Package org.biojava.bio.gui

Class DistributionLogo

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

org.biojava.bio.gui.DistributionLogo

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable

public class DistributionLogo
extends JComponent

The GUI component for rendering a DistributionLogo. By default, this uses the text logo style - with letters stacked on top of one another, scaled by the total information in the dist, and uses a PlainStyle colorer that outlines in black, and fills in grey.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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 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
DistributionLogo()	Create a new DistributionLogo object.

Method Summary

Modifier and Type	Method	Description
static double	entropy(Distribution dist, Symbol s)	Calculate the information content of a symbol in bits.
BlockPainter	getBlockPainter()
Distribution	getDistribution()	Retrieve the currently rendered dist.
LogoPainter	getLogoPainter()	Retrieve the current logo painter.
RenderingHints	getRenderingHints()
SymbolStyle	getStyle()	Retrieve the current style.
boolean	isScaleByInformation()
void	paintComponent(Graphics g)	Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.
void	setBlockPainter(BlockPainter blockPainter)
void	setDistribution(Distribution dist)	Set the dist to render.
void	setLogoPainter(LogoPainter logoPainter)	Set the logo painter.
void	setRenderingHints(RenderingHints renderingHints)
void	setScaleByInformation(boolean scale)
void	setStyle(SymbolStyle style)	Set the symbol style.
static double	totalBits(Distribution dist)	Retrieve the maximal number of bits possible for this type of dist.
static double	totalInformation(Distribution dist)	Calculates the total information of the dist in bits.

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, getUI, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, 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, updateUI

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, getAccessibleContext, 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, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, 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

Constructor Detail

DistributionLogo

public DistributionLogo()

Create a new DistributionLogo object. It will set up all the properties except the dist to render.

Method Detail

getDistribution

public Distribution getDistribution()

Retrieve the currently rendered dist.

Returns:

a Distribution

setDistribution

public void setDistribution(Distribution dist)
                     throws IllegalAlphabetException

Set the dist to render.

The dist must be over a FiniteAlphabet so that we can draw the numbers for each Symbol.

Parameters:

dist - the new Distribution to render

Throws:

IllegalAlphabetException

getLogoPainter

public LogoPainter getLogoPainter()

Retrieve the current logo painter.

Returns:

the LogoPainter used to render the dist

setLogoPainter

public void setLogoPainter(LogoPainter logoPainter)

Set the logo painter.

This will alter the way that the dist is rendered to screen.

Parameters:

logoPainter - the new logoPainter

getStyle

public SymbolStyle getStyle()

Retrieve the current style.

Returns:

the current SymbolStyle

setStyle

public void setStyle(SymbolStyle style)

Set the symbol style.

This will change the outline and fill paints for the logos

Parameters:

style - the new SymbolStyle to use

isScaleByInformation

public boolean isScaleByInformation()

setScaleByInformation

public void setScaleByInformation(boolean scale)

getBlockPainter

public BlockPainter getBlockPainter()

setBlockPainter

public void setBlockPainter(BlockPainter blockPainter)

entropy

public static double entropy(Distribution dist,
                             Symbol s)
                      throws IllegalSymbolException

Calculate the information content of a symbol in bits.

Parameters:

s - the symbol to calculate for

dist - the Distribution that the symbol comes from and in whose context the information content will be calculated.

Throws:

IllegalSymbolException - if r is not within the dist.

totalBits

public static double totalBits(Distribution dist)

Retrieve the maximal number of bits possible for this type of dist.

Returns:

maximum bits as a double

totalInformation

public static double totalInformation(Distribution dist)

Calculates the total information of the dist in bits.

This calculates totalBits - sum_r(entropy(r))

Returns:

the total information in the dist

paintComponent

public void paintComponent(Graphics g)

Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.

Overrides:

paintComponent in class JComponent

getRenderingHints

public RenderingHints getRenderingHints()

setRenderingHints

public void setRenderingHints(RenderingHints renderingHints)