradientForColor)

isShowBorders

public boolean isShowBorders()

setShowBorders

public void setShowBorders(boolean showBorders)

isShowBox

public boolean isShowBox()

setShowBox

public void setShowBox(boolean showBox)

finalize

public void finalize()
              throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable