org.biojava.bio.structure.gui
Class ScaleableMatrixPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.biojava.bio.structure.gui.ScaleableMatrixPanel

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener

Direct Known Subclasses:

DotPlotPanel

public class ScaleableMatrixPanel
extends javax.swing.JPanel
implements javax.swing.event.ChangeListener, java.awt.event.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

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

protected javax.swing.JComboBox	coloring
protected java.util.Map<java.lang.String,ContinuousColorMapper>	gradients
protected JMatrixPanel	mPanel
protected javax.swing.JScrollPane	scroll
protected javax.swing.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(java.awt.event.ActionEvent e)
protected static java.util.Map<java.lang.String,ContinuousColorMapper>	createGradients()
AlternativeAlignment[]	getAlternativeAligs()
ContinuousColorMapper	getCellColor()
FragmentPair[]	getFragmentPairs()
Matrix	getMatrix()
JMatrixPanel	getMatrixPanel()
int	getSelectedAlignmentPos()
static void	main(java.lang.String[] args)
void	setAlternativeAligs(AlternativeAlignment[] aligs)
void	setCellColor(ContinuousColorMapper cellColor)
void	setFragmentPairs(FragmentPair[] pairs)
void	setMatrix(Matrix matrix)
void	setSelectedAlignmentPos(int selectedAlignmentPos)
void	stateChanged(javax.swing.event.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 javax.swing.JSlider slider

scroll

protected javax.swing.JScrollPane scroll

coloring

protected javax.swing.JComboBox coloring

gradients

protected java.util.Map<java.lang.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(java.lang.String[] args)

createGradients

protected static java.util.Map<java.lang.String,ContinuousColorMapper> createGradients()

stateChanged

public void stateChanged(javax.swing.event.ChangeEvent e)

Specified by:

stateChanged in interface javax.swing.event.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(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e -

See Also:

ActionListener.actionPerformed(java.awt.event.ActionEvent)