Class NMR_JmolPanel
java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
org.openscience.jmol.app.jmolpanel.JmolPanel
org.openscience.jmol.app.janocchio.NMR_JmolPanel
- All Implemented Interfaces:
ImageObserver
,MenuContainer
,Serializable
,Accessible
,JsonNioClient
,SplashInterface
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescription(package private) class
class
class
class
private class
(package private) class
class
class
class
(package private) class
class
class
class
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
Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel
Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
Nested classes/interfaces inherited from interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
JsonNioClient.TouchHandler
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Field Summary
FieldsModifier and TypeFieldDescription(package private) static Point
static final String
protected static File
private static final String
(package private) JFileChooser
(package private) static Boolean
(package private) boolean
private static final String
private static final String
(package private) static final int
(package private) NmrApplet
private NMR_DisplayPanel
private NmrGuiMap
(package private) FileChooser
private static final String
(package private) JFileChooser
private static final String
(package private) JFileChooser
private static final String
(package private) JFileChooser
private static final String
(package private) JFileChooser
private static final String
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
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
Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Fields inherited from interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
TYPES
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
checkLoadAndRun
(String structureFile, Object fileData, String fileType) (package private) void
protected void
protected GuiMap
protected StatusBar
protected JToolBar
Create the toolbar.protected boolean
doClose
(boolean saveSize) protected static void
dumpContainer
(Container c, String s) private static String
(package private) javajs.util.BS[]
protected void
(package private) NmrMolecule
getDistanceJMolecule
(javajs.util.BS mol, String[] labelArray, boolean forNOE) int
protected ImageIcon
void
protected void
getMenuItem
(String name) Fetch the menu item that was created for the given command.int
protected String
getStringX
(String cmd) static File
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) int
getViewerRow
(int row, int type) protected String
protected void
(package private) void
notifyScriptCallback
(String script) void
readNmrData
(File file) void
readNmrDataJSON
(File file) (package private) void
runScriptWithCallback
(Thread t, String command) protected void
protected void
(package private) void
setCurrentDirectoryAll
(File cDir) protected void
setFrameLocation
(Point loc, JmolPanel parent) protected void
protected String
setMenuKeys
(String key, String tokens) opportunity to adjust menus for a custom applicationprotected void
protected void
protected void
setupDnD()
protected void
protected static String[]
Take the given string and chop it up into a series of strings on whitespace boundries.void
writeNmrData
(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, getConsole, getInstanceWithParams, getJavaConsole, getJmolProperty, getJsonNioServer, getPluginOption, getPreference, isServer, newToolbar, nioClosed, print, processNioMessage, report, say, serverCycle, setCommandHooks, setMenuState, setPluginOption, setStatus, showStatus, updateConsoleFont
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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
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
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 Details
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MIN_SIZE
static final int MIN_SIZE- See Also:
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nmrDisplay
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mainSplitPane
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noeTable
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coupleTable
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frameCounter
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labelSetter
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populationDisplay
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frameDeltaDisplay
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currentDir
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openChooser
FileChooser openChooser -
exportChooser
JFileChooser exportChooser -
saveNmrChooser
JFileChooser saveNmrChooser -
readNmrChooser
JFileChooser readNmrChooser -
saveNamfisChooser
JFileChooser saveNamfisChooser -
readNamfisChooser
JFileChooser readNamfisChooser -
nmrApplet
NmrApplet nmrApplet -
isApplet
boolean isApplet -
nmrguimap
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border
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haveBorder
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htGuiChanges
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saveNmrAction
- See Also:
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readNmrAction
- See Also:
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detachAppletAction
- See Also:
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reattachAppletAction
- See Also:
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writeNamfisAction
- See Also:
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readNamfisAction
- See Also:
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jumpBestFrameAction
- See Also:
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labelNmrAction
- See Also:
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chemFileProperty
- See Also:
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htMessageCallbacks
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Constructor Details
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NMR_JmolPanel
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Method Details
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getMenuItem
Description copied from class:JmolPanel
Fetch the menu item that was created for the given command.- Overrides:
getMenuItem
in 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
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getAllMolecules
javajs.util.BS[] getAllMolecules() -
getWindowName
- Overrides:
getWindowName
in classJmolPanel
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getFrameActions
- Overrides:
getFrameActions
in classJmolPanel
- Returns:
- A list of Actions that is understood by the upper level application
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getStringX
- Overrides:
getStringX
in classJmolPanel
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getIconX
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createGuiMap
- Overrides:
createGuiMap
in classJmolPanel
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createStatusBar
- Overrides:
createStatusBar
in classJmolPanel
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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 classJmolPanel
- Returns:
- The toolbar
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createDisplayAndAddStatusListener
protected void createDisplayAndAddStatusListener()- Overrides:
createDisplayAndAddStatusListener
in classJmolPanel
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setupModelAdapterAndViewer
protected void setupModelAdapterAndViewer()- Overrides:
setupModelAdapterAndViewer
in classJmolPanel
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getDialogs
protected void getDialogs()- Overrides:
getDialogs
in classJmolPanel
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getMeasurementTable
protected void getMeasurementTable()- Overrides:
getMeasurementTable
in classJmolPanel
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setupDisplay
protected void setupDisplay()- Overrides:
setupDisplay
in classJmolPanel
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setFrameLocation
- Overrides:
setFrameLocation
in classJmolPanel
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setIntoFrame
protected void setIntoFrame()- Overrides:
setIntoFrame
in classJmolPanel
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setupConsole
protected void setupConsole()- Overrides:
setupConsole
in classJmolPanel
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setupDnD
protected void setupDnD() -
setAtomChooser
protected void setAtomChooser()- Overrides:
setAtomChooser
in classJmolPanel
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launchMainFrame
protected void launchMainFrame()- Overrides:
launchMainFrame
in classJmolPanel
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saveWindowSizes
protected void saveWindowSizes()- Overrides:
saveWindowSizes
in classJmolPanel
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getJavaConsole
public void getJavaConsole()- Overrides:
getJavaConsole
in classJmolPanel
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setMenuKeys
Description copied from class:JmolPanel
opportunity to adjust menus for a custom application- Overrides:
setMenuKeys
in classJmolPanel
- Parameters:
key
-tokens
-- Returns:
- possibly changed token string
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doClose
protected boolean doClose(boolean saveSize) -
setCurrentDirectoryAll
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getMinindex
public int getMinindex() -
getCurrentStructureFile
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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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dumpContainer
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tokenize
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
- Throws:
IOException
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readNmrData
- Throws:
Exception
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readNmrDataJSON
- Throws:
Exception
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checkLoadAndRun
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firstLineOf
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runScriptWithCallback
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notifyScriptCallback
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getFrameAtomCount
public int getFrameAtomCount() -
getViewerMeasurement
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getViewerRow
int getViewerRow(int row, int type) -
clearViewerSelection
void clearViewerSelection()
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