cct.dialogs
Class JEditorFrame

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      cct.dialogs.JEditorFrame

All Implemented Interfaces:

ParentInterface, AtomProperties, OperationsOnAtoms, PDBBankFetcherInterface, ShadowClientInterface, java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class JEditorFrame
extends javax.swing.JFrame
implements OperationsOnAtoms, AtomProperties, java.awt.event.ActionListener, ParentInterface, PDBBankFetcherInterface, ShadowClientInterface

Title: Computational Chemistry Tookit

Description:

This is the main interface for the Jamberoo (JMolEditor) By default, is redirected to the internal window. To disable this feature set cct.dialogs.JEditorFrame@redirectStderr = false in the cct.properties file

Copyright: Copyright (c) 2005-2009 Dr. Vladislav Vassiliev

Company: ANU

See Also:

Serialized Form

Nested Class Summary

(package private) class	JEditorFrame.AtomColorScheme_actionAdapter
(package private) class	JEditorFrame.JEditorFrame_deleteMoleculeButton_actionAdapter
(package private) class	JEditorFrame.JEditorFrame_jButton3_actionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuAnalyze_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuDB_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuFileEdit_ActionAdapter Title: Picking
(package private) class	JEditorFrame.JEditorFrame_jMenuFileExit_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuFileOpenAs_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuFileSaveAs_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuHelpAbout_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_jMenuView_ActionAdapter
(package private) class	JEditorFrame.JEditorFrame_openFileButton_actionAdapter

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

javax.swing.JFrame.AccessibleJFrame

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

java.awt.Frame.AccessibleAWTFrame

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

java.awt.Window.AccessibleAWTWindow

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

(package private) J3DTabbedWorld	j3dTabbedWorld
(package private) static MemoryMonitor	memorymonitor
protected javax.swing.JMenuItem	trajectoryAnalysis
protected TrajectoryAnalysisDialog	trajectoryAnalysisDialog

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface cct.modelling.OperationsOnAtoms

FIXED_ATOM, ROTATE_ATOM, ROTATE_GROUP, RULE_DIFFERENCE, RULE_INTERSECTION, RULE_UNION, SELECT_ATOMS, SELECT_MOLECULES, SELECT_MONOMERS, SELECTED_ADD_ATOMS, SELECTED_ADD_FRAGMENT, SELECTED_ADD_MOLECULE, SELECTED_CHANGE_ATOM_LABELS_COLOR, SELECTED_CHANGE_ATOM_LABELS_SIZE, SELECTED_CREATE_CENTROID, SELECTED_DELETE_ATOMS, SELECTED_DISPLAY_ATOMS, SELECTED_FILL_VALENCES_WITH_HYDROGENS, SELECTED_LABEL_ATOMS, SELECTED_MODIFY_ANGLES, SELECTED_MODIFY_ATOMS, SELECTED_MODIFY_BONDS, SELECTED_MODIFY_DIHEDRALS, SELECTED_NOTHING, SELECTED_SOLVATE_CAP, SELECTED_SOLVATE_SHELL, SELECTED_UNDISPLAY_ATOMS, SELECTED_UNLABEL_ATOMS, SELECTION_FOUR_ATOMS_ONLY, SELECTION_ONE_ATOM_ONLY, SELECTION_SPOT_ONLY, SELECTION_THREE_ATOMS_ONLY, SELECTION_TWO_ATOMS_ONLY, SELECTION_UNLIMITED, TRANSLATE_ATOM, TRANSLATE_GROUP

Fields inherited from interface cct.modelling.AtomProperties

GEOMETRY_LINEAR, GEOMETRY_TETRAHEDRAL, GEOMETRY_TRIGONAL

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

JEditorFrame(java.lang.String title)

JEditorFrame(java.lang.String[] args)

JEditorFrame(java.lang.String title, java.lang.String[] args)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent actionEvent)
java.lang.String	addMenuItem(java.lang.String menuName, javax.swing.JMenuItem menuItem)
(package private) void	buildAnalyzeMenu()
(package private) void	buildEditMenu()
void	changeAtomColorScheme(java.awt.event.ActionEvent e)
void	changeLookAndFeel(java.awt.event.ActionEvent e)
void	childFinished(java.lang.Object child) To inform parent that its child process finished its execution
(package private) java.lang.String	chooseFileDialog(java.lang.String fileType, java.lang.String formatDescr, int dialogType)
void	deleteMoleculeButton_actionPerformed(java.awt.event.ActionEvent e)
void	fetchStructure(java.lang.String host, java.lang.String entry_directory, java.lang.String code)
java.awt.Component	getComponent() Gets parent component (if any)
Java3dUniverse	getJ3DUniverse()
javax.swing.JToolBar	getJToolBar()
javax.swing.JMenuItem	getMenuItem(java.lang.String menuName, java.lang.String menuItemName) Gets menu item with ActionCommand name "menuItemName" from the menu with ActionCommand name "menuName"
MoleculeInterface	getMolecule()
java.awt.Frame	getParentFrame()
float[][]	getVirtualWorldCoordinates(MoleculeInterface molec) Transforms coordinates of atoms of the arbitrary molecule into current virtual world space
(package private) boolean	guessAndOpenFile(Java3dUniverse j3d)
boolean	hasMenuItem(java.lang.String menuName, java.lang.String menuItemName) Check whether menu with ActionCommand "menuName" has menu item with ActionCommand "menuItemName"
void	interceptStderr(boolean enable) Enables/disables redirection of stderr.
boolean	isMoleculeLoaded() Checks whether molecule loaded or not
void	jButton3_actionPerformed(java.awt.event.ActionEvent e)
(package private) void	jMenuAnalyze_actionPerformed(java.awt.event.ActionEvent actionEvent)
(package private) void	jMenuDB_actionPerformed(java.awt.event.ActionEvent actionEvent)
(package private) void	jMenuFileEdit_actionPerformed(java.awt.event.ActionEvent actionEvent)
(package private) void	jMenuFileExit_actionPerformed(java.awt.event.ActionEvent actionEvent) File | Exit action performed.
(package private) void	jMenuFileOpenAs_actionPerformed(java.awt.event.ActionEvent actionEvent) File | Exit action performed.
(package private) void	jMenuFileSaveAs_actionPerformed(java.awt.event.ActionEvent actionEvent)
(package private) void	jMenuHelpAbout_actionPerformed(java.awt.event.ActionEvent actionEvent) Help | About action performed.
(package private) void	jMenuView_actionPerformed(java.awt.event.ActionEvent actionEvent)
void	loadFromSFTP(java.awt.event.ActionEvent e)
(package private) void	openFile(Java3dUniverse j3d, CHEMISTRY_FILE_FORMAT fileType, java.lang.String fileName)
(package private) void	openFile(Java3dUniverse j3d, java.lang.String fileType)
void	openFileButton_actionPerformed(java.awt.event.ActionEvent e) Program tries to guess and open all supported molecular file formats
void	openMoleculeFile(java.lang.String title, Java3dUniverse j3d)
(package private) void	processArguments(java.lang.String[] args)
javax.swing.JMenuItem	removeMenuItem(java.lang.String menuName, java.lang.String menuItemName)
void	saveImageAs(java.awt.event.ActionEvent e)
void	setDefaultHelper()
void	setFileBrowser(java.lang.String host, java.lang.String username, FileBrowserInterface file_browser)
void	setHelper(HelperInterface h)
void	setKnownHosts(java.lang.String[] hosts)
void	setMolecule(Molecule m)
void	setMolecule(MoleculeInterface m)
void	submitGaussianJob(java.awt.event.ActionEvent e)
void	submitMolecule(java.awt.event.ActionEvent e)

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

j3dTabbedWorld

J3DTabbedWorld j3dTabbedWorld

trajectoryAnalysis

protected javax.swing.JMenuItem trajectoryAnalysis

trajectoryAnalysisDialog

protected TrajectoryAnalysisDialog trajectoryAnalysisDialog

memorymonitor

static MemoryMonitor memorymonitor

Constructor Detail

JEditorFrame

public JEditorFrame(java.lang.String title,
                    java.lang.String[] args)

JEditorFrame

public JEditorFrame(java.lang.String[] args)

JEditorFrame

public JEditorFrame(java.lang.String title)

Method Detail

processArguments

void processArguments(java.lang.String[] args)

setDefaultHelper

public void setDefaultHelper()

setHelper

public void setHelper(HelperInterface h)

jMenuFileOpenAs_actionPerformed

void jMenuFileOpenAs_actionPerformed(java.awt.event.ActionEvent actionEvent)

File | Exit action performed.

Parameters:

actionEvent - ActionEvent

openFile

void openFile(Java3dUniverse j3d,
              CHEMISTRY_FILE_FORMAT fileType,
              java.lang.String fileName)

openFile

void openFile(Java3dUniverse j3d,
              java.lang.String fileType)

jMenuFileSaveAs_actionPerformed

void jMenuFileSaveAs_actionPerformed(java.awt.event.ActionEvent actionEvent)

isMoleculeLoaded

public boolean isMoleculeLoaded()

Checks whether molecule loaded or not

Returns:

boolean "true" if loaded and "false" otherwise

jMenuFileEdit_actionPerformed

void jMenuFileEdit_actionPerformed(java.awt.event.ActionEvent actionEvent)

Parameters:

actionEvent - ActionEvent

jMenuAnalyze_actionPerformed

void jMenuAnalyze_actionPerformed(java.awt.event.ActionEvent actionEvent)

jMenuView_actionPerformed

void jMenuView_actionPerformed(java.awt.event.ActionEvent actionEvent)

jMenuDB_actionPerformed

void jMenuDB_actionPerformed(java.awt.event.ActionEvent actionEvent)

buildEditMenu

void buildEditMenu()

buildAnalyzeMenu

void buildAnalyzeMenu()

chooseFileDialog

java.lang.String chooseFileDialog(java.lang.String fileType,
                                  java.lang.String formatDescr,
                                  int dialogType)

Parameters:

fileType - String

formatDescr - String

Returns:

String

jMenuFileExit_actionPerformed

void jMenuFileExit_actionPerformed(java.awt.event.ActionEvent actionEvent)

File | Exit action performed.

Parameters:

actionEvent - ActionEvent

jMenuHelpAbout_actionPerformed

void jMenuHelpAbout_actionPerformed(java.awt.event.ActionEvent actionEvent)

Help | About action performed.

Parameters:

actionEvent - ActionEvent

deleteMoleculeButton_actionPerformed

public void deleteMoleculeButton_actionPerformed(java.awt.event.ActionEvent e)

changeAtomColorScheme

public void changeAtomColorScheme(java.awt.event.ActionEvent e)

saveImageAs

public void saveImageAs(java.awt.event.ActionEvent e)

submitMolecule

public void submitMolecule(java.awt.event.ActionEvent e)

submitGaussianJob

public void submitGaussianJob(java.awt.event.ActionEvent e)

changeLookAndFeel

public void changeLookAndFeel(java.awt.event.ActionEvent e)

openFileButton_actionPerformed

public void openFileButton_actionPerformed(java.awt.event.ActionEvent e)

Program tries to guess and open all supported molecular file formats

Parameters:

e - ActionEvent

guessAndOpenFile

boolean guessAndOpenFile(Java3dUniverse j3d)

getVirtualWorldCoordinates

public float[][] getVirtualWorldCoordinates(MoleculeInterface molec)

Transforms coordinates of atoms of the arbitrary molecule into current virtual world space

Parameters:

molec - MoleculeInterface - Molecule

Returns:

float[][] - cartesian coordinates float[number_of_atoms][3]

addMenuItem

public java.lang.String addMenuItem(java.lang.String menuName,
                                    javax.swing.JMenuItem menuItem)

getJToolBar

public javax.swing.JToolBar getJToolBar()

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent actionEvent)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

fetchStructure

public void fetchStructure(java.lang.String host,
                           java.lang.String entry_directory,
                           java.lang.String code)

Specified by:

fetchStructure in interface PDBBankFetcherInterface

openMoleculeFile

public void openMoleculeFile(java.lang.String title,
                             Java3dUniverse j3d)

hasMenuItem

public boolean hasMenuItem(java.lang.String menuName,
                           java.lang.String menuItemName)
                    throws java.lang.Exception

Check whether menu with ActionCommand "menuName" has menu item with ActionCommand "menuItemName"

Parameters:

menuName - String - menu ActionCommand name

menuItemName - String menu item ActionCommand name

Returns:

boolean true - a menu has a given menu item, false otherwise

Throws:

java.lang.Exception - if there is no such menu in menubar

getMenuItem

public javax.swing.JMenuItem getMenuItem(java.lang.String menuName,
                                         java.lang.String menuItemName)
                                  throws java.lang.Exception

Gets menu item with ActionCommand name "menuItemName" from the menu with ActionCommand name "menuName"

Parameters:

menuName - String

menuItemName - String

Returns:

JMenuItem

Throws:

java.lang.Exception

removeMenuItem

public javax.swing.JMenuItem removeMenuItem(java.lang.String menuName,
                                            java.lang.String menuItemName)
                                     throws java.lang.Exception

Throws:

java.lang.Exception

getMolecule

public MoleculeInterface getMolecule()

getJ3DUniverse

public Java3dUniverse getJ3DUniverse()

setMolecule

public void setMolecule(Molecule m)

setMolecule

public void setMolecule(MoleculeInterface m)

jButton3_actionPerformed

public void jButton3_actionPerformed(java.awt.event.ActionEvent e)

childFinished

public void childFinished(java.lang.Object child)

Description copied from interface: ParentInterface

To inform parent that its child process finished its execution

Specified by:

childFinished in interface ParentInterface

Parameters:

child - Object - Some ID of a child given by parent

interceptStderr

public void interceptStderr(boolean enable)

Enables/disables redirection of stderr.

Parameters:

enable - boolean - if true, redirects sdterr to the errors log panel and adds "Errors Log" menu item to the File menu. if false, remove menu item from the File menu and directs sdterr to the standard stream

getComponent

public java.awt.Component getComponent()

Description copied from interface: ParentInterface

Gets parent component (if any)

Specified by:

getComponent in interface ParentInterface

Specified by:

getComponent in interface ShadowClientInterface

Returns:

Component

getParentFrame

public java.awt.Frame getParentFrame()

Specified by:

getParentFrame in interface ParentInterface

setKnownHosts

public void setKnownHosts(java.lang.String[] hosts)

Specified by:

setKnownHosts in interface ShadowClientInterface

setFileBrowser

public void setFileBrowser(java.lang.String host,
                           java.lang.String username,
                           FileBrowserInterface file_browser)

Specified by:

setFileBrowser in interface ShadowClientInterface

loadFromSFTP

public void loadFromSFTP(java.awt.event.ActionEvent e)