org.biojava.bio.structure.gui
Class ScaleableMatrixPanel

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by org.biojava.bio.structure.gui.ScaleableMatrixPanel
All Implemented Interfaces:
ActionListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, ChangeListener
Direct Known Subclasses:
DotPlotPanel

public class ScaleableMatrixPanel
extends JPanel
implements ChangeListener, ActionListener

A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm. It adds a JSlider to a JMatrixPanel. see also JMatrixPanel.

See Also:
Serialized Form

Nested Class Summary
protected  class ScaleableMatrixPanel.GradientRenderer
          A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.
 
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
protected  JComboBox coloring
           
protected  Map<String,ContinuousColorMapper> gradients
           
protected  JMatrixPanel mPanel
           
protected  JScrollPane scroll
           
protected  JSlider slider
           
protected static int SLIDER_STEPS
           
 
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
ScaleableMatrixPanel()
           
 
Method Summary
 void actionPerformed(ActionEvent e)
           
protected static Map<String,ContinuousColorMapper> createGradients()
           
 AlternativeAlignment[] getAlternativeAligs()
           
 ContinuousColorMapper getCellColor()
           
 FragmentPair[] getFragmentPairs()
           
 Matrix getMatrix()
           
 JMatrixPanel getMatrixPanel()
           
 int getSelectedAlignmentPos()
           
static void main(String[] args)
           
 void setAlternativeAligs(AlternativeAlignment[] aligs)
           
 void setCellColor(ContinuousColorMapper cellColor)
           
 void setFragmentPairs(FragmentPair[] pairs)
           
 void setMatrix(Matrix matrix)
           
 void setSelectedAlignmentPos(int selectedAlignmentPos)
           
 void stateChanged(ChangeEvent e)
           
 
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

mPanel

protected JMatrixPanel mPanel

slider

protected JSlider slider

scroll

protected JScrollPane scroll

coloring

protected JComboBox coloring

gradients

protected Map<String,ContinuousColorMapper> gradients

SLIDER_STEPS

protected static final int SLIDER_STEPS
See Also:
Constant Field Values
Constructor Detail

ScaleableMatrixPanel

public ScaleableMatrixPanel()
Method Detail

main

public static void main(String[] args)

createGradients

protected static Map<String,ContinuousColorMapper> createGradients()

stateChanged

public void stateChanged(ChangeEvent e)
Specified by:
stateChanged in interface ChangeListener

getMatrix

public Matrix getMatrix()

setMatrix

public void setMatrix(Matrix matrix)

getMatrixPanel

public JMatrixPanel getMatrixPanel()

getFragmentPairs

public FragmentPair[] getFragmentPairs()

setFragmentPairs

public void setFragmentPairs(FragmentPair[] pairs)

getAlternativeAligs

public AlternativeAlignment[] getAlternativeAligs()

setAlternativeAligs

public void setAlternativeAligs(AlternativeAlignment[] aligs)

getSelectedAlignmentPos

public int getSelectedAlignmentPos()

setSelectedAlignmentPos

public void setSelectedAlignmentPos(int selectedAlignmentPos)

getCellColor

public ContinuousColorMapper getCellColor()
Returns:
the color mapping of the JMatrixPanel

setCellColor

public void setCellColor(ContinuousColorMapper cellColor)
Parameters:
cellColor - the color mapping of the JMatrixPanel

actionPerformed

public void actionPerformed(ActionEvent e)
Specified by:
actionPerformed in interface ActionListener
Parameters:
e -
See Also:
ActionListener.actionPerformed(java.awt.event.ActionEvent)