gui
Class JPreview

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  gui.JPreview

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class JPreview
extends javax.swing.JPanel

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JComponent.AccessibleJComponent

Field Summary

java.util.Vector

pdbFiles

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, 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

JPreview(JWorkPanel workPanel)
The JPreview is a container wich handles the specific JmolViewer in restricted mode used by cell microcosmos editor to preview different PDB-files.

Method Summary

void	computePDBManipulation(Protein givenProtein) Computes the yTranslation and the RotationMatrix of the PDB.
void	fetchPDBManipulationFromProtein(Protein givenProtein) Computes the yTranslation and the RotationMatrix of the PDB.
JmolPdbPreview	getJmolMemViewer()
javax.swing.JPanel	getMembraneJPanel()
boolean	getShowTransparentLipids() Gives an info, whether all transparents will be displayed or not.
JWorkPanel	getWorkPanel()
void	handlePopupMenu(int x, int y)
void	notifyAtomPicked(int atomIndex, java.lang.String strInfo)
void	notifyFileLoaded(java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.Object clientFile, java.lang.String errorMessage)
void	notifyFrameChanged(int frameNo)
void	notifyMeasurementsChanged()
void	notifyScriptTermination(java.lang.String statusMessage, int msWalltime)
void	scriptEcho(java.lang.String strEcho)
void	scriptStatus(java.lang.String strStatus)
void	setJmolMemViewer(JmolPdbPreview jmolMemViewer)
void	setMembraneJPanel(javax.swing.JPanel membraneJPanel)
void	setPDB(java.util.Vector pdb) Contains the pdb for the pdb-viewer in a vector
void	setShowTransparentLipids(boolean showLipids) Sets whether all transparents lipids will be displayed or not.
void	setStatusMessage(java.lang.String statusMessage)
void	showConsole(boolean showConsole)
void	showInfo() This is only a test-method!
void	showPdbFile(java.lang.String filepath) Reads a PDB file, wich is visualized in pdb-viewer
void	showUrl(java.lang.String url)
void	showViewerPdbFile(java.lang.String filepath, JmolPdbPreview viewer) Reads a PDB file, wich is visualized in the given viewer
void	switchViewerTo(javax.swing.JPanel viewerToShow) This method switches between the two viewer
void	updatePreview()

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, 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, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, 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, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, 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, 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, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

pdbFiles

public java.util.Vector pdbFiles

Constructor Detail

JPreview

public JPreview(JWorkPanel workPanel)

The JPreview is a container wich handles the specific JmolViewer in restricted mode used by cell microcosmos editor to preview different PDB-files. If wanted it is possible to switch to a standard Jmolviewer to use a viewer which runs not in restricted mode. Often used functions are accesible from different buttons on the JPreview panel.

Parameters:

workPanel - The used JWorkPanel contains informations about other objects wich will be needed by JPreview.

Method Detail

computePDBManipulation

public void computePDBManipulation(Protein givenProtein)

Computes the yTranslation and the RotationMatrix of the PDB. It gets the RotationMatrix from the JmolViewer and writes it to the protein.

Parameters:

givenProtein - The use pdb as Protein object.

fetchPDBManipulationFromProtein

public void fetchPDBManipulationFromProtein(Protein givenProtein)

Computes the yTranslation and the RotationMatrix of the PDB. It gets the RotationMatrix from the protein and writes it to the JmolViewer.

Parameters:

givenProtein - The use pdb as Protein object.

updatePreview

public void updatePreview()

switchViewerTo

public void switchViewerTo(javax.swing.JPanel viewerToShow)

This method switches between the two viewer

Parameters:

viewerToShow - The viewer wich should be visualized

showPdbFile

public void showPdbFile(java.lang.String filepath)

Reads a PDB file, wich is visualized in pdb-viewer

Parameters:

filepath -

showViewerPdbFile

public void showViewerPdbFile(java.lang.String filepath,
                              JmolPdbPreview viewer)

Reads a PDB file, wich is visualized in the given viewer

Parameters:

filepath - Path of the file to display

viewer - The viewer wich should visualize the given file

setPDB

public void setPDB(java.util.Vector pdb)

Contains the pdb for the pdb-viewer in a vector

Parameters:

pdb - The vector, wich contains the pdb

showInfo

public void showInfo()

This is only a test-method! Just visualize some Jmol informations and properties. Not longer used and this one will be deleted at the next release!

getShowTransparentLipids

public boolean getShowTransparentLipids()

Gives an info, whether all transparents will be displayed or not.

Returns:

Returns true if all transparent lipids are shown. If it returns false only the ones on the left and on the right are shown

setShowTransparentLipids

public void setShowTransparentLipids(boolean showLipids)

Sets whether all transparents lipids will be displayed or not.

Parameters:

showLipids - Set this to true and all transparent lipids will be displayed.

notifyFileLoaded

public void notifyFileLoaded(java.lang.String fullPathName,
                             java.lang.String fileName,
                             java.lang.String modelName,
                             java.lang.Object clientFile,
                             java.lang.String errorMessage)

setStatusMessage

public void setStatusMessage(java.lang.String statusMessage)

scriptEcho

public void scriptEcho(java.lang.String strEcho)

scriptStatus

public void scriptStatus(java.lang.String strStatus)

notifyScriptTermination

public void notifyScriptTermination(java.lang.String statusMessage,
                                    int msWalltime)

handlePopupMenu

public void handlePopupMenu(int x,
                            int y)

notifyMeasurementsChanged

public void notifyMeasurementsChanged()

notifyFrameChanged

public void notifyFrameChanged(int frameNo)

notifyAtomPicked

public void notifyAtomPicked(int atomIndex,
                             java.lang.String strInfo)

showUrl

public void showUrl(java.lang.String url)

showConsole

public void showConsole(boolean showConsole)

getWorkPanel

public JWorkPanel getWorkPanel()

Returns:

Returns the workPanel.

getMembraneJPanel

public javax.swing.JPanel getMembraneJPanel()

Returns:

Returns the membraneJPanel.

setMembraneJPanel

public void setMembraneJPanel(javax.swing.JPanel membraneJPanel)

Parameters:

membraneJPanel - The membraneJPanel to set.

getJmolMemViewer

public JmolPdbPreview getJmolMemViewer()

Returns:

Returns the jmolMemViewer.

setJmolMemViewer

public void setJmolMemViewer(JmolPdbPreview jmolMemViewer)

Parameters:

jmolMemViewer - The jmolMemViewer to set.