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)

Class ScaleableMatrixPanel

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JPanel

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Details

mPanel

slider

scroll

coloring

gradients

SLIDER_STEPS

Constructor Details

ScaleableMatrixPanel

Method Details

main

createGradients

stateChanged

getMatrix

setMatrix

getMatrixPanel

getFragmentPairs

setFragmentPairs

getAlternativeAligs

setAlternativeAligs

getSelectedAlignmentPos

setSelectedAlignmentPos

getCellColor

setCellColor

actionPerformed