Package ubic.basecode.graphics

Class MatrixDisplay<R,C>

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

ubic.basecode.graphics.MatrixDisplay<R,C>

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class MatrixDisplay<R,C>
extends JPanel

A visual component for displaying a color matrix

Author:

Will Braynen

See Also:

Serialized Form

Nested Class Summary

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

JPanel.AccessibleJPanel

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
protected Dimension	m_cellSize
protected int	m_columnLabelHeight
protected int	m_defaultResolution
protected int	m_fontGutter
protected int	m_fontSize
protected boolean	m_isShowLabels
protected boolean	m_isShowScale
protected Font	m_labelFont
protected int	m_labelGutter
protected int	m_maxColumnLength
protected int	m_maxFontSize
protected int	m_ratioWidth
protected int	m_resolution
protected int	m_rowLabelWidth
protected int	m_textSize

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Constructor	Description
MatrixDisplay(DoubleMatrix<R,C> matrix)
MatrixDisplay(ColorMatrix<R,C> matrix)

Method Summary

Modifier and Type	Method	Description
protected Dimension	computeSize(boolean showLabels, boolean showScalebar)	compute the size of the matrix in pixels.
protected void	drawColumnNames(Graphics g, boolean leaveRoomForScalebar)	Draws column names vertically (turned 90 degrees counter-clockwise)
protected void	drawMatrix(ColorMatrix<R,C> matrix, Graphics g, boolean leaveRoomForLabels, boolean leaveRoomForScalebar)	Gets called from #paintComponent and #saveImage.
protected void	drawRowNames(Graphics g, boolean showScalebar)	Draws row names (horizontally)
protected void	drawScaleBar(Graphics g, Dimension d, double displayMin, double displayMax)
Color	getColor(int row, int column)
Color[]	getColorMap()
ColorMatrix<R,C>	getColorMatrix()
int	getColumnCount()
Object	getColumnName(int column)
String[]	getColumnNames()
double	getDisplayMax()
double	getDisplayMin()
double	getDisplayRange()
DoubleMatrix<R,C>	getMatrix()
double	getMax()
int	getMaxColumnLength()
double	getMin()
Color	getMissingColor()
double	getRawValue(int row, int column)
double[]	getRow(int row)
double[]	getRowByName(R rowName)
int	getRowCount()
int	getRowHeight()
int	getRowIndexByName(R rowName)
Object	getRowName(int row)
String[]	getRowNames()
boolean	getStandardizedEnabled()
double	getValue(int row, int column)
void	init(ColorMatrix<R,C> matrix)
protected void	initSize()	Sets the display size
static <R,C> MatrixDisplay<R,C>	newInstance(ColorMatrix<R,C> matrix)
protected void	paintComponent(Graphics g)
void	resetRowKeys()
void	saveImage(String outPngFilename)	Saves the image to a png file.
void	saveImage(String outPngFilename, boolean showLabels, boolean showScale)
void	saveImage(ColorMatrix<R,C> matrix, String outPngFilename, boolean showLabels, boolean showScalebar, boolean standardize)
void	saveImageToPng(ColorMatrix<R,C> matrix, OutputStream stream, boolean showLabels, boolean showScalebar, boolean standardize)
void	setCellSize(Dimension d)
void	setColorMap(Color[] colorMap)
void	setDisplayRange(double min, double max)
void	setLabelsVisible(boolean isShowLabels)	If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
void	setMatrix(ColorMatrix<R,C> matrix)
void	setMaxColumnLength(int columnLength)
void	setRowHeight(int height)
void	setRowKeys(int[] rowKeys)
void	setScaleBarVisible(boolean isShowScale)
void	setStandardizedEnabled(boolean showStandardizedMatrix)
void	writeToPng(ColorMatrix<R,C> matrix, OutputStream stream, boolean showLabels, boolean showScalebar)

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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, 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, 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

m_cellSize

protected Dimension m_cellSize

m_columnLabelHeight

protected int m_columnLabelHeight

m_defaultResolution

protected final int m_defaultResolution

See Also:

Constant Field Values

m_fontGutter

protected int m_fontGutter

m_fontSize

protected int m_fontSize

m_isShowLabels

protected boolean m_isShowLabels

m_isShowScale

protected boolean m_isShowScale

m_labelFont

protected Font m_labelFont

m_labelGutter

protected int m_labelGutter

m_maxColumnLength

protected int m_maxColumnLength

m_maxFontSize

protected final int m_maxFontSize

See Also:

Constant Field Values

m_ratioWidth

protected int m_ratioWidth

m_resolution

protected int m_resolution

m_rowLabelWidth

protected int m_rowLabelWidth

m_textSize

protected int m_textSize

Constructor Detail

MatrixDisplay

public MatrixDisplay(ColorMatrix<R,C> matrix)

MatrixDisplay

public MatrixDisplay(DoubleMatrix<R,C> matrix)

Method Detail

newInstance

public static <R,C> MatrixDisplay<R,C> newInstance(ColorMatrix<R,C> matrix)

getColor

public Color getColor(int row,
                      int column)

getColorMap

public Color[] getColorMap()

Returns:

the current color map

getColorMatrix

public ColorMatrix<R,C> getColorMatrix()

getColumnCount

public int getColumnCount()

getColumnName

public Object getColumnName(int column)

getColumnNames

public String[] getColumnNames()

getDisplayMax

public double getDisplayMax()

getDisplayMin

public double getDisplayMin()

getDisplayRange

public double getDisplayRange()

getMatrix

public DoubleMatrix<R,C> getMatrix()

getMax

public double getMax()

Returns:

the largest value in the matrix

getMaxColumnLength

public int getMaxColumnLength()

Returns:

the m_maxColumnLength

getMin

public double getMin()

Returns:

the smallest value in the matrix

getMissingColor

public Color getMissingColor()

Returns:

the color used for missing values

getRawValue

public double getRawValue(int row,
                          int column)

getRow

public double[] getRow(int row)

getRowByName

public double[] getRowByName(R rowName)

getRowCount

public int getRowCount()

getRowHeight

public int getRowHeight()

getRowIndexByName

public int getRowIndexByName(R rowName)

getRowName

public Object getRowName(int row)

getRowNames

public String[] getRowNames()

getStandardizedEnabled

public boolean getStandardizedEnabled()

getValue

public double getValue(int row,
                       int column)

init

public void init(ColorMatrix<R,C> matrix)

resetRowKeys

public void resetRowKeys()

saveImage

public void saveImage(ColorMatrix<R,C> matrix,
                      String outPngFilename,
                      boolean showLabels,
                      boolean showScalebar,
                      boolean standardize)
               throws IOException

Parameters:

outPngFilename - String

showLabels - boolean

standardize - normalize to deviation 1, mean 0. FIXME this is not used?

Throws:

IOException

saveImage

public void saveImage(String outPngFilename)
               throws IOException

Saves the image to a png file.

Parameters:

outPngFilename - String

Throws:

IOException

saveImage

public void saveImage(String outPngFilename,
                      boolean showLabels,
                      boolean showScale)
               throws IOException

Parameters:

outPngFilename -

showLabels -

Throws:

IOException

saveImageToPng

public void saveImageToPng(ColorMatrix<R,C> matrix,
                           OutputStream stream,
                           boolean showLabels,
                           boolean showScalebar,
                           boolean standardize)
                    throws IOException

Parameters:

stream -

showLabels -

standardize -

Throws:

IOException

setCellSize

public void setCellSize(Dimension d)

setColorMap

public void setColorMap(Color[] colorMap)

Parameters:

colorMap - an array of colors which define the midpoints in the color map; this can be one of the constants defined in the ColorMap class, like ColorMap.REDGREEN_COLORMAP and ColorMap.BLACKBODY_COLORMAP

setDisplayRange

public void setDisplayRange(double min,
                            double max)

Parameters:

min -

max -

setLabelsVisible

public void setLabelsVisible(boolean isShowLabels)

If this display component has already been added to the GUI, it will be resized to fit or exclude the row names

Parameters:

isShowLabels - boolean

setMatrix

public void setMatrix(ColorMatrix<R,C> matrix)

Parameters:

matrix - the new matrix to use; will resize this display component as necessary

setMaxColumnLength

public void setMaxColumnLength(int columnLength)

Parameters:

columnLength - the m_maxColumnLength to set

setRowHeight

public void setRowHeight(int height)

setRowKeys

public void setRowKeys(int[] rowKeys)

setScaleBarVisible

public void setScaleBarVisible(boolean isShowScale)

setStandardizedEnabled

public void setStandardizedEnabled(boolean showStandardizedMatrix)

writeToPng

public void writeToPng(ColorMatrix<R,C> matrix,
                       OutputStream stream,
                       boolean showLabels,
                       boolean showScalebar)
                throws IOException

Parameters:

matrix -

stream -

showLabels -

showScalebar -

Throws:

IOException

computeSize

protected Dimension computeSize(boolean showLabels,
                                boolean showScalebar)

compute the size of the matrix in pixels.

Parameters:

withLabels -

Returns:

drawColumnNames

protected void drawColumnNames(Graphics g,
                               boolean leaveRoomForScalebar)

Draws column names vertically (turned 90 degrees counter-clockwise)

Parameters:

g - Graphics

drawMatrix

protected void drawMatrix(ColorMatrix<R,C> matrix,
                          Graphics g,
                          boolean leaveRoomForLabels,
                          boolean leaveRoomForScalebar)

Gets called from #paintComponent and #saveImage. Does not draw the labels.

Parameters:

g - Graphics

leaveRoomForLabels - boolean

drawRowNames

protected void drawRowNames(Graphics g,
                            boolean showScalebar)

Draws row names (horizontally)

Parameters:

g - Graphics

showScalebar -

drawScaleBar

protected void drawScaleBar(Graphics g,
                            Dimension d,
                            double displayMin,
                            double displayMax)

Parameters:

g -

d -

initSize

protected void initSize()

Sets the display size

paintComponent

protected void paintComponent(Graphics g)

Overrides:

paintComponent in class JComponent