Package chemaxon.marvin.beans
Class MarvinPane
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- javax.swing.JComponent
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- javax.swing.JRootPane
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- chemaxon.marvin.beans.MarvinPane
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- All Implemented Interfaces:
ComponentListener
,ImageObserver
,MenuContainer
,PropertyChangeListener
,Serializable
,EventListener
,Accessible
- Direct Known Subclasses:
MSketchPane
,MViewPane
@PublicAPI public abstract class MarvinPane extends JRootPane implements PropertyChangeListener, ComponentListener
Ancestor of the Marvin Beans.- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class javax.swing.JRootPane
JRootPane.AccessibleJRootPane, JRootPane.RootLayout
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Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
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Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
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Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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Field Summary
Fields Modifier and Type Field Description protected chemaxon.marvin.common.swing.MolPanel
molPanel
Underlying panel.protected String
params
Parameter string.protected static Container
topLevelContainer
The top level container of the panestatic String
VERSION
Marvin version.-
Fields inherited from class javax.swing.JRootPane
COLOR_CHOOSER_DIALOG, contentPane, defaultButton, ERROR_DIALOG, FILE_CHOOSER_DIALOG, FRAME, glassPane, INFORMATION_DIALOG, layeredPane, menuBar, NONE, PLAIN_DIALOG, QUESTION_DIALOG, WARNING_DIALOG
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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
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Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
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Constructor Summary
Constructors Modifier Constructor Description protected
MarvinPane()
Constructor.
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods Modifier and Type Method Description void
addActionListener(ActionListener l)
Adds an action listener.JMenu
addHelpMenu(Container m)
Adds the help menu to a parent menu.void
addMenuBarChangeListener(chemaxon.marvin.common.swing.MenuBarChangeListener l)
Adds a menubar change listener.JMenu
addToolsMenu(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(ComponentEvent ev)
Hides windows if the parent frame is hidden.void
componentMoved(ComponentEvent ev)
Does nothing.void
componentResized(ComponentEvent ev)
Does nothing.void
componentShown(ComponentEvent ev)
Shows windows if the parent frame is hidden.static JMenu
createMenu(ResourceBundle rc, String key)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.createMenuabstract 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.int
getAtomNumberingType()
Determines the atom numbering.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
getBoldBondWidth()
Gets the C-C bold bond width in pt units.double
getBondLength()
Gets the C-C bond length in pt units.double
getBondSpacing()
Gets the bond spacing.double
getBondWidth()
Deprecated.as of Marvin 4.1, replaced bygetBondSpacing()
int
getChiralitySupport()
Gets chirality support level.int
getCleanDim()
Gets the number of space dimensions for cleaning.String
getColorScheme()
Gets the color scheme.chemaxon.marvin.common.swing.action.CommonActions
getCommonActions()
Deprecated.int
getDebug()
Gets the debugging level.File
getDirectory()
Sets the working directory.int
getDispopts()
Gets display options.String
getDownWedge()
Gets the wedge bond display convention.File
getFile()
Gets the current molecule file.String
getFormat()
Gets the default molecule file format.String
getImplicitH()
Query the display method of implicit hydrogens.long
getInvisibleSets()
Gets the visibility of the specified atom sets.boolean
getLabels()
Deprecated.use isAtomSymbolsVisible() insteadboolean
getLonePairsVisible()
Tests whether lone pairs are visible.double
getMarginSize()
Gets the documents margin size.Color
getMolbg()
Gets the molecule background color.chemaxon.marvin.common.swing.MolPanel
getMolPanel()
Returns the underlying panel.String
getParameter(String key)
Gets a parameter.String
getParams()
Gets the parameter string.boolean
getPopupMenusEnabled()
Are popup menus enabled?boolean
getReadGlobalGUIProperties()
Deprecated.since Marvin 5.1 when this and thegetSaveGlobalGUIProperties()
function have been merged.String
getRendering()
Gets the rendering style.static ResourceBundle
getResourceBundle(String name)
Utility method to get a resource bundle.boolean
getSaveGlobalGUIProperties()
Checks whether we have to read GUI properties from a .MRV fileColor
getSetColor(int i)
Deprecated.as of Marvin 3.3, replaced by getAtomSetColordouble
getStickThickness()
Gets the stick thickness.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(Action action, ResourceBundle rc, String key, KeyStroke accel)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.initActionstatic void
initButton(AbstractButton b, ResourceBundle rc, String key)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.initButtonboolean
isAtomMappingVisible()
Determines the visibility of the atom mapping.boolean
isAtomNumbersVisible()
Deprecated.in 6.2.0.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() insteadboolean
isGrinvVisible()
Gets the visibility of the graph invariants.boolean
isMPVisible()
Gets the M/P display option.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?boolean
isSgroupDataFormatted()
Returns whether the Sgroup data is formatted.void
propertyChange(PropertyChangeEvent ev)
Handles "ancestor" events or sets parameters if a bean property is changed.protected static MDocument
readDoc(ObjectInput in)
void
readExternal(ObjectInput in)
Restores object state.protected static Molecule
readMol(ObjectInput in)
protected static void
readResources(Class<?> cl, String fname)
Reads resources from the specified file.void
removeActionListener(ActionListener l)
Removes an action listener.void
setAtomMappingVisible(boolean v)
Shows or hides the atom mapping.void
setAtomNumberingType(int type)
Sets the atom numbering.void
setAtomNumbersVisible(boolean v)
Deprecated.in 6.2.0.void
setAtomSetColor(int i, 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
setBoldBondWidth(double w)
Sets the bold bond width.void
setBondLength(double l)
Sets the bond length.void
setBondLengthVisible(boolean v)
Sets the bond length display option.void
setBondSetColor(int i, Color color)
Sets the color of a bond set.void
setBondSpacing(double w)
Sets the bond spacing.void
setBondWidth(double w)
Deprecated.as of Marvin 4.1, replaced bysetBondSpacing(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(String s)
Sets the color scheme.void
setDebug(int debug)
Switches on the debug messages.void
setDirectory(File wd)
Sets the working directory, if the Load/Save is in Last Opened Mode.void
setDispopts(int f)
Sets display options.void
setDownWedge(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
setEzVisible(boolean v)
Sets the E/Z display option.void
setFile(File f)
Sets the current molecule file but does not load it.void
setFormat(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) insteadvoid
setGrinvVisible(boolean v)
Shows or hides the graph invariants.void
setImplicitH(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) insteadvoid
setLonePairsVisible(boolean v)
Shows or hides (implicit) lone pairs.void
setMarginSize(double size)
Sets the documents margin size.void
setMolbg(Color c)
Sets the molecule background color.void
setMPVisible(boolean v)
Sets the M/P display option.void
setParams(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(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, Color color)
Deprecated.as of Marvin 3.3, replaced by setAtomSetColorvoid
setSetColoringEnabled(boolean v)
Enable or disable atom/bond set coloring.void
setSgroupDataFormatted(boolean isFormatted)
Sets if the Sgroup data to be formatted.void
setStickThickness(double d)
Sets the stick thickness.void
setTopLevelContainer(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(String msg, Throwable ex)
Show error dialog.void
showFileDialog(String what, Molecule mol)
Shows an Open or Save file dialog.void
showFileOpenDialog()
Shows file open dialog.void
writeExternal(ObjectOutput out)
Saves object state.protected static void
writeMol(ObjectOutput out, Molecule mol)
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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
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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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isPaintingForPrint, isPaintingOrigin, 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
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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, transferFocusDownCycle, validate, validateTree
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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
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Field Detail
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VERSION
public static final String VERSION
Marvin version.
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molPanel
protected chemaxon.marvin.common.swing.MolPanel molPanel
Underlying panel.
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params
protected String params
Parameter string.
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topLevelContainer
protected static Container topLevelContainer
The top level container of the pane
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Method Detail
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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
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addActionListener
public void addActionListener(ActionListener l)
Adds an action listener.- Parameters:
l
- the action listener- Since:
- Marvin 3.3
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removeActionListener
public void removeActionListener(ActionListener l)
Removes an action listener.- Parameters:
l
- the action listener- Since:
- Marvin 3.3
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init
protected void init(chemaxon.marvin.common.swing.MolPanel m)
Initializes the content pane.- Parameters:
m
- the MolPanel
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init
protected void init(chemaxon.marvin.common.swing.MolPanel m, boolean start)
Initializes the content pane.- Parameters:
m
- the MolPanelstart
- enable (true
) or disable (false
) molecule/template structure/abbreviated group loading- Since:
- Marvin 3.4.2, 08/03/2004
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getMolPanel
public chemaxon.marvin.common.swing.MolPanel getMolPanel()
Returns the underlying panel.- Returns:
- the underlying panel
- Throws:
chemaxon.license.LicenseException
- if there is not any license set for using Marvin Beans in the given context. From Marvin 6.2- Since:
- Marvin 5.0
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propertyChange
public void propertyChange(PropertyChangeEvent ev)
Handles "ancestor" events or sets parameters if a bean property is changed.- Specified by:
propertyChange
in interfacePropertyChangeListener
- Parameters:
ev
- the event object
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componentResized
public void componentResized(ComponentEvent ev)
Does nothing.- Specified by:
componentResized
in interfaceComponentListener
- Parameters:
ev
- the event object
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componentMoved
public void componentMoved(ComponentEvent ev)
Does nothing.- Specified by:
componentMoved
in interfaceComponentListener
- Parameters:
ev
- the event object
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componentShown
public void componentShown(ComponentEvent ev)
Shows windows if the parent frame is hidden.- Specified by:
componentShown
in interfaceComponentListener
- Parameters:
ev
- the event object
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componentHidden
public void componentHidden(ComponentEvent ev)
Hides windows if the parent frame is hidden.- Specified by:
componentHidden
in interfaceComponentListener
- Parameters:
ev
- the event object
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getPopupMenusEnabled
public boolean getPopupMenusEnabled()
Are popup menus enabled?- Returns:
- true if the popup menus are enabled, else false
- Since:
- Marvin 2.9.12
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arePopupMenusEnabled
public boolean arePopupMenusEnabled()
Are popup menus enabled?- Returns:
- true if the popup menus are enabled, else false
- Since:
- Marvin 3.3
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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)
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getParams
public String getParams()
Gets the parameter string.- Returns:
- the parameter string
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setParams
public void setParams(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
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getParameter
public String getParameter(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
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getMolbg
public Color getMolbg()
Gets the molecule background color.- Returns:
- the color
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setMolbg
public void setMolbg(Color c)
Sets the molecule background color.- Parameters:
c
- the color
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getAtomsize
public double getAtomsize()
Gets the atom size.- Returns:
- the atom size in C-C bond length units
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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
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getBoldBondWidth
public double getBoldBondWidth()
Gets the C-C bold bond width in pt units.- Returns:
- the bold bond width of C-C bonds.
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setBoldBondWidth
public void setBoldBondWidth(double w)
Sets the bold bond width.- Parameters:
w
- the bold bond width of C-C bonds in pt units.
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getBondLength
public double getBondLength()
Gets the C-C bond length in pt units.- Returns:
- the bond Length of C-C bonds.
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setBondLength
public void setBondLength(double l)
Sets the bond length.- Parameters:
l
- the bond length of C-C bonds in pt units.
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getBondSpacing
public double getBondSpacing()
Gets the bond spacing.- Returns:
- the bond spacing in C-C bond length units.
- Since:
- Marvin 4.1, 10/19/2005
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setBondSpacing
public void setBondSpacing(double w)
Sets the 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
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getCleanDim
public int getCleanDim()
Gets the number of space dimensions for cleaning.- Returns:
- 2 or 3
- Since:
- Marvin 3.1.3
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setCleanDim
public void setCleanDim(int d)
Sets the space dimensions for cleaning.- Parameters:
d
- 2 or 3- Since:
- Marvin 3.1.3
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getDispopts
public int getDispopts()
Gets display options.- Returns:
- the display options
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setDispopts
public void setDispopts(int f)
Sets display options.- Parameters:
f
- the display options
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getColorScheme
public String getColorScheme()
Gets the color scheme.- Returns:
MONO_SCHEME_S
,CPK_SCHEME_S
,SHAPELY_SCHEME_S
orGROUP_SCHEME_S
.- See Also:
COLOR_SCHEMES
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setColorScheme
public void setColorScheme(String s)
Sets the color scheme.- Parameters:
s
-MONO_SCHEME_S
,CPK_SCHEME_S
,SHAPELY_SCHEME_S
orGROUP_SCHEME_S
.- See Also:
DispOptConsts.COLOR_SCHEMES
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isSetColoringEnabled
public boolean isSetColoringEnabled()
Is the atom/bond set coloring enabled?- Returns:
- true if enabled, false if disabled
- Since:
- Marvin 3.3
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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
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getRendering
public String getRendering()
Gets the rendering style.- Returns:
WIREFRAME_RENDERING_S
,STICKS_RENDERING_S
,BALLSTICK_RENDERING_S
orSPACEFILL_RENDERING_S
.- See Also:
DispOptConsts.RENDERING_STYLES
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setRendering
public void setRendering(String s)
Sets the rendering style.- Parameters:
s
-WIREFRAME_RENDERING_S
,STICKS_RENDERING_S
,BALLSTICK_RENDERING_S
orSPACEFILL_RENDERING_S
.- See Also:
DispOptConsts.RENDERING_STYLES
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getWireThickness
public double getWireThickness()
Gets the line thickness for wireframe mode.- Returns:
- wire thickness in Angstroms
- Since:
- Marvin 3.4, 06/08/2004
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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
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getStickThickness
public double getStickThickness()
Gets the stick thickness.- Returns:
- stick thickness in Angstroms
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setStickThickness
public void setStickThickness(double d)
Sets the stick thickness.- Parameters:
d
- stick thickness in Angstroms
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getBallRadius
public double getBallRadius()
Gets the ball radius in units of covalent radius.- Returns:
- the ball radius
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setBallRadius
public void setBallRadius(double r)
Sets the ball radius in units of covalent radius.- Parameters:
r
- the ball radius
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getDownWedge
public String getDownWedge()
Gets the wedge bond display convention.- Returns:
- "mdl" or "daylight"
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setDownWedge
public void setDownWedge(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"
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isAtomNumbersVisible
@Deprecated public boolean isAtomNumbersVisible()
Deprecated.in 6.2.0. Use getAtomNumberingType() instead.Determines the visibility of the atom numbers.- Returns:
- true if atom numbers are visible.
- Since:
- Marvin 2.9.13
-
getAtomNumberingType
public int getAtomNumberingType()
Determines the atom numbering.- Returns:
- 0: off, 1: Atom numbers, 2: IUPAC numbering.
- Since:
- Marvin 6.2.0
-
setAtomNumbersVisible
@Deprecated public void setAtomNumbersVisible(boolean v)
Deprecated.in 6.2.0. Use setAtomNumberingType() insteadShows or hides the atom numbers.- Parameters:
v
- shows the atom numbers if true, else hide them.
-
setAtomNumberingType
public void setAtomNumberingType(int type)
Sets the atom numbering.- Parameters:
type
- 0: off 1: Atom numbers 2: IUPAC numbering.- Since:
- Marvin 6.2.0
-
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
-
setMarginSize
public void setMarginSize(double size)
Sets the documents margin size.- Parameters:
size
- the size of the margin- Since:
- Marvin 15.2.23, 2/16/2015
-
getMarginSize
public double getMarginSize()
Gets the documents margin size.- Returns:
- the margin size
- Since:
- Marvin 15.2.23, 2/16/2015
-
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 String getImplicitH()
Query the display method of implicit hydrogens.- Returns:
IMPLICITH_OFF_S
,IMPLICITH_HETERO_S
,IMPLICITH_HETEROTERM_S
orIMPLICITH_ALL_S
.- See Also:
DispOptConsts.IMPLICITH_LEVELS
-
setImplicitH
public void setImplicitH(String s)
Sets the display method of implicit hydrogens.- Parameters:
s
-IMPLICITH_OFF_S
,IMPLICITH_HETERO_S
,IMPLICITH_HETEROTERM_S
orIMPLICITH_ALL_S
.- See Also:
DispOptConsts.IMPLICITH_LEVELS
-
getChiralitySupport
public int getChiralitySupport()
Gets chirality support level.- Always show atom chirality (R/S) and highlight possible chiral centers as well:
StereoConstants.CHIRALITYSUPPORT_ALL_POSSIBLE
- Always show atom chirality (R/S):
StereoConstants.CHIRALITYSUPPORT_ALL
- Show atom chirality if chiral flag is set for the molecule or the atom's enhanced stereo
type is absolute:
StereoConstants.CHIRALITYSUPPORT_SELECTED
- Do not show atom chirality (R/S):
StereoConstants.CHIRALITYSUPPORT_NONE
- Returns:
- the chirality support level.
- Always show atom chirality (R/S) and highlight possible chiral centers as well:
-
setChiralitySupport
public void setChiralitySupport(int l)
Sets chirality support to show or hide the R/S labels.- Always show atom chirality (R/S) and highlight possible chiral centers as well:
StereoConstants.CHIRALITYSUPPORT_ALL_POSSIBLE
- Always show atom chirality (R/S):
StereoConstants.CHIRALITYSUPPORT_ALL
- Show atom chirality if chiral flag is set for the molecule or the atom's enhanced stereo
type is absolute:
StereoConstants.CHIRALITYSUPPORT_SELECTED
- Do not show atom chirality (R/S):
StereoConstants.CHIRALITYSUPPORT_NONE
- Parameters:
l
- chirality support level.
- Always show atom chirality (R/S) and highlight possible chiral centers as well:
-
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
-
isMPVisible
public boolean isMPVisible()
Gets the M/P display option.- Returns:
- show (true) or hide (false)
-
setMPVisible
public void setMPVisible(boolean v)
Sets the M/P display option.- Parameters:
v
- show (true) or hide (false) M/p
-
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 Color getAtomSetColor(int i)
Gets the color of an atom set.- Parameters:
i
- atom set sequence number (0, ...,SETSEQ_MAX
)- Returns:
- the color
- Since:
- Marvin 3.3
-
setAtomSetColor
public void setAtomSetColor(int i, Color color)
Sets the color of an atom set.- Parameters:
i
- atom set sequence number (0, ...,SETSEQ_MAX
)color
- the color- Since:
- Marvin 3.3
-
setBondSetColor
public void setBondSetColor(int i, Color color)
Sets the color of a bond set.- Parameters:
i
- bond set sequence number (1, ...,SETSEQ_MAX
)color
- the color- Since:
- Marvin 3.3
-
getFormat
public String getFormat()
Gets the default molecule file format.- Returns:
- the format or "DEFAULT" if it is not specified
-
setFormat
public void setFormat(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 File getFile()
Gets the current molecule file.- Returns:
- the file
-
setFile
public void setFile(File f)
Sets the current molecule file but does not load it.- Parameters:
f
- the file
-
showFileDialog
public void showFileDialog(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 File getDirectory()
Sets the working directory.- Returns:
- the working directory
- Since:
- Marvin 3.0
-
setDirectory
public void setDirectory(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
@Deprecated public chemaxon.marvin.common.swing.action.CommonActions getCommonActions()
Deprecated.Gets the common actions.- Returns:
- the actions
- Since:
- Marvin 5.0, 11/17/2006
-
addToolsMenu
@Deprecated public JMenu addToolsMenu(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 JMenu addHelpMenu(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 ResourceBundle getResourceBundle(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(String msg, Throwable ex)
Show error dialog.- Parameters:
msg
- error messageex
- the exception- Since:
- Marvin 3.5, 10/26/2004
-
readResources
protected static void readResources(Class<?> cl, String fname)
Reads resources from the specified file.- Parameters:
cl
- the class to read resources forfname
- resource filename- Since:
- Marvin 3.0
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Saves object state. For internal use only! This method does not implement the Externalizable interface. It is called by the writeExternal method of theMSketch
andMView
classes, which do implement it.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur- Since:
- Marvin 3.5, 2004/11/01
-
readExternal
public void readExternal(ObjectInput in) throws IOException
Restores object state. For internal use only! This method does not implement the Externalizable interface. It is called by the readExternal method of theMSketch
andMView
classes, which do implement it.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.- Since:
- Marvin 3.5, 2004/11/01
-
writeMol
protected static void writeMol(ObjectOutput out, Molecule mol) throws IOException
- Throws:
IOException
-
readMol
protected static Molecule readMol(ObjectInput in) throws IOException
- Throws:
IOException
-
readDoc
protected static MDocument readDoc(ObjectInput in) throws IOException
- Throws:
IOException
-
getBondWidth
@Deprecated public double getBondWidth()
Deprecated.as of Marvin 4.1, replaced bygetBondSpacing()
Gets bond spacing.- Returns:
- the bond spacing in bond length units
-
setBondWidth
@Deprecated public void setBondWidth(double w)
Deprecated.as of Marvin 4.1, replaced bysetBondSpacing(double)
Sets bond spacing.- Parameters:
w
- bond spacing in bond length units
-
getSetColor
@Deprecated public Color getSetColor(int i)
Deprecated.as of Marvin 3.3, replaced by getAtomSetColor- Parameters:
i
- atom set sequence number (0, ...,SETSEQ_MAX
)- Returns:
- the color
-
setSetColor
@Deprecated public void setSetColor(int i, Color color)
Deprecated.as of Marvin 3.3, replaced by setAtomSetColor- Parameters:
i
- atom set sequence number (0, ...,SETSEQ_MAX
)color
- the color
-
getLabels
@Deprecated public boolean getLabels()
Deprecated.use isAtomSymbolsVisible() instead
-
setLabels
@Deprecated public void setLabels(boolean v)
Deprecated.use setAtomSymbolsVisible(v) instead
-
isGrinv
@Deprecated 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
@Deprecated 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
@Deprecated public static JMenu createMenu(ResourceBundle rc, String key)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.createMenu- Parameters:
rc
- the resourceskey
- name of the label resource- Returns:
- the menu
- Since:
- Marvin 3.3
-
initButton
@Deprecated public static void initButton(AbstractButton b, ResourceBundle rc, String key)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.initButton- Parameters:
b
- the buttonrc
- the resourceskey
- name of the resource- Since:
- Marvin 3.3
-
initAction
@Deprecated public static void initAction(Action action, ResourceBundle rc, String key, KeyStroke accel)
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.initAction- Parameters:
action
- the actionrc
- the resourceskey
- name of the resourceaccel
- the accelerator or null- Since:
- Marvin 3.3
-
setTopLevelContainer
public void setTopLevelContainer(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 Container getTopLevelContainer()
- Returns:
- the top level container (if set) or null
-
getReadGlobalGUIProperties
@Deprecated public boolean getReadGlobalGUIProperties()
Deprecated.since Marvin 5.1 when this and thegetSaveGlobalGUIProperties()
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 classJComponent
- 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()
-
setSgroupDataFormatted
public void setSgroupDataFormatted(boolean isFormatted)
Sets if the Sgroup data to be formatted. The default value is true- Parameters:
isFormatted
-
-
isSgroupDataFormatted
public boolean isSgroupDataFormatted()
Returns whether the Sgroup data is formatted.
-
-