edu.stanford.math.plex

Class BCPlot

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

edu.stanford.math.plex.BCPlot

All Implemented Interfaces:

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

public class BCPlot
extends javax.swing.JPanel

The BCPlot class does simple plotting of PersistenceIntervals.

Version:

$Id$

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	BCPlot.DrawingPane The component inside the scroll pane.
protected class	BCPlot.fileSaveMenuHandler
protected class	BCPlot.Ruler

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

Fields

Modifier and Type	Field and Description
protected java.lang.String	backgroundImageName
protected java.awt.Color	barcodeBarColor
protected int	barcodeBarHeight
protected int	barcodeBarSpacing
protected BCPlot.DrawingPane	barcodePane
protected java.awt.Rectangle	baseRegionUsedForPlotLegendRulerLabels
protected java.awt.image.BufferedImage	bufferedImage
protected static int	CIRCLE_SIZE
protected static int	DEFAULT_BARS_PER_PAGE
protected javax.swing.Action	fileSaveMenuHandler
protected static int	FIXED_RULER_HEIGHT
protected BCPlot.Ruler	fixedRuler
protected java.awt.Color	fixedRulerBorderColor
protected java.awt.Color	fixedRulerColor
protected java.awt.Font	fixedRulerFont
protected java.awt.Color	fixedRulerFontColor
protected java.awt.FontMetrics	fixedRulerFontMetrics
protected java.awt.Color	fixedRulerMajorTickColor
protected java.awt.Color	fixedRulerMinorTickColor
protected int	fullVisualizationHeight
protected int	fullVisualizationWidth
protected int	gridHeight
protected java.lang.Boolean	gridIsVisible
protected java.awt.Font	gridRulerFont
protected java.awt.Color	gridRulerFontColor
protected java.awt.FontMetrics	gridRulerFontMetrics
protected java.awt.Color	gridTickMajorColor
protected java.awt.Color	gridTickMinorColor
protected int	gridWidth
protected int	heightOfBaseRegionUsedForPlotLegendRulerLabels
protected java.awt.Font	labelFont
protected java.awt.Color	labelFontColor
protected java.awt.FontMetrics	labelFontMetrics
protected int	leftMargin
protected java.awt.Font	legendMajorFont
protected java.awt.Color	legendMajorFontColor
protected java.awt.FontMetrics	legendMajorFontMetrics
protected java.lang.String	legendMajorString
protected java.awt.Font	legendMinorFont
protected java.awt.Color	legendMinorFontColor
protected java.awt.FontMetrics	legendMinorFontMetrics
protected java.lang.String	legendMinorString
protected static int	MAX_DISPLAYABLE_BARS
protected static int	MAX_GRID_HEIGHT_PER_PAGE
protected double	pixelsPerUnit
protected java.lang.Boolean	plotBeingSaved
protected boolean	plotTypeScatter
protected double	plotUpperBound
protected double[][]	plotValue
protected int	rightMargin
protected static long	serialVersionUID
protected java.lang.Boolean	thereIsaBackgroundImage
protected int	tickGap
protected int	tickMajorPlacement
protected java.awt.Color	tickUpperBoundColor
protected double	unitsPerPixel
protected java.awt.Color	upperBoundFontColor
protected int	upperMargin
protected int	widthOfSideRegionUsedForPlotLegendRulerLabels

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

Constructors

Modifier	Constructor and Description
protected	BCPlot()
protected	BCPlot(double[][] values, double upperBound, boolean forceScatter)

Method Summary

Methods

Modifier and Type	Method and Description
protected javax.swing.JMenuBar	createMenuBar()
static void	doPlot(java.lang.String label, double[][] intervals, double upperBound) Make a barcode plot -- call via Plex.plot().
static void	doScatter(java.lang.String label, double[][] intervals, double upperBound) Make a barcode scatterplot -- call via Plex.scatter().
protected java.lang.String[]	getFormats()
int	getMaxDisplayableBars() Returns the maximum number of barcodes that can be "plotted".
protected static java.lang.String	illegal_interval_string(int i, double a, double b)
protected void	initJFrame()
protected static void	plot(java.lang.String legend, double[][] values, double upperBound, boolean forceScatter) Create the plot window and display results.
protected void	setMajorLegend(java.lang.String s) Sets the Major Legend
protected void	validate(double[][] numbers, double upperBound) Validate the upperBound and the values used for the Barcode Plot

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, 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, setPreferredSize, 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, 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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

CIRCLE_SIZE

protected static final int CIRCLE_SIZE

See Also:

Constant Field Values

serialVersionUID

protected static final long serialVersionUID

See Also:

Constant Field Values

plotTypeScatter

protected boolean plotTypeScatter

fixedRuler

protected BCPlot.Ruler fixedRuler

FIXED_RULER_HEIGHT

protected static final int FIXED_RULER_HEIGHT

See Also:

Constant Field Values

MAX_GRID_HEIGHT_PER_PAGE

protected static final int MAX_GRID_HEIGHT_PER_PAGE

See Also:

Constant Field Values

MAX_DISPLAYABLE_BARS

protected static final int MAX_DISPLAYABLE_BARS

See Also:

Constant Field Values

DEFAULT_BARS_PER_PAGE

protected static final int DEFAULT_BARS_PER_PAGE

See Also:

Constant Field Values

barcodePane

protected BCPlot.DrawingPane barcodePane

fileSaveMenuHandler

protected javax.swing.Action fileSaveMenuHandler

baseRegionUsedForPlotLegendRulerLabels

protected java.awt.Rectangle baseRegionUsedForPlotLegendRulerLabels

heightOfBaseRegionUsedForPlotLegendRulerLabels

protected int heightOfBaseRegionUsedForPlotLegendRulerLabels

widthOfSideRegionUsedForPlotLegendRulerLabels

protected int widthOfSideRegionUsedForPlotLegendRulerLabels

leftMargin

protected int leftMargin

rightMargin

protected int rightMargin

legendMajorString

protected java.lang.String legendMajorString

legendMinorString

protected java.lang.String legendMinorString

fullVisualizationWidth

protected int fullVisualizationWidth

gridWidth

protected int gridWidth

gridHeight

protected int gridHeight

fullVisualizationHeight

protected int fullVisualizationHeight

plotValue

protected double[][] plotValue

plotUpperBound

protected double plotUpperBound

gridRulerFontColor

protected java.awt.Color gridRulerFontColor

tickUpperBoundColor

protected java.awt.Color tickUpperBoundColor

gridTickMinorColor

protected java.awt.Color gridTickMinorColor

gridTickMajorColor

protected java.awt.Color gridTickMajorColor

upperBoundFontColor

protected java.awt.Color upperBoundFontColor

labelFontColor

protected java.awt.Color labelFontColor

legendMinorFontColor

protected java.awt.Color legendMinorFontColor

legendMajorFontColor

protected java.awt.Color legendMajorFontColor

fixedRulerBorderColor

protected java.awt.Color fixedRulerBorderColor

fixedRulerColor

protected java.awt.Color fixedRulerColor

barcodeBarColor

protected java.awt.Color barcodeBarColor

fixedRulerFontColor

protected java.awt.Color fixedRulerFontColor

fixedRulerMinorTickColor

protected java.awt.Color fixedRulerMinorTickColor

fixedRulerMajorTickColor

protected java.awt.Color fixedRulerMajorTickColor

labelFont

protected java.awt.Font labelFont

legendMinorFont

protected java.awt.Font legendMinorFont

legendMajorFont

protected java.awt.Font legendMajorFont

gridRulerFont

protected java.awt.Font gridRulerFont

fixedRulerFont

protected java.awt.Font fixedRulerFont

legendMinorFontMetrics

protected java.awt.FontMetrics legendMinorFontMetrics

legendMajorFontMetrics

protected java.awt.FontMetrics legendMajorFontMetrics

fixedRulerFontMetrics

protected java.awt.FontMetrics fixedRulerFontMetrics

labelFontMetrics

protected java.awt.FontMetrics labelFontMetrics

gridRulerFontMetrics

protected java.awt.FontMetrics gridRulerFontMetrics

upperMargin

protected int upperMargin

barcodeBarHeight

protected int barcodeBarHeight

barcodeBarSpacing

protected int barcodeBarSpacing

gridIsVisible

protected java.lang.Boolean gridIsVisible

plotBeingSaved

protected java.lang.Boolean plotBeingSaved

unitsPerPixel

protected double unitsPerPixel

pixelsPerUnit

protected double pixelsPerUnit

tickMajorPlacement

protected int tickMajorPlacement

tickGap

protected int tickGap

bufferedImage

protected java.awt.image.BufferedImage bufferedImage

thereIsaBackgroundImage

protected java.lang.Boolean thereIsaBackgroundImage

backgroundImageName

protected java.lang.String backgroundImageName

Constructor Detail

BCPlot

protected BCPlot()

BCPlot

protected BCPlot(double[][] values,
      double upperBound,
      boolean forceScatter)

Method Detail

getMaxDisplayableBars

public int getMaxDisplayableBars()

Returns the maximum number of barcodes that can be "plotted".

setMajorLegend

protected void setMajorLegend(java.lang.String s)

Sets the Major Legend

illegal_interval_string

protected static java.lang.String illegal_interval_string(int i,
                                       double a,
                                       double b)

validate

protected void validate(double[][] numbers,
            double upperBound)

Validate the upperBound and the values used for the Barcode Plot

initJFrame

protected void initJFrame()

createMenuBar

protected javax.swing.JMenuBar createMenuBar()

getFormats

protected java.lang.String[] getFormats()

plot

protected static void plot(java.lang.String legend,
        double[][] values,
        double upperBound,
        boolean forceScatter)

Create the plot window and display results. For thread safety, this method should be invoked from the event-dispatching thread.

doPlot

public static void doPlot(java.lang.String label,
          double[][] intervals,
          double upperBound)

Make a barcode plot -- call via Plex.plot().

Parameters:

label - Window label.

intervals - An array of double[2] of [x,y] intervals to plot.

upperBound - Display the range from 0 to upperBound.

See Also:

Plex.plot(edu.stanford.math.plex.PersistenceInterval[], java.lang.String, double)

doScatter

public static void doScatter(java.lang.String label,
             double[][] intervals,
             double upperBound)

Make a barcode scatterplot -- call via Plex.scatter().

Parameters:

label - Window label.

intervals - An array of double[2] of x,y points to plot.

upperBound - Display the square from 0 to upperBound.

See Also:

Plex.scatter(edu.stanford.math.plex.PersistenceInterval[], java.lang.String, double)