Class NMR_JmolPanel

Method Details

• getMenuItem

  public JMenuItem getMenuItem(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, String[] labelArray, boolean forNOE)

• getAllMolecules

  javajs.util.BS[] getAllMolecules()

• getWindowName

  protected String getWindowName()

  Overrides:

  getWindowName in class JmolPanel

• getFrameActions

  protected List<Action> getFrameActions()

  Overrides:

  getFrameActions in class JmolPanel

  Returns:

  A list of Actions that is understood by the upper level application

• getStringX

  protected String getStringX(String cmd)

  Overrides:

  getStringX in class JmolPanel

• getIconX

  protected ImageIcon getIconX(String img)

  Overrides:

  getIconX in class JmolPanel

• createGuiMap

  protected GuiMap createGuiMap()

  Overrides:

  createGuiMap in class JmolPanel

• createStatusBar

  protected StatusBar createStatusBar()

  Overrides:

  createStatusBar in class JmolPanel

• createToolBar

  protected 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

• createDisplayAndAddStatusListener

  protected void createDisplayAndAddStatusListener()

  Overrides:

  createDisplayAndAddStatusListener in class JmolPanel

• setupModelAdapterAndViewer

  protected void setupModelAdapterAndViewer()

  Overrides:

  setupModelAdapterAndViewer in class JmolPanel

• getDialogs

  protected void getDialogs()

  Overrides:

  getDialogs in class JmolPanel

• getMeasurementTable

  protected void getMeasurementTable()

  Overrides:

  getMeasurementTable in class JmolPanel

• setupDisplay

  protected void setupDisplay()

  Overrides:

  setupDisplay in class JmolPanel

• setFrameLocation

  protected void setFrameLocation(Point loc, JmolPanel parent)

  Overrides:

  setFrameLocation in class JmolPanel

• setIntoFrame

  protected void setIntoFrame()

  Overrides:

  setIntoFrame in class JmolPanel

• setupConsole

  protected void setupConsole()

  Overrides:

  setupConsole in class JmolPanel

• setupDnD

  protected void setupDnD()

  Overrides:

  setupDnD in class JmolPanel

• setAtomChooser

  protected void setAtomChooser()

  Overrides:

  setAtomChooser in class JmolPanel

• launchMainFrame

  protected void launchMainFrame()

  Overrides:

  launchMainFrame in class JmolPanel

• saveWindowSizes

  protected void saveWindowSizes()

  Overrides:

  saveWindowSizes in class JmolPanel

• getJavaConsole

  public void getJavaConsole()

  Overrides:

  getJavaConsole in class JmolPanel

• setMenuKeys

  protected String setMenuKeys(String key, 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(File cDir)

• getMinindex

  public int getMinindex()

• getCurrentStructureFile

  public String getCurrentStructureFile()

• getUserDirectory

  public static 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(Container c, String s)

• tokenize

  protected static String[] tokenize(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(File file) throws IOException

  Throws:

  IOException

• readNmrData

  public void readNmrData(File file) throws Exception

  Throws:

  Exception

• readNmrDataJSON

  public void readNmrDataJSON(File file) throws Exception

  Throws:

  Exception

• checkLoadAndRun

  private void checkLoadAndRun(String structureFile, Object fileData, String fileType)

• firstLineOf

  private static String firstLineOf(String s)

• runScriptWithCallback

  void runScriptWithCallback(Thread t, String command)

• notifyScriptCallback

  void notifyScriptCallback(String script)

• getFrameAtomCount

  public int getFrameAtomCount()

• getViewerMeasurement

  Atom[] getViewerMeasurement(int vRow, int type)

• getViewerRow

  int getViewerRow(int row, int type)

• clearViewerSelection

  void clearViewerSelection()