Package org.biojava.nbio.structure.gui

Class ScaleableMatrixPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

org.biojava.nbio.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

Nested Classes

Modifier and Type	Class	Description
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

Fields

Modifier and Type	Field	Description
protected JComboBox	coloring
protected Map<String,ContinuousColorMapper>	gradients
protected JMatrixPanel	mPanel
protected JScrollPane	scroll
protected JSlider	slider
protected static final int	SLIDER_STEPS

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
ScaleableMatrixPanel()

Method Summary

Modifier and Type	Method	Description
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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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

Field Details

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 Details

ScaleableMatrixPanel

public ScaleableMatrixPanel()

Method Details

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)