Package chemaxon.marvin.beans

Class MarvinPane

    • Field Detail

      • VERSION

        public static final String VERSION
        Marvin version.

      • molPanel

        protected chemaxon.marvin.common.swing.MolPanel molPanel
        Underlying panel.

      • params

        protected String params
        Parameter string.

      • topLevelContainer

        protected static 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​(ActionListener l)
        Adds an action listener.
        Parameters:
        l - the action listener
        Since:
        Marvin 3.3

      • removeActionListener

        public void removeActionListener​(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
        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

      • 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 String getParams()
        Gets the parameter string.
        Returns:
        the parameter string

      • 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

      • 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

      • getMolbg

        public Color getMolbg()
        Gets the molecule background color.
        Returns:
        the color

      • setMolbg

        public void setMolbg​(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

      • getBoldBondWidth

        public double getBoldBondWidth()
        Gets the C-C bold bond width in pt units.
        Returns:
        the bold bond width of C-C bonds.

      • setBoldBondWidth

        public void setBoldBondWidth​(double w)
        Sets the bold bond width.
        Parameters:
        w - the bold bond width of C-C bonds in pt units.

      • getBondLength

        public double getBondLength()
        Gets the C-C bond length in pt units.
        Returns:
        the bond Length of C-C bonds.

      • setBondLength

        public void setBondLength​(double l)
        Sets the bond length.
        Parameters:
        l - the bond length of C-C bonds in pt units.

      • 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

      • 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

      • 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

      • 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

      • 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 String getDownWedge()
        Gets the wedge bond display convention.
        Returns:
        "mdl" or "daylight"

      • 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"

      • 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() instead
        Shows 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

      • 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 message
        ex - 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 for
        fname - 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 the MSketch and MView 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 the MSketch and MView 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 occur
        ClassNotFoundException - If the class for an object being restored cannot be found.
        Since:
        Marvin 3.5, 2004/11/01

      • getBondWidth

        @Deprecated
public double getBondWidth()
        Deprecated.
        as of Marvin 4.1, replaced by getBondSpacing()
        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 by setBondSpacing(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 resources
        key - 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 button
        rc - the resources
        key - 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 action
        rc - the resources
        key - name of the resource
        accel - 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 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

      • 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 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()

      • 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.