chemaxon.marvin.beans
Class MarvinPane

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JRootPane
                  chemaxon.marvin.beans.MarvinPane

All Implemented Interfaces:

java.awt.event.ComponentListener, java.awt.event.KeyListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

Direct Known Subclasses:

MSketchPane, MViewPane

public abstract class MarvinPane
extends javax.swing.JRootPane
implements java.awt.event.KeyListener, java.beans.PropertyChangeListener, java.awt.event.ComponentListener

Ancestor of the Marvin Beans.

Version:

5.2, 02/11/2009

Author:

Peter Csizmadia, Tamas Vertse

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JRootPane.AccessibleJRootPane, javax.swing.JRootPane.RootLayout

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

javax.swing.JComponent.AccessibleJComponent

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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected chemaxon.marvin.common.swing.MolPanel	molPanel Underlying panel.
protected java.lang.String	params Parameter string.
protected static java.awt.Container	topLevelContainer The top level container of the pane
static java.lang.String	VERSION Marvin version.

Fields inherited from class javax.swing.JRootPane

COLOR_CHOOSER_DIALOG, contentPane, defaultButton, defaultPressAction, defaultReleaseAction, ERROR_DIALOG, FILE_CHOOSER_DIALOG, FRAME, glassPane, INFORMATION_DIALOG, layeredPane, menuBar, NONE, PLAIN_DIALOG, QUESTION_DIALOG, WARNING_DIALOG

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

protected

MarvinPane() Constructor.

Method Summary

void	addActionListener(java.awt.event.ActionListener l) Adds an action listener.
javax.swing.JMenu	addHelpMenu(java.awt.Container m) Adds the help menu to a parent menu.
void	addMenuBarChangeListener(chemaxon.marvin.common.swing.MenuBarChangeListener l) Adds a menubar change listener.
javax.swing.JMenu	addToolsMenu(java.awt.Container m) Deprecated. Not used.
boolean	arePopupMenusEnabled() Are popup menus enabled?
void	beginHourglass() Changes the cursor to hourglass at the beginning of a long operation.
void	closeWindows() Closes all windows opened by this MarvinPane.
void	componentHidden(java.awt.event.ComponentEvent ev) Hides windows if the parent frame is hidden.
void	componentMoved(java.awt.event.ComponentEvent ev) Does nothing.
void	componentResized(java.awt.event.ComponentEvent ev) Does nothing.
void	componentShown(java.awt.event.ComponentEvent ev) Shows windows if the parent frame is hidden.
static javax.swing.JMenu	createMenu(java.util.ResourceBundle rc, java.lang.String key) Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.createMenu
abstract void	doPaste() Invokes Paste actions.
void	endHourglass() Changes the hourglass cursor back to normal at the end of a long operation.
void	exit() Closes all windows opened by this MarvinPane and saves user initialization file.
boolean	getAtomNumbersVisible() Deprecated. as of Marvin 2.9.13, replaced by isAtomNumbersVisible.
java.awt.Color	getAtomSetColor(int i) Gets the color of an atom set.
double	getAtomsize() Gets the atom size.
double	getBallRadius() Gets the ball radius in units of covalent radius.
double	getBondSpacing() Gets the double bond spacing.
double	getBondWidth() Deprecated. as of Marvin 4.1, replaced by getBondSpacing()
int	getChiralitySupport() Gets chirality support level.
int	getCleanDim() Gets the number of space dimensions for cleaning.
java.lang.String	getColorScheme() Gets the color scheme.
chemaxon.marvin.common.swing.CommonActions	getCommonActions() Deprecated.
int	getDebug() Gets the debugging level.
java.io.File	getDirectory() Sets the working directory.
int	getDispopts() Gets display options.
int	getDispQuality() Gets the display quality.
java.lang.String	getDownWedge() Gets the wedge bond display convention.
boolean	getExplicitH() Deprecated. since 5.4 returns false. will be unsupported in 5.5
java.io.File	getFile() Gets the current molecule file.
java.lang.String	getFormat() Gets the default molecule file format.
java.lang.String	getImplicitH() Query the display method of implicit hydrogens.
long	getInvisibleSets() Gets the visibility of the specified atom sets.
boolean	getLabels() Deprecated. use isAtomSymbolsVisible() instead
boolean	getLonePairsVisible() Tests whether lone pairs are visible.
java.awt.Color	getMolbg() Gets the molecule background color.
chemaxon.marvin.common.swing.MolPanel	getMolPanel() Returns the underlying panel.
java.lang.String	getParameter(java.lang.String key) Gets a parameter.
java.lang.String	getParams() Gets the parameter string.
boolean	getPopupMenusEnabled() Are popup menus enabled?
boolean	getReadGlobalGUIProperties() Deprecated. since Marvin 5.1 when this and the getSaveGlobalGUIProperties() function have been merged.
java.lang.String	getRendering() Gets the rendering style.
static java.util.ResourceBundle	getResourceBundle(java.lang.String name) Utility method to get a resource bundle.
boolean	getSaveGlobalGUIProperties() Checks whether we have to read GUI properties from a .MRV file
java.awt.Color	getSetColor(int i) Deprecated. as of Marvin 3.3, replaced by getAtomSetColor
double	getStickThickness() Gets the stick thickness.
java.awt.Container	getTopLevelContainer()
UserSettings	getUserSettings() Gets the user settings object.
double	getWireThickness() Gets the line thickness for wireframe mode.
protected void	init(chemaxon.marvin.common.swing.MolPanel m) Initializes the content pane.
protected void	init(chemaxon.marvin.common.swing.MolPanel m, boolean start) Initializes the content pane.
static void	initAction(javax.swing.Action action, java.util.ResourceBundle rc, java.lang.String key, javax.swing.KeyStroke accel) Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initAction
static void	initButton(javax.swing.AbstractButton b, java.util.ResourceBundle rc, java.lang.String key) Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initButton
boolean	isAtomMappingVisible() Determines the visibility of the atom mapping.
boolean	isAtomNumbersVisible() Determines the visibility of the atom numbers.
boolean	isAtomSymbolsVisible() Tests the visibility of the atom symbols in 3D.
boolean	isBondLengthVisible() Gets the bond length display option.
boolean	isExitCanceled() Check whether exiting is allowed or not.
boolean	isExperimentalEnabled() Tests whether experimental features are enabled.
boolean	isEzVisible() Gets the E/Z display option.
boolean	isGrinv() Deprecated. as of Marvin 3.5, use isGrinvVisible() instead
boolean	isGrinvVisible() Gets the visibility of the graph invariants.
boolean	isPrintEnabled() Determines if the File->Print menu item is enabled or not.
boolean	isRgroupsVisible() Determines the visibility of R-group defintions.
boolean	isSaveIniEnabled() Automatically saves user settings to an initialization file.
boolean	isSetColoringEnabled() Is the atom/bond set coloring enabled?
void	keyPressed(java.awt.event.KeyEvent ev) Handles key events.
void	keyReleased(java.awt.event.KeyEvent ev) Handles key events.
void	keyTyped(java.awt.event.KeyEvent ev) Handles key events.
void	propertyChange(java.beans.PropertyChangeEvent ev) Handles "ancestor" events or sets parameters if a bean property is changed.
protected static MDocument	readDoc(java.io.ObjectInput in)
void	readExternal(java.io.ObjectInput in) Restores object state.
protected static Molecule	readMol(java.io.ObjectInput in)
protected static void	readResources(java.lang.Class cl, java.lang.String fname) Reads resources from the specified file.
void	removeActionListener(java.awt.event.ActionListener l) Removes an action listener.
void	setAtomMappingVisible(boolean v) Shows or hides the atom mapping.
void	setAtomNumbersVisible(boolean v) Shows or hides the atom numbers.
void	setAtomSetColor(int i, java.awt.Color color) Sets the color of an atom set.
void	setAtomsize(double r) Sets the atom size.
void	setAtomSymbolsVisible(boolean v) Shows or hides the atom symbols in 3D.
void	setBallRadius(double r) Sets the ball radius in units of covalent radius.
void	setBondLengthVisible(boolean v) Sets the bond length display option.
void	setBondSetColor(int i, java.awt.Color color) Sets the color of a bond set.
void	setBondSpacing(double w) Sets the double bond spacing.
void	setBondWidth(double w) Deprecated. as of Marvin 4.1, replaced by setBondSpacing(double)
void	setChiralitySupport(int l) Sets chirality support to show or hide the R/S labels.
void	setCleanDim(int d) Sets the space dimensions for cleaning.
void	setColorScheme(java.lang.String s) Sets the color scheme.
void	setDebug(int debug) Switches on the debug messages.
void	setDirectory(java.io.File wd) Sets the working directory, if the Load/Save is in Last Opened Mode.
void	setDispopts(int f) Sets display options.
void	setDispQuality(int q) Sets the display quality.
void	setDownWedge(java.lang.String s) Sets the wedge bond display convention.
void	setEnabled(boolean b) Enables or disables this component, depending on the value of the parameter b.
void	setExperimentalEnabled(boolean v) Enable or disable experimental features.
void	setExplicitH(boolean show) Deprecated. since 5.4 does nothing, will not be supported after 5.5
void	setEzVisible(boolean v) Sets the E/Z display option.
void	setFile(java.io.File f) Sets the current molecule file but does not load it.
void	setFormat(java.lang.String fmt) Sets the default molecule file format.
void	setGlobalGUIProperties(MPropertyContainer gp)
void	setGrinv(boolean v) Deprecated. as of Marvin 3.5, use setGrinvVisible(boolean) instead
void	setGrinvVisible(boolean v) Shows or hides the graph invariants.
void	setImplicitH(java.lang.String s) Sets the display method of implicit hydrogens.
void	setInvisibleSets(long v) Sets the visibility of the specified atom sets.
void	setLabels(boolean v) Deprecated. use setAtomSymbolsVisible(v) instead
void	setLonePairsVisible(boolean v) Shows or hides (implicit) lone pairs.
void	setMolbg(java.awt.Color c) Sets the molecule background color.
void	setParams(java.lang.String s) Sets the parameter string.
void	setPopupMenusEnabled(boolean b) Allows popup menus.
void	setPrintEnabled(boolean b) Set the accessibility of the Print menu item in the File menu.
void	setRendering(java.lang.String s) Sets the rendering style.
void	setRgroupsVisible(boolean b) Shows or hides R-group definitions.
void	setSaveIniEnabled(boolean v) Enables or disables automatic preference saving.
void	setSetColor(int i, java.awt.Color color) Deprecated. as of Marvin 3.3, replaced by setAtomSetColor
void	setSetColoringEnabled(boolean v) Enable or disable atom/bond set coloring.
void	setStickThickness(double d) Sets the stick thickness.
void	setTopLevelContainer(java.awt.Container tlc) Sets the top level container (JFrame, JDialog, etc) of the pane.
void	setUserSettings(UserSettings settings) Sets the user settings object.
void	setWireThickness(double d) Sets the line thickness for wireframe mode.
void	showErrorDialog(java.lang.String msg, java.lang.Throwable ex) Show error dialog.
void	showFileDialog(java.lang.String what, Molecule mol) Shows an Open or Save file dialog.
void	showFileOpenDialog() Shows file open dialog.
void	writeExternal(java.io.ObjectOutput out) Saves object state.
protected static void	writeMol(java.io.ObjectOutput out, Molecule mol)

Methods inherited from class javax.swing.JRootPane

addImpl, addNotify, createContentPane, createGlassPane, createLayeredPane, createRootLayout, getAccessibleContext, getContentPane, getDefaultButton, getGlassPane, getJMenuBar, getLayeredPane, getMenuBar, getUI, getUIClassID, getWindowDecorationStyle, isOptimizedDrawingEnabled, isValidateRoot, paramString, removeNotify, setContentPane, setDefaultButton, setDoubleBuffered, setGlassPane, setJMenuBar, setLayeredPane, setMenuBar, setUI, setWindowDecorationStyle, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, 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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, 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, 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, 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, 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, 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, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, 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

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

Field Detail

VERSION

public static final java.lang.String VERSION

Marvin version.

molPanel

protected chemaxon.marvin.common.swing.MolPanel molPanel

Underlying panel.

params

protected java.lang.String params

Parameter string.

topLevelContainer

protected static java.awt.Container topLevelContainer

The top level container of the pane

Constructor Detail

MarvinPane

protected MarvinPane()

Constructor.

Method Detail

addMenuBarChangeListener

public void addMenuBarChangeListener(chemaxon.marvin.common.swing.MenuBarChangeListener l)

Adds a menubar change listener.

Parameters:

l - the menubar change listener

Since:

Marvin 4.1, 11/14/2005

addActionListener

public void addActionListener(java.awt.event.ActionListener l)

Adds an action listener.

Parameters:

l - the action listener

Since:

Marvin 3.3

removeActionListener

public void removeActionListener(java.awt.event.ActionListener l)

Removes an action listener.

Parameters:

l - the action listener

Since:

Marvin 3.3

init

protected void init(chemaxon.marvin.common.swing.MolPanel m)

Initializes the content pane.

Parameters:

m - the MolPanel

init

protected void init(chemaxon.marvin.common.swing.MolPanel m,
                    boolean start)

Initializes the content pane.

Parameters:

m - the MolPanel

start - enable (true) or disable (false) molecule/template structure/abbreviated group loading

Since:

Marvin 3.4.2, 08/03/2004

getMolPanel

public chemaxon.marvin.common.swing.MolPanel getMolPanel()

Returns the underlying panel.

Returns:

the underlying panel

Since:

Marvin 5.0

keyPressed

public void keyPressed(java.awt.event.KeyEvent ev)

Handles key events. @param ev the event object

Specified by:

keyPressed in interface java.awt.event.KeyListener

keyTyped

public void keyTyped(java.awt.event.KeyEvent ev)

Handles key events. @param ev the event object

Specified by:

keyTyped in interface java.awt.event.KeyListener

keyReleased

public void keyReleased(java.awt.event.KeyEvent ev)

Handles key events. @param ev the event object

Specified by:

keyReleased in interface java.awt.event.KeyListener

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent ev)

Handles "ancestor" events or sets parameters if a bean property is changed.

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

Parameters:

ev - the event object

componentResized

public void componentResized(java.awt.event.ComponentEvent ev)

Does nothing.

Specified by:

componentResized in interface java.awt.event.ComponentListener

Parameters:

ev - the event object

componentMoved

public void componentMoved(java.awt.event.ComponentEvent ev)

Does nothing.

Specified by:

componentMoved in interface java.awt.event.ComponentListener

Parameters:

ev - the event object

componentShown

public void componentShown(java.awt.event.ComponentEvent ev)

Shows windows if the parent frame is hidden.

Specified by:

componentShown in interface java.awt.event.ComponentListener

Parameters:

ev - the event object

componentHidden

public void componentHidden(java.awt.event.ComponentEvent ev)

Hides windows if the parent frame is hidden.

Specified by:

componentHidden in interface java.awt.event.ComponentListener

Parameters:

ev - the event object

getPopupMenusEnabled

public boolean getPopupMenusEnabled()

Are popup menus enabled?

Returns:

true if the popup menus are enabled, else false

Since:

Marvin 2.9.12

arePopupMenusEnabled

public boolean arePopupMenusEnabled()

Are popup menus enabled?

Returns:

true if the popup menus are enabled, else false

Since:

Marvin 3.3

setPopupMenusEnabled

public void setPopupMenusEnabled(boolean b)

Allows popup menus. If you would like to use your own popup menu add MouseListener to the canvas of MarvinSketch or MarvinView and set builtin popup menus disabled.
Example:

//Create custom popup menu
...
sketchPane.getCanvasComponent().addMouseListener(actionListener);
sketchPane.setPopupMenusEnabled(false); //avoid to display both popup menus

Parameters:

b - True sets popup menus enabled, false sets them disabled.

Since:

Marvin 2.9.12

See Also:

MSketchPane.getCanvasComponent(), MViewPane.getVisibleCellComponent(int)

getParams

public java.lang.String getParams()

Gets the parameter string.

Returns:

the parameter string

setParams

public void setParams(java.lang.String s)

Sets the parameter string. Must be called before any other property setting method.
Example: MarvinView Table View Example
See also: MViewParams
Code example:

        molPanel.setParams(
"rows=2\n"+
"cols=2\n"+
"layout0=:2:2:M:1:0:1:1:c:b:1:1:L:0:0:1:1:c:n:0:1\n"+
"param0=:M:100:100:L:10b\n"+
"\n"+
"# MarvinSketch properties also have to be specified here for the\n"+
"# sketcher windows that can be launched using Edit/Structure.\n"+
"extrabonds=arom,wedge\n");

Parameters:

s - the parameter string

getParameter

public java.lang.String getParameter(java.lang.String key)

Gets a parameter. The return value is based on the contents of the parameter string, the bean properties file (MSketchPane.properties or MViewPane.properties) and the user's MarvinSketch configuration file (in case of MSketchPane).

Parameters:

key - the parameter name

Returns:

the value

getMolbg

public java.awt.Color getMolbg()

Gets the molecule background color.

Returns:

the color

setMolbg

public void setMolbg(java.awt.Color c)

Sets the molecule background color.

Parameters:

c - the color

getAtomsize

public double getAtomsize()

Gets the atom size.

Returns:

the atom size in C-C bond length units

setAtomsize

public void setAtomsize(double r)

Sets the atom size.

size = atomsize*1.54 Å = atomsize*scale points

Parameters:

r - the atom size in C-C bond length units

getBondSpacing

public double getBondSpacing()

Gets the double bond spacing.

Returns:

the bond spacing in C-C bond length units.

Since:

Marvin 4.1, 10/19/2005

setBondSpacing

public void setBondSpacing(double w)

Sets the double bond spacing.

width = w*1.54 Å = w*scale pixels

Parameters:

w - the bond spacing in C-C bond length units.

Since:

Marvin 4.1, 10/19/2005

getCleanDim

public int getCleanDim()

Gets the number of space dimensions for cleaning.

Returns:

2 or 3

Since:

Marvin 3.1.3

setCleanDim

public void setCleanDim(int d)

Sets the space dimensions for cleaning.

Parameters:

d - 2 or 3

Since:

Marvin 3.1.3

getDispopts

public int getDispopts()

Gets display options.

Returns:

the display options

setDispopts

public void setDispopts(int f)

Sets display options.

Parameters:

f - the display options

getColorScheme

public java.lang.String getColorScheme()

Gets the color scheme.

Returns:

MONO_SCHEME_S, CPK_SCHEME_S, SHAPELY_SCHEME_S or GROUP_SCHEME_S.

See Also:

DispOptConsts.COLOR_SCHEMES

setColorScheme

public void setColorScheme(java.lang.String s)

Sets the color scheme.

Parameters:

s - MONO_SCHEME_S, CPK_SCHEME_S, SHAPELY_SCHEME_S or GROUP_SCHEME_S.

See Also:

DispOptConsts.COLOR_SCHEMES

isSetColoringEnabled

public boolean isSetColoringEnabled()

Is the atom/bond set coloring enabled?

Returns:

true if enabled, false if disabled

Since:

Marvin 3.3

setSetColoringEnabled

public void setSetColoringEnabled(boolean v)

Enable or disable atom/bond set coloring.

Parameters:

v - true to enable, false to disable

Since:

Marvin 3.3

getRendering

public java.lang.String getRendering()

Gets the rendering style.

Returns:

WIREFRAME_RENDERING_S, WIREKNOBS_RENDERING_S, STICKS_RENDERING_S, BALLSTICK_RENDERING_S or SPACEFILL_RENDERING_S.

See Also:

DispOptConsts.RENDERING_STYLES

setRendering

public void setRendering(java.lang.String s)

Sets the rendering style.

Parameters:

s - WIREFRAME_RENDERING_S, WIREKNOBS_RENDERING_S, STICKS_RENDERING_S, BALLSTICK_RENDERING_S or SPACEFILL_RENDERING_S.

See Also:

DispOptConsts.RENDERING_STYLES

getDispQuality

public int getDispQuality()

Gets the display quality.

• 0 - low quality, fast rendering
• 1 - high quality (antialiasing), slower rendering

Returns:

the display quality

Since:

Marvin 3.5, 23/08/2004

setDispQuality

public void setDispQuality(int q)

Sets the display quality.

• 0 - low quality, fast rendering
• 1 - high quality (antialiasing), slower rendering

Parameters:

q - the display quality

Since:

Marvin 3.5, 23/08/2004

getWireThickness

public double getWireThickness()

Gets the line thickness for wireframe mode.

Returns:

wire thickness in Angstroms

Since:

Marvin 3.4, 06/08/2004

setWireThickness

public void setWireThickness(double d)

Sets the line thickness for wireframe mode.

Parameters:

d - wire thickness in Angstroms

Since:

Marvin 3.4, 06/08/2004

getStickThickness

public double getStickThickness()

Gets the stick thickness.

Returns:

stick thickness in Angstroms

setStickThickness

public void setStickThickness(double d)

Sets the stick thickness.

Parameters:

d - stick thickness in Angstroms

getBallRadius

public double getBallRadius()

Gets the ball radius in units of covalent radius.

Returns:

the ball radius

setBallRadius

public void setBallRadius(double r)

Sets the ball radius in units of covalent radius.

Parameters:

r - the ball radius

getDownWedge

public java.lang.String getDownWedge()

Gets the wedge bond display convention.

Returns:

"mdl" or "daylight"

setDownWedge

public void setDownWedge(java.lang.String s)

Sets the wedge bond display convention. Down wedge points downward in MDL's convention ("mdl"), upward (at the chiral center) in Daylight's ("daylight").

Parameters:

s - "mdl" or "daylight"

isAtomNumbersVisible

public boolean isAtomNumbersVisible()

Determines the visibility of the atom numbers.

Returns:

true if atom numbers are visible.

Since:

Marvin 2.9.13

setAtomNumbersVisible

public void setAtomNumbersVisible(boolean v)

Shows or hides the atom numbers.

Parameters:

v - shows the atom numbers if true, else hide them.

isAtomMappingVisible

public boolean isAtomMappingVisible()

Determines the visibility of the atom mapping.

Returns:

true if the atom mapping is visible.

Since:

Marvin 2.10.5

setAtomMappingVisible

public void setAtomMappingVisible(boolean v)

Shows or hides the atom mapping.

Parameters:

v - shows the atom mapping if true, else hide it.

isAtomSymbolsVisible

public boolean isAtomSymbolsVisible()

Tests the visibility of the atom symbols in 3D.

Returns:

true if the atom symbols are visible.

Since:

Marvin 3.0

See Also:

DispOptConsts.ATSYM_FLAG

setAtomSymbolsVisible

public void setAtomSymbolsVisible(boolean v)

Shows or hides the atom symbols in 3D.

Parameters:

v - shows the atom symbols if true, else hide them

Since:

Marvin 3.0

See Also:

DispOptConsts.ATSYM_FLAG

getLonePairsVisible

public boolean getLonePairsVisible()

Tests whether lone pairs are visible.

Returns:

true if lone pairs are visible, false otherwise

Since:

Marvin 4.0

setLonePairsVisible

public void setLonePairsVisible(boolean v)

Shows or hides (implicit) lone pairs.

Parameters:

v - true show, false hides lone pairs

Since:

Marvin 4.0

isGrinvVisible

public boolean isGrinvVisible()

Gets the visibility of the graph invariants.

Returns:

true if graph invariants are visible.

Since:

Marvin 3.5, 11/01/2004

setGrinvVisible

public void setGrinvVisible(boolean v)

Shows or hides the graph invariants.

Parameters:

v - true to show the graph invariants, false to hide them.

Since:

Marvin 3.5, 11/01/2004

getImplicitH

public java.lang.String getImplicitH()

Query the display method of implicit hydrogens.

Returns:

IMPLICITH_OFF_S, IMPLICITH_HETERO_S, IMPLICITH_HETEROTERM_S or IMPLICITH_ALL_S.

See Also:

DispOptConsts.IMPLICITH_LEVELS

setImplicitH

public void setImplicitH(java.lang.String s)

Sets the display method of implicit hydrogens.

Parameters:

s - IMPLICITH_OFF_S, IMPLICITH_HETERO_S, IMPLICITH_HETEROTERM_S or IMPLICITH_ALL_S.

See Also:

DispOptConsts.IMPLICITH_LEVELS

getExplicitH

@Deprecated
public boolean getExplicitH()

Deprecated. since 5.4 returns false. will be unsupported in 5.5

Are explicit hydrogens shown?

Returns:

true if shown, false if hidden

setExplicitH

@Deprecated
public void setExplicitH(boolean show)

Deprecated. since 5.4 does nothing, will not be supported after 5.5

Sets the display method of explicit hydrogens.

Parameters:

show - true to show, false to hide explicit hydrogens

getChiralitySupport

public int getChiralitySupport()

Gets chirality support level.

Returns:

the chirality support level.

See Also:

StereoConstants.CHIRALITYSUPPORT_NONE, StereoConstants.CHIRALITYSUPPORT_SELECTED, StereoConstants.CHIRALITYSUPPORT_ALL

setChiralitySupport

public void setChiralitySupport(int l)

Sets chirality support to show or hide the R/S labels.

Parameters:

l - chirality support level.

See Also:

StereoConstants.CHIRALITYSUPPORT_NONE, StereoConstants.CHIRALITYSUPPORT_SELECTED, StereoConstants.CHIRALITYSUPPORT_ALL

isEzVisible

public boolean isEzVisible()

Gets the E/Z display option.

Returns:

show (true) or hide (false)

setEzVisible

public void setEzVisible(boolean v)

Sets the E/Z display option.

Parameters:

v - show (true) or hide (false) E/Z

isBondLengthVisible

public boolean isBondLengthVisible()

Gets the bond length display option.

Returns:

show (true) or hide (false)

Since:

Marvin 3.5, 23/08/2004

setBondLengthVisible

public void setBondLengthVisible(boolean v)

Sets the bond length display option.

Parameters:

v - show (true) or hide (false)

Since:

Marvin 3.5, 23/08/2004

See Also:

DispOptConsts.BONDLEN_FLAG

getInvisibleSets

public long getInvisibleSets()

Gets the visibility of the specified atom sets.

Returns:

the invisibility mask

setInvisibleSets

public void setInvisibleSets(long v)

Sets the visibility of the specified atom sets. Set n is invisible if the n-th bit of the specified 64 bit number is 1.

Parameters:

v - invisibility mask

See Also:

getInvisibleSets()

getAtomSetColor

public java.awt.Color getAtomSetColor(int i)

Gets the color of an atom set.

Parameters:

i - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

Returns:

the color

Since:

Marvin 3.3

setAtomSetColor

public void setAtomSetColor(int i,
                            java.awt.Color color)

Sets the color of an atom set.

Parameters:

i - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

color - the color

Since:

Marvin 3.3

setBondSetColor

public void setBondSetColor(int i,
                            java.awt.Color color)

Sets the color of a bond set.

Parameters:

i - bond set sequence number (1, ..., MolBond.SETSEQ_MAX)

color - the color

Since:

Marvin 3.3

getFormat

public java.lang.String getFormat()

Gets the default molecule file format.

Returns:

the format or "DEFAULT" if it is not specified

setFormat

public void setFormat(java.lang.String fmt)

Sets the default molecule file format. This setting also determine the format of molecule source in the Edit Source window.

Parameters:

fmt - the format string or null

getFile

public java.io.File getFile()

Gets the current molecule file.

Returns:

the file

setFile

public void setFile(java.io.File f)

Sets the current molecule file but does not load it.

Parameters:

f - the file

showFileDialog

public void showFileDialog(java.lang.String what,
                           Molecule mol)

Shows an Open or Save file dialog.

Parameters:

what - "open", "save" or "saveAs"

mol - the molecule to save or null

getDebug

public int getDebug()

Gets the debugging level.

Returns:

the debugging level

setDebug

public void setDebug(int debug)

Switches on the debug messages.

Parameters:

debug - debug level

closeWindows

public void closeWindows()

Closes all windows opened by this MarvinPane.

isExitCanceled

public boolean isExitCanceled()

Check whether exiting is allowed or not.

Returns:

true if the use cancels the exit operation, false otherwise

Since:

Marvin 3.1.4

exit

public void exit()

Closes all windows opened by this MarvinPane and saves user initialization file.

getUserSettings

public UserSettings getUserSettings()

Gets the user settings object.

Returns:

the user settings object

Since:

Marvin 3.0

setUserSettings

public void setUserSettings(UserSettings settings)

Sets the user settings object.

Parameters:

settings - the user settings object

Since:

Marvin 3.0

isSaveIniEnabled

public boolean isSaveIniEnabled()

Automatically saves user settings to an initialization file.

Returns:

true if enabled, false if disabled

Since:

Marvin 2.8.3

setSaveIniEnabled

public void setSaveIniEnabled(boolean v)

Enables or disables automatic preference saving.

Parameters:

v - true to enable, false to disable

Since:

Marvin 2.8.3

getDirectory

public java.io.File getDirectory()

Sets the working directory.

Returns:

the working directory

Since:

Marvin 3.0

setDirectory

public void setDirectory(java.io.File wd)

Sets the working directory, if the Load/Save is in Last Opened Mode.

Parameters:

wd - the working directory

Since:

Marvin 3.0

isExperimentalEnabled

public boolean isExperimentalEnabled()

Tests whether experimental features are enabled.

Returns:

true if experimental features are enabled, false otherwise

Since:

Marvin 3.5, 11/04/2004

setExperimentalEnabled

public void setExperimentalEnabled(boolean v)

Enable or disable experimental features.

Parameters:

v - true enables, false disables experimental features

Since:

Marvin 3.5, 11/04/2004

showFileOpenDialog

public void showFileOpenDialog()

Shows file open dialog.

Since:

Marvin 3.0

getCommonActions

public chemaxon.marvin.common.swing.CommonActions getCommonActions()

Deprecated.

Gets the common actions.

Returns:

the actions

Since:

Marvin 5.0, 11/17/2006

addToolsMenu

public javax.swing.JMenu addToolsMenu(java.awt.Container m)

Deprecated. Not used.

Adds the Tools menu.

Parameters:

m - the parent menu or menu bar

Returns:

the created menu

Since:

Marvin 3.4, 05/03/2004

addHelpMenu

public javax.swing.JMenu addHelpMenu(java.awt.Container m)

Adds the help menu to a parent menu.

Parameters:

m - the parent menu or menu bar

Returns:

the created menu

Since:

Marvin 3.4, 05/03/2004

getResourceBundle

public static java.util.ResourceBundle getResourceBundle(java.lang.String name)

Utility method to get a resource bundle. If the "LOCALES" resource is set and the current locale is listed, then also loads resources for to the corrent locale.

Parameters:

name - resource file path

Returns:

the resource bundle

Since:

Marvin 3.3

beginHourglass

public void beginHourglass()

Changes the cursor to hourglass at the beginning of a long operation.

Since:

Marvin 3.5, 10/31/2004

endHourglass

public void endHourglass()

Changes the hourglass cursor back to normal at the end of a long operation.

Since:

Marvin 3.5, 10/31/2004

showErrorDialog

public void showErrorDialog(java.lang.String msg,
                            java.lang.Throwable ex)

Show error dialog.

Parameters:

msg - error message

ex - the exception

Since:

Marvin 3.5, 10/26/2004

readResources

protected static void readResources(java.lang.Class cl,
                                    java.lang.String fname)

Reads resources from the specified file.

Parameters:

cl - the class to read resources for

fname - resource filename

Since:

Marvin 3.0

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves object state. For internal use only! This method does not implement the Externalizable interface. It is called by the writeExternal method of the MSketch and MView classes, which do implement it.

Parameters:

out - the stream to write the object to

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Since:

Marvin 3.5, 2004/11/01

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Restores object state. For internal use only! This method does not implement the Externalizable interface. It is called by the readExternal method of the MSketch and MView classes, which do implement it.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

java.io.IOException - if I/O errors occur

java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.

Since:

Marvin 3.5, 2004/11/01

writeMol

protected static void writeMol(java.io.ObjectOutput out,
                               Molecule mol)
                        throws java.io.IOException

Throws:

java.io.IOException

readMol

protected static Molecule readMol(java.io.ObjectInput in)
                           throws java.io.IOException

Throws:

java.io.IOException

readDoc

protected static MDocument readDoc(java.io.ObjectInput in)
                            throws java.io.IOException

Throws:

java.io.IOException

getBondWidth

public double getBondWidth()

Deprecated. as of Marvin 4.1, replaced by getBondSpacing()

Gets bond spacing.

Returns:

the bond spacing in bond length units

setBondWidth

public void setBondWidth(double w)

Deprecated. as of Marvin 4.1, replaced by setBondSpacing(double)

Sets bond spacing.

Parameters:

w - bond spacing in bond length units

getSetColor

public java.awt.Color getSetColor(int i)

Deprecated. as of Marvin 3.3, replaced by getAtomSetColor

Parameters:

i - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

Returns:

the color

setSetColor

public void setSetColor(int i,
                        java.awt.Color color)

Deprecated. as of Marvin 3.3, replaced by setAtomSetColor

Parameters:

i - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

color - the color

getLabels

public boolean getLabels()

Deprecated. use isAtomSymbolsVisible() instead

setLabels

public void setLabels(boolean v)

Deprecated. use setAtomSymbolsVisible(v) instead

getAtomNumbersVisible

public boolean getAtomNumbersVisible()

Deprecated. as of Marvin 2.9.13, replaced by isAtomNumbersVisible.

isGrinv

public boolean isGrinv()

Deprecated. as of Marvin 3.5, use isGrinvVisible() instead

Returns:

true if graph invariants are visible.

Since:

Marvin 2.10.3

setGrinv

public void setGrinv(boolean v)

Deprecated. as of Marvin 3.5, use setGrinvVisible(boolean) instead

Parameters:

v - true to show the graph invariants, false to hide them.

Since:

Marvin 2.10.3

createMenu

public static javax.swing.JMenu createMenu(java.util.ResourceBundle rc,
                                           java.lang.String key)

Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.createMenu

Parameters:

rc - the resources

key - name of the label resource

Returns:

the menu

Since:

Marvin 3.3

initButton

public static void initButton(javax.swing.AbstractButton b,
                              java.util.ResourceBundle rc,
                              java.lang.String key)

Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initButton

Parameters:

b - the button

rc - the resources

key - name of the resource

Since:

Marvin 3.3

initAction

public static void initAction(javax.swing.Action action,
                              java.util.ResourceBundle rc,
                              java.lang.String key,
                              javax.swing.KeyStroke accel)

Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initAction

Parameters:

action - the action

rc - the resources

key - name of the resource

accel - the accelerator or null

Since:

Marvin 3.3

setTopLevelContainer

public void setTopLevelContainer(java.awt.Container tlc)

Sets the top level container (JFrame, JDialog, etc) of the pane. If the container (window) size is to be restored from the .mrv file this also have to be set when adding the MarvinPane instance to the content pane of the container.

Parameters:

tlc - the top level container

getTopLevelContainer

public java.awt.Container getTopLevelContainer()

Returns:

the top level container (if set) or null

getReadGlobalGUIProperties

public boolean getReadGlobalGUIProperties()

Deprecated. since Marvin 5.1 when this and the getSaveGlobalGUIProperties() function have been merged.

Checks whether we have to read GUI properties from a .MRV file

Returns:

true if we have a molPanel and according to its settings want to save properties

Since:

Marvin 5.0

getSaveGlobalGUIProperties

public boolean getSaveGlobalGUIProperties()

Checks whether we have to read GUI properties from a .MRV file

Returns:

true if we have a molPanel and according to its settings want to save properties

Since:

Marvin 5.1

setGlobalGUIProperties

public void setGlobalGUIProperties(MPropertyContainer gp)

setEnabled

public void setEnabled(boolean b)

Enables or disables this component, depending on the value of the parameter b. An enabled component can respond to user input and generate events. Components are enabled initially by default.
Note: Overwrites JComponent.setEnabled(boolean).

Overrides:

setEnabled in class javax.swing.JComponent

Parameters:

b - If true, this component is enabled; otherwise this component is disabled.

Since:

Marvin 4.1.6

doPaste

public abstract void doPaste()

Invokes Paste actions.

Since:

Marvin 5.0

setRgroupsVisible

public void setRgroupsVisible(boolean b)

Shows or hides R-group definitions.

Parameters:

b - true to show, false to hide R-group definitions.

Since:

Marvin 5.0.4 05/21/2008

isRgroupsVisible

public boolean isRgroupsVisible()

Determines the visibility of R-group defintions.

Returns:

True if visible, else false.

Since:

Marvin 5.0.4 05/21/2008

isPrintEnabled

public boolean isPrintEnabled()

Determines if the File->Print menu item is enabled or not.

Returns:

True, if Print is enabled in the menu, else false.

Since:

5.4 09/06/2010

See Also:

setPrintEnabled(boolean)

setPrintEnabled

public void setPrintEnabled(boolean b)

Set the accessibility of the Print menu item in the File menu.

Parameters:

b - True to enable print operation from the file menu. False to set it to disabled.

Since:

5.4 09/06/2010

See Also:

isPrintEnabled()