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java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--javax.swing.JComponent | +--org.biojava.bio.gui.DistributionLogo
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.
Inner classes inherited from class javax.swing.JComponent |
javax.swing.JComponent.AccessibleJComponent |
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 |
Constructor Summary | |
DistributionLogo()
Create a new DistributionLogo object. |
Method Summary | |
double |
entropy(Symbol r)
Calculate the information content of a symbol in bits. |
Distribution |
getDistribution()
Retrieve the currently rendered dist. |
LogoPainter |
getLogoPainter()
Retrieve the current logo painter. |
SymbolStyle |
getStyle()
Retrieve the current style. |
void |
paintComponent(java.awt.Graphics g)
Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area. |
void |
setDistribution(Distribution dist)
Set the dist to render. |
void |
setLogoPainter(LogoPainter logoPainter)
Set the logo painter. |
void |
setStyle(SymbolStyle style)
Set the symbol style. |
double |
totalBits()
Retrieve the maximal number of bits possible for this type of dist. |
double |
totalInformation()
Calculates the total information of the dist in bits. |
Methods inherited from class javax.swing.JComponent |
addAncestorListener,
addNotify,
addPropertyChangeListener,
addPropertyChangeListener,
addVetoableChangeListener,
computeVisibleRect,
contains,
createToolTip,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
firePropertyChange,
fireVetoableChange,
getAccessibleContext,
getActionForKeyStroke,
getAlignmentX,
getAlignmentY,
getAutoscrolls,
getBorder,
getBounds,
getClientProperty,
getComponentGraphics,
getConditionForKeyStroke,
getDebugGraphicsOptions,
getGraphics,
getHeight,
getInsets,
getInsets,
getLocation,
getMaximumSize,
getMinimumSize,
getNextFocusableComponent,
getPreferredSize,
getRegisteredKeyStrokes,
getRootPane,
getSize,
getToolTipLocation,
getToolTipText,
getToolTipText,
getTopLevelAncestor,
getUIClassID,
getVisibleRect,
getWidth,
getX,
getY,
grabFocus,
hasFocus,
isDoubleBuffered,
isFocusCycleRoot,
isFocusTraversable,
isLightweightComponent,
isManagingFocus,
isOpaque,
isOptimizedDrawingEnabled,
isPaintingTile,
isRequestFocusEnabled,
isValidateRoot,
paint,
paintBorder,
paintChildren,
paintImmediately,
paintImmediately,
paramString,
print,
printAll,
processComponentKeyEvent,
processFocusEvent,
processKeyEvent,
processMouseMotionEvent,
putClientProperty,
registerKeyboardAction,
registerKeyboardAction,
removeAncestorListener,
removeNotify,
removePropertyChangeListener,
removePropertyChangeListener,
removeVetoableChangeListener,
repaint,
repaint,
requestDefaultFocus,
requestFocus,
resetKeyboardActions,
reshape,
revalidate,
scrollRectToVisible,
setAlignmentX,
setAlignmentY,
setAutoscrolls,
setBackground,
setBorder,
setDebugGraphicsOptions,
setDoubleBuffered,
setEnabled,
setFont,
setForeground,
setMaximumSize,
setMinimumSize,
setNextFocusableComponent,
setOpaque,
setPreferredSize,
setRequestFocusEnabled,
setToolTipText,
setUI,
setVisible,
unregisterKeyboardAction,
update,
updateUI |
Methods inherited from class java.awt.Container |
add,
add,
add,
add,
add,
addContainerListener,
addImpl,
countComponents,
deliverEvent,
doLayout,
findComponentAt,
findComponentAt,
getComponent,
getComponentAt,
getComponentAt,
getComponentCount,
getComponents,
getLayout,
insets,
invalidate,
isAncestorOf,
layout,
list,
list,
locate,
minimumSize,
paintComponents,
preferredSize,
printComponents,
processContainerEvent,
processEvent,
remove,
remove,
removeAll,
removeContainerListener,
setCursor,
setLayout,
validate,
validateTree |
Methods inherited from class java.awt.Component |
action,
add,
addComponentListener,
addFocusListener,
addInputMethodListener,
addKeyListener,
addMouseListener,
addMouseMotionListener,
bounds,
checkImage,
checkImage,
coalesceEvents,
contains,
createImage,
createImage,
disable,
disableEvents,
dispatchEvent,
enable,
enable,
enableEvents,
enableInputMethods,
getBackground,
getBounds,
getColorModel,
getComponentOrientation,
getCursor,
getDropTarget,
getFont,
getFontMetrics,
getForeground,
getInputContext,
getInputMethodRequests,
getLocale,
getLocation,
getLocationOnScreen,
getName,
getParent,
getPeer,
getSize,
getToolkit,
getTreeLock,
gotFocus,
handleEvent,
hide,
imageUpdate,
inside,
isDisplayable,
isEnabled,
isLightweight,
isShowing,
isValid,
isVisible,
keyDown,
keyUp,
list,
list,
list,
location,
lostFocus,
mouseDown,
mouseDrag,
mouseEnter,
mouseExit,
mouseMove,
mouseUp,
move,
nextFocus,
paintAll,
postEvent,
prepareImage,
prepareImage,
processComponentEvent,
processInputMethodEvent,
processMouseEvent,
remove,
removeComponentListener,
removeFocusListener,
removeInputMethodListener,
removeKeyListener,
removeMouseListener,
removeMouseMotionListener,
repaint,
repaint,
repaint,
resize,
resize,
setBounds,
setBounds,
setComponentOrientation,
setDropTarget,
setLocale,
setLocation,
setLocation,
setName,
setSize,
setSize,
show,
show,
size,
toString,
transferFocus |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
wait,
wait,
wait |
Constructor Detail |
public DistributionLogo()
Method Detail |
public Distribution getDistribution()
public void setDistribution(Distribution dist) throws IllegalAlphabetException
The dist must be over a FiniteAlphabet so that we can draw the numbers for each Symbol.
dist
- the new Distribution to renderpublic LogoPainter getLogoPainter()
public void setLogoPainter(LogoPainter logoPainter)
This will alter the way that the dist is rendered to screen.
logoPainter
- the new logoPainterpublic SymbolStyle getStyle()
public void setStyle(SymbolStyle style)
This will change the outline and fill paints for the logos
style
- the new SymbolStyle to usepublic double entropy(Symbol r) throws IllegalSymbolException
r
- the symbol to calculate forpublic double totalBits()
public double totalInformation()
This calculates totalBits - sum_r(entropy(r))
public void paintComponent(java.awt.Graphics g)
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