Class NMR_JmolPanel
- 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.JPanel
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- org.openscience.jmol.app.jmolpanel.JmolPanel
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- org.openscience.jmol.app.janocchio.NMR_JmolPanel
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- All Implemented Interfaces:
ImageObserver,MenuContainer,Serializable,Accessible,JsonNioClient,SplashInterface
public class NMR_JmolPanel extends JmolPanel
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description (package private) classNMR_JmolPanel.AtomSetChooserActionclassNMR_JmolPanel.DetachAppletActionclassNMR_JmolPanel.JumpBestFrameActionclassNMR_JmolPanel.LabelNmrActionprivate classNMR_JmolPanel.MoleculeDependentAction(package private) classNMR_JmolPanel.MyStatusListenerclassNMR_JmolPanel.ReadNamfisActionclassNMR_JmolPanel.ReadNmrActionclassNMR_JmolPanel.ReattachAppletAction(package private) classNMR_JmolPanel.SaveNmrActionclassNMR_JmolPanel.ViewCoupleTableActionclassNMR_JmolPanel.ViewNoeTableActionclassNMR_JmolPanel.WriteNamfisAction-
Nested classes/interfaces inherited from class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolPanel.AboutAction, JmolPanel.ActionChangedListener, JmolPanel.AnimButton, JmolPanel.AppCloser, JmolPanel.CloseAction, JmolPanel.ConsoleAction, JmolPanel.CopyImageAction, JmolPanel.CopyScriptAction, JmolPanel.CreditsAction, JmolPanel.ExecuteScriptAction, JmolPanel.ExitAction, JmolPanel.ExportAction, JmolPanel.GaussianAction, JmolPanel.NewAction, JmolPanel.NewwinAction, JmolPanel.OpenAction, JmolPanel.OpenMolAction, JmolPanel.OpenPdbAction, JmolPanel.OpenUrlAction, JmolPanel.PasteClipboardAction, JmolPanel.PovrayAction, JmolPanel.PrintAction, JmolPanel.RecentFilesAction, JmolPanel.ResizeAction, JmolPanel.ScriptEditorAction, JmolPanel.ScriptWindowAction, JmolPanel.SurfaceToolAction, JmolPanel.ToWebAction, JmolPanel.UguideAction, JmolPanel.ViewMeasurementTableAction, JmolPanel.WhatsNewAction, JmolPanel.WriteAction
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Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel
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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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Nested classes/interfaces inherited from interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
JsonNioClient.TouchHandler
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Field Summary
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Fields inherited from class org.openscience.jmol.app.jmolpanel.JmolPanel
aboutAction, allowJavaConsole, appletContext, atomSetChooser, atomsetchooserAction, bannerFrame, clientService, closeAction, commands, consoleAction, consoleframe, copyImageAction, copyImageActionProperty, copyScriptAction, copyScriptActionProperty, creditsAction, display, EDITOR_WINDOW_NAME, editorAction, executeScriptAction, exitAction, exportAction, exportActionProperty, FILE_OPEN_WINDOW_NAME, frame, gaussianAction, gaussianDialog, guimap, historyFile, imageType, isPlugin, jmolApp, kioskFrame, measurementTable, menuItems, modelAdapter, myStatusListener, newAction, newwinAction, numWindows, openAction, openmolAction, openpdbAction, openurlAction, OUTSOCKET, pasteClipboardAction, pasteClipboardActionProperty, pcs, pluginFile, povrayAction, povrayActionProperty, preferencesDialog, printAction, printActionProperty, qualityJPG, qualityPNG, recentFiles, recentFilesAction, resizeAction, screenSize, SCRIPT_WINDOW_NAME, splash, startupHeight, startupWidth, status, surfaceTool, SURFACETOOL_WINDOW_NAME, surfaceToolAction, surfaceToolActionProperty, toolbar, toWebAction, toWebActionProperty, uguideAction, viewMeasurementTableAction, vwr, vwrOptions, WEB_MAKER_WINDOW_NAME, whatsnewAction, windowName, writeAction, writeActionProperty
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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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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private voidcheckLoadAndRun(String structureFile, Object fileData, String fileType)(package private) voidclearViewerSelection()protected voidcreateDisplayAndAddStatusListener()protected GuiMapcreateGuiMap()protected StatusBarcreateStatusBar()protected JToolBarcreateToolBar()Create the toolbar.protected booleandoClose(boolean saveSize)protected static voiddumpContainer(Container c, String s)private static StringfirstLineOf(String s)(package private) javajs.util.BS[]getAllMolecules()StringgetCurrentStructureFile()protected voidgetDialogs()(package private) NmrMoleculegetDistanceJMolecule(javajs.util.BS mol, String[] labelArray, boolean forNOE)protected List<Action>getFrameActions()intgetFrameAtomCount()protected ImageIcongetIconX(String img)voidgetJavaConsole()protected voidgetMeasurementTable()JMenuItemgetMenuItem(String name)Fetch the menu item that was created for the given command.intgetMinindex()protected StringgetStringX(String cmd)static FilegetUserDirectory()Returns a new File referenced by the property 'user.dir', or null if the property is not defined.(package private) Atom[]getViewerMeasurement(int vRow, int type)(package private) intgetViewerRow(int row, int type)protected StringgetWindowName()protected voidlaunchMainFrame()(package private) voidnotifyScriptCallback(String script)voidreadNmrData(File file)voidreadNmrDataJSON(File file)(package private) voidrunScriptWithCallback(Thread t, String command)protected voidsaveWindowSizes()protected voidsetAtomChooser()(package private) voidsetCurrentDirectoryAll(File cDir)protected voidsetFrameLocation(Point loc, JmolPanel parent)protected voidsetIntoFrame()protected StringsetMenuKeys(String key, String tokens)opportunity to adjust menus for a custom applicationprotected voidsetupConsole()protected voidsetupDisplay()protected voidsetupDnD()protected voidsetupModelAdapterAndViewer()protected static String[]tokenize(String input)Take the given string and chop it up into a series of strings on whitespace boundries.voidwriteNmrData(File file)-
Methods inherited from class org.openscience.jmol.app.jmolpanel.JmolPanel
addHelpMenuBar, addJmolProperties, addJmolProperty, addJmolWindowInfo, addJmolWindowInnerInfo, addMacrosMenu, addNormalMenuBar, addPluginMenu, createMenu, createMenubar, createMenuItem, createToolbarButton, getAction, getAndRegisterPlugin, getInstanceWithParams, getJavaConsole, getJmolProperty, getJsonNioServer, getPluginOption, getPreference, isServer, newToolbar, nioClosed, nioSync, print, processNioMessage, report, say, serverCycle, setCommandHooks, setMenuState, setPluginOption, setStatus, showStatus, syncScript, updateConsoleFont
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Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, 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, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, 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, addImpl, 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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MIN_SIZE
static final int MIN_SIZE
- See Also:
- Constant Field Values
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nmrDisplay
private NMR_DisplayPanel nmrDisplay
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mainSplitPane
public JSplitPane mainSplitPane
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noeTable
public NoeTable noeTable
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coupleTable
public CoupleTable coupleTable
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frameCounter
public FrameCounter frameCounter
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labelSetter
public LabelSetter labelSetter
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populationDisplay
public PopulationDisplay populationDisplay
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frameDeltaDisplay
public FrameDeltaDisplay frameDeltaDisplay
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currentDir
protected static File currentDir
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openChooser
FileChooser openChooser
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exportChooser
JFileChooser exportChooser
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saveNmrChooser
JFileChooser saveNmrChooser
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readNmrChooser
JFileChooser readNmrChooser
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saveNamfisChooser
JFileChooser saveNamfisChooser
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readNamfisChooser
JFileChooser readNamfisChooser
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nmrApplet
NmrApplet nmrApplet
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isApplet
boolean isApplet
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nmrguimap
private NmrGuiMap nmrguimap
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border
static Point border
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haveBorder
static Boolean haveBorder
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saveNmrAction
private static final String saveNmrAction
- See Also:
- Constant Field Values
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readNmrAction
private static final String readNmrAction
- See Also:
- Constant Field Values
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detachAppletAction
private static final String detachAppletAction
- See Also:
- Constant Field Values
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reattachAppletAction
private static final String reattachAppletAction
- See Also:
- Constant Field Values
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writeNamfisAction
private static final String writeNamfisAction
- See Also:
- Constant Field Values
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readNamfisAction
private static final String readNamfisAction
- See Also:
- Constant Field Values
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jumpBestFrameAction
private static final String jumpBestFrameAction
- See Also:
- Constant Field Values
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labelNmrAction
private static final String labelNmrAction
- See Also:
- Constant Field Values
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chemFileProperty
public static final String chemFileProperty
- See Also:
- Constant Field Values
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Method Detail
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getMenuItem
public JMenuItem getMenuItem(String name)
Description copied from class:JmolPanelFetch the menu item that was created for the given command.- Overrides:
getMenuItemin classJmolPanel- Parameters:
name- Name of the action.- Returns:
- item created for the given command or null if one wasn't created.
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getDistanceJMolecule
NmrMolecule getDistanceJMolecule(javajs.util.BS mol, String[] labelArray, boolean forNOE)
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getAllMolecules
javajs.util.BS[] getAllMolecules()
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getWindowName
protected String getWindowName()
- Overrides:
getWindowNamein classJmolPanel
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getFrameActions
protected List<Action> getFrameActions()
- Overrides:
getFrameActionsin classJmolPanel- Returns:
- A list of Actions that is understood by the upper level application
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getStringX
protected String getStringX(String cmd)
- Overrides:
getStringXin classJmolPanel
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createGuiMap
protected GuiMap createGuiMap()
- Overrides:
createGuiMapin classJmolPanel
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createStatusBar
protected StatusBar createStatusBar()
- Overrides:
createStatusBarin classJmolPanel
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createToolBar
protected JToolBar createToolBar()
Description copied from class:JmolPanelCreate the toolbar. By default this reads the resource file for the definition of the toolbars.- Overrides:
createToolBarin classJmolPanel- Returns:
- The toolbar
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createDisplayAndAddStatusListener
protected void createDisplayAndAddStatusListener()
- Overrides:
createDisplayAndAddStatusListenerin classJmolPanel
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setupModelAdapterAndViewer
protected void setupModelAdapterAndViewer()
- Overrides:
setupModelAdapterAndViewerin classJmolPanel
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getDialogs
protected void getDialogs()
- Overrides:
getDialogsin classJmolPanel
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getMeasurementTable
protected void getMeasurementTable()
- Overrides:
getMeasurementTablein classJmolPanel
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setupDisplay
protected void setupDisplay()
- Overrides:
setupDisplayin classJmolPanel
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setFrameLocation
protected void setFrameLocation(Point loc, JmolPanel parent)
- Overrides:
setFrameLocationin classJmolPanel
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setIntoFrame
protected void setIntoFrame()
- Overrides:
setIntoFramein classJmolPanel
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setupConsole
protected void setupConsole()
- Overrides:
setupConsolein classJmolPanel
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setAtomChooser
protected void setAtomChooser()
- Overrides:
setAtomChooserin classJmolPanel
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launchMainFrame
protected void launchMainFrame()
- Overrides:
launchMainFramein classJmolPanel
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saveWindowSizes
protected void saveWindowSizes()
- Overrides:
saveWindowSizesin classJmolPanel
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getJavaConsole
public void getJavaConsole()
- Overrides:
getJavaConsolein classJmolPanel
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setMenuKeys
protected String setMenuKeys(String key, String tokens)
Description copied from class:JmolPanelopportunity to adjust menus for a custom application- Overrides:
setMenuKeysin classJmolPanel- Returns:
- possibly changed token string
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setCurrentDirectoryAll
void setCurrentDirectoryAll(File cDir)
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getMinindex
public int getMinindex()
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getCurrentStructureFile
public String getCurrentStructureFile()
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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
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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
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writeNmrData
public void writeNmrData(File file) throws IOException
- Throws:
IOException
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checkLoadAndRun
private void checkLoadAndRun(String structureFile, Object fileData, String fileType)
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notifyScriptCallback
void notifyScriptCallback(String script)
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getFrameAtomCount
public int getFrameAtomCount()
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getViewerMeasurement
Atom[] getViewerMeasurement(int vRow, int type)
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getViewerRow
int getViewerRow(int row, int type)
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clearViewerSelection
void clearViewerSelection()
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