org.biojava.spice.jmol
Class StructurePanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.biojava.spice.jmol.StructurePanel

All Implemented Interfaces:

Accessible, ImageObserver, JmolCommander, MenuContainer, Serializable

public class StructurePanel

extends JPanel

implements JmolCommander

A panel that provides a wrapper around the Jmol viewer. The code for this is heavily inspired by http://cvs.sourceforge.net/viewcvs.py/jmol/Jmol/examples/Integration.java?view=markup - the Jmol example of how to integrate Jmol into an application.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JPanel

JPanel.AccessibleJPanel

Nested classes inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

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

StructurePanel()

Method Summary

void	addJmolStatusListener(JmolStatusListener listener) Add a JmolStatus listener to Jmol
void	clearDisplay()
void	clearListeners() remove the listeners from Jmol again.
void	executeCmd(String command) Send a RASMOL like command to Jmol
Matrix	getJmolRotation() get the rotation out of Jmol
Structure	getStructure() return the currently displayed structure object
JmolViewer	getViewer() returns the JmolViewer
void	initJmolDisplay() call this upon startup.
void	paint(Graphics g) paint Jmol
void	reset() reset the Jmol display
void	rotateJmol(Matrix jmolRotation) send a rotation to Jmol
void	setStructure(Structure structure) display a new PDB structure in Jmol

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, transferFocusBackward, 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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

StructurePanel

public StructurePanel()

Method Detail

reset

public void reset()

reset the Jmol display

initJmolDisplay

public void initJmolDisplay()

call this upon startup. This is a workaround to a bug in Jmol.

addJmolStatusListener

public void addJmolStatusListener(JmolStatusListener listener)

Add a JmolStatus listener to Jmol

Parameters:

listener -

See Also:

JmolSpiceTranslator

clearListeners

public void clearListeners()

remove the listeners from Jmol again.

clearDisplay

public void clearDisplay()

getViewer

public JmolViewer getViewer()

returns the JmolViewer

Returns:

the viewer

paint

public void paint(Graphics g)

paint Jmol

executeCmd

public void executeCmd(String command)

Send a RASMOL like command to Jmol

Specified by:

executeCmd in interface JmolCommander

Parameters:

command - - a String containing a RASMOL like command. e.g. "select protein; cartoon on;"

getJmolRotation

public Matrix getJmolRotation()

get the rotation out of Jmol

Returns:

the jmol rotation matrix

rotateJmol

public void rotateJmol(Matrix jmolRotation)

send a rotation to Jmol

Parameters:

jmolRotation -

getStructure

public Structure getStructure()

return the currently displayed structure object

Returns:

the currently displayed structure

setStructure

public void setStructure(Structure structure)

display a new PDB structure in Jmol

Parameters:

structure - a Biojava structure object