Class NMR_JmolPanel

    • Field Detail

      • mainSplitPane

        public javax.swing.JSplitPane mainSplitPane
      • currentDir

        protected static java.io.File currentDir
      • exportChooser

        javax.swing.JFileChooser exportChooser
      • saveNmrChooser

        javax.swing.JFileChooser saveNmrChooser
      • readNmrChooser

        javax.swing.JFileChooser readNmrChooser
      • saveNamfisChooser

        javax.swing.JFileChooser saveNamfisChooser
      • readNamfisChooser

        javax.swing.JFileChooser readNamfisChooser
      • isApplet

        boolean isApplet
      • border

        static java.awt.Point border
      • haveBorder

        static java.lang.Boolean haveBorder
      • htGuiChanges

        static java.util.Set<java.lang.String> htGuiChanges
      • detachAppletAction

        private static final java.lang.String detachAppletAction
        See Also:
        Constant Field Values
      • reattachAppletAction

        private static final java.lang.String reattachAppletAction
        See Also:
        Constant Field Values
      • writeNamfisAction

        private static final java.lang.String writeNamfisAction
        See Also:
        Constant Field Values
      • readNamfisAction

        private static final java.lang.String readNamfisAction
        See Also:
        Constant Field Values
      • jumpBestFrameAction

        private static final java.lang.String jumpBestFrameAction
        See Also:
        Constant Field Values
      • chemFileProperty

        public static final java.lang.String chemFileProperty
        See Also:
        Constant Field Values
      • htMessageCallbacks

        protected java.util.Map<java.lang.String,​java.lang.Thread> htMessageCallbacks
    • Constructor Detail

      • NMR_JmolPanel

        public NMR_JmolPanel​(JmolApp jmolApp,
                             Splash splash,
                             javax.swing.JFrame frame,
                             Jmol parent,
                             int startupWidth,
                             int startupHeight,
                             java.util.Map<java.lang.String,​java.lang.Object> vwrOptions,
                             java.awt.Point loc)
    • Method Detail

      • getMenuItem

        public javax.swing.JMenuItem getMenuItem​(java.lang.String name)
        Description copied from class: JmolPanel
        Fetch the menu item that was created for the given command.
        Overrides:
        getMenuItem in class JmolPanel
        Parameters:
        name - Name of the action.
        Returns:
        item created for the given command or null if one wasn't created.
      • getDistanceJMolecule

        NmrMolecule getDistanceJMolecule​(javajs.util.BS mol,
                                         java.lang.String[] labelArray,
                                         boolean forNOE)
      • getAllMolecules

        javajs.util.BS[] getAllMolecules()
      • getFrameActions

        protected java.util.List<javax.swing.Action> getFrameActions()
        Overrides:
        getFrameActions in class JmolPanel
        Returns:
        A list of Actions that is understood by the upper level application
      • getStringX

        protected java.lang.String getStringX​(java.lang.String cmd)
        Overrides:
        getStringX in class JmolPanel
      • getIconX

        protected javax.swing.ImageIcon getIconX​(java.lang.String img)
        Overrides:
        getIconX in class JmolPanel
      • createToolBar

        protected javax.swing.JToolBar createToolBar()
        Description copied from class: JmolPanel
        Create the toolbar. By default this reads the resource file for the definition of the toolbars.
        Overrides:
        createToolBar in class JmolPanel
        Returns:
        The toolbar
      • setMenuKeys

        protected java.lang.String setMenuKeys​(java.lang.String key,
                                               java.lang.String tokens)
        Description copied from class: JmolPanel
        opportunity to adjust menus for a custom application
        Overrides:
        setMenuKeys in class JmolPanel
        Returns:
        possibly changed token string
      • doClose

        protected boolean doClose​(boolean saveSize)
        Overrides:
        doClose in class JmolPanel
      • setCurrentDirectoryAll

        void setCurrentDirectoryAll​(java.io.File cDir)
      • getMinindex

        public int getMinindex()
      • getCurrentStructureFile

        public java.lang.String getCurrentStructureFile()
      • getUserDirectory

        public static java.io.File getUserDirectory()
        Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
        Returns:
        a File to the user directory
      • dumpContainer

        protected static void dumpContainer​(java.awt.Container c,
                                            java.lang.String s)
      • tokenize

        protected static java.lang.String[] tokenize​(java.lang.String input)
        Take the given string and chop it up into a series of strings on whitespace boundries. This is useful for trying to get an array of strings out of the resource file.
        Parameters:
        input - String to chop
        Returns:
        Strings chopped on whitespace boundries
      • writeNmrData

        public void writeNmrData​(java.io.File file)
                          throws java.io.IOException
        Throws:
        java.io.IOException
      • readNmrData

        public void readNmrData​(java.io.File file)
                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readNmrDataJSON

        public void readNmrDataJSON​(java.io.File file)
                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkLoadAndRun

        private void checkLoadAndRun​(java.lang.String structureFile,
                                     java.lang.Object fileData,
                                     java.lang.String fileType)
      • firstLineOf

        private static java.lang.String firstLineOf​(java.lang.String s)
      • runScriptWithCallback

        void runScriptWithCallback​(java.lang.Thread t,
                                   java.lang.String command)
      • notifyScriptCallback

        void notifyScriptCallback​(java.lang.String script)
      • getFrameAtomCount

        public int getFrameAtomCount()
      • getViewerMeasurement

        Atom[] getViewerMeasurement​(int vRow,
                                    int type)
      • getViewerRow

        int getViewerRow​(int row,
                         int type)
      • clearViewerSelection

        void clearViewerSelection()