Package org.openscience.jmol.app.janocchio

Class NoeTable

  • All Implemented Interfaces:
    java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.SwingConstants
    public class NoeTable
extends javax.swing.JTabbedPane
    See Also:
    Serialized Form

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      (package private) class  NoeTable.NoeListWindowListener  
      (package private) class  NoeTable.NoeTableModel  

      • Nested classes/interfaces inherited from class javax.swing.JTabbedPane

        javax.swing.JTabbedPane.AccessibleJTabbedPane, javax.swing.JTabbedPane.ModelListener

      • Nested classes/interfaces inherited from class javax.swing.JComponent

        javax.swing.JComponent.AccessibleJComponent

      • Nested classes/interfaces inherited from class java.awt.Container

        java.awt.Container.AccessibleAWTContainer

      • Nested classes/interfaces inherited from class java.awt.Component

        java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

    • Constructor Summary

      Constructors 
      Constructor Description
      NoeTable​(NMR_JmolPanel nmrPanel, javax.swing.JFrame parentFrame)
      Constructor

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void activate()  
      void addMol()  
      void allocateExpNoes​(int numAtoms)  
      void allocateLabelArray​(int numAtoms)  
      private void calcFrameDelta()  
      (package private) int calcNatomsPerModel()
      TODO This assumes we have the same structure in each model.
      protected void centerDialog()  
      (package private) boolean checkNoe​(int i)  
      void close()  
      (package private) javax.swing.JComponent constructDismissButtonPanel()  
      (package private) javax.swing.JComponent constructNoeButtonPanel()  
      (package private) javax.swing.JComponent constructNoeTable()  
      double getCorrelationTime()
      get the correlation time in seconds
      double getCutoff()
      get the cutoff distance
      java.lang.String getExpDist​(int i, int j)  
      java.lang.String getExpNoe​(int i, int j)  
      boolean getlexpNoes()  
      int[] getMeasurementCountPlusIndices​(int row)  
      double getMixingTime()
      get the mixing time
      double getNMRfreq()
      gets the NMR frequency
      double getNoeExprefValue()  
      int[] getnoeNPrefIndices()  
      boolean getNoesy()  
      double getRedValue()  
      double getRhoStar()  
      int getRowCount()  
      protected int getViewerRow​(int i)  
      double getYellowValue()  
      void setCorrelationTime​(double t)
      set the correlation time to be used in the NOE calculation
      void setCutoff​(double c)
      sets the cutoff distance beyond which atom interactions are not considered
      void setExpDist​(java.lang.String value, int i, int j)  
      void setExpNoe​(java.lang.String value, int i, int j)  
      void setFrameDeltaDisplay​(FrameDeltaDisplay frameDeltaDisplay)  
      void setLabelArray​(java.lang.String[] labelArray)  
      void setlrefSingle​(boolean l)  
      void setMixingTime​(double t)
      sets the mixing time for the NOE experiment
      void setmolCDKuptodate​(boolean value)  
      void setNMRfreq​(double f)
      set the NMR frequency for the NOE simulation
      void setNoeExprefValue​(double value)  
      void setNoeNPrefIndices​(int[] noeNPrefIndices)  
      void setNoesy​(boolean b)  
      void setRedValue​(double value)  
      void setRhoStar​(double c)  
      void setYellowValue​(double value)  
      (package private) void updateNoeTableData()  
      (package private) void updateNoeTableStructure()  
      void updateTables()  

      • Methods inherited from class javax.swing.JTabbedPane

        add, add, add, add, add, addChangeListener, addTab, addTab, addTab, createChangeListener, fireStateChanged, getAccessibleContext, getBackgroundAt, getBoundsAt, getChangeListeners, getComponentAt, getDisabledIconAt, getDisplayedMnemonicIndexAt, getForegroundAt, getIconAt, getMnemonicAt, getModel, getSelectedComponent, getSelectedIndex, getTabComponentAt, getTabCount, getTabLayoutPolicy, getTabPlacement, getTabRunCount, getTitleAt, getToolTipText, getToolTipTextAt, getUI, getUIClassID, indexAtLocation, indexOfComponent, indexOfTab, indexOfTab, indexOfTabComponent, insertTab, isEnabledAt, paramString, remove, remove, removeAll, removeChangeListener, removeTabAt, setBackgroundAt, setComponentAt, setDisabledIconAt, setDisplayedMnemonicIndexAt, setEnabledAt, setForegroundAt, setIconAt, setMnemonicAt, setModel, setSelectedComponent, setSelectedIndex, setTabComponentAt, setTabLayoutPolicy, setTabPlacement, setTitleAt, setToolTipTextAt, 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, 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

        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, 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

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • labelArray

        java.lang.String[] labelArray

      • molCDKuptodate

        boolean molCDKuptodate

      • natomsPerModel

        int natomsPerModel

      • expNoes

        java.lang.String[][] expNoes

      • expDists

        java.lang.String[][] expDists

      • lexpNoes

        boolean lexpNoes

      • freq

        double freq

      • tau

        double tau

      • tMix

        double tMix

      • cutoff

        double cutoff

      • rhoStar

        double rhoStar

      • noesy

        boolean noesy

      • yellowValue

        double yellowValue

      • redValue

        double redValue

      • noeTable

        javax.swing.JTable noeTable

      • noeSelection

        private javax.swing.ListSelectionModel noeSelection

      • selectedNoeRow

        int[] selectedNoeRow

      • noedeleteButton

        javax.swing.JButton noedeleteButton

      • noedeleteAllButton

        private javax.swing.JButton noedeleteAllButton

      • noesetRefButton

        javax.swing.JButton noesetRefButton

      • expOrDistButton

        javax.swing.JComboBox<java.lang.String> expOrDistButton

      • noeNPrefValue

        double noeNPrefValue

      • noeNPrefIndices

        int[] noeNPrefIndices

      • noeExprefValue

        double noeExprefValue

      • lrefSingle

        boolean lrefSingle

    • Constructor Detail

      • NoeTable

        public NoeTable​(NMR_JmolPanel nmrPanel,
                javax.swing.JFrame parentFrame)
        Constructor
        Parameters:
        parentFrame - the parent frame
        nmrPanel - the NMRViewer in which the animation will take place (?)

    • Method Detail

      • constructNoeTable

        javax.swing.JComponent constructNoeTable()

      • constructNoeButtonPanel

        javax.swing.JComponent constructNoeButtonPanel()

      • constructDismissButtonPanel

        javax.swing.JComponent constructDismissButtonPanel()

      • centerDialog

        protected void centerDialog()

      • close

        public void close()

      • activate

        public void activate()

      • updateNoeTableData

        void updateNoeTableData()

      • updateNoeTableStructure

        void updateNoeTableStructure()

      • getRowCount

        public int getRowCount()

      • getMeasurementCountPlusIndices

        public int[] getMeasurementCountPlusIndices​(int row)

      • calcFrameDelta

        private void calcFrameDelta()

      • updateTables

        public void updateTables()

      • getViewerRow

        protected int getViewerRow​(int i)

      • checkNoe

        boolean checkNoe​(int i)

      • calcNatomsPerModel

        int calcNatomsPerModel()
        TODO This assumes we have the same structure in each model.
        Returns:
        average number of atoms per model ??

      • addMol

        public void addMol()

      • setmolCDKuptodate

        public void setmolCDKuptodate​(boolean value)

      • allocateLabelArray

        public void allocateLabelArray​(int numAtoms)

      • allocateExpNoes

        public void allocateExpNoes​(int numAtoms)

      • getExpNoe

        public java.lang.String getExpNoe​(int i,
                                  int j)

      • getExpDist

        public java.lang.String getExpDist​(int i,
                                   int j)

      • setExpNoe

        public void setExpNoe​(java.lang.String value,
                      int i,
                      int j)

      • setExpDist

        public void setExpDist​(java.lang.String value,
                       int i,
                       int j)

      • setLabelArray

        public void setLabelArray​(java.lang.String[] labelArray)

      • setCorrelationTime

        public void setCorrelationTime​(double t)
        set the correlation time to be used in the NOE calculation
        Parameters:
        t - the correlation time in seconds. Typical value would be 80E-12.

      • setMixingTime

        public void setMixingTime​(double t)
        sets the mixing time for the NOE experiment
        Parameters:
        t - the mixing time in seconds. Typically 0.5-1.5 seconds for small molecules

      • setNMRfreq

        public void setNMRfreq​(double f)
        set the NMR frequency for the NOE simulation
        Parameters:
        f - the frequency in MHz

      • setCutoff

        public void setCutoff​(double c)
        sets the cutoff distance beyond which atom interactions are not considered
        Parameters:
        c - the cutoff distance in Angstroms

      • setRhoStar

        public void setRhoStar​(double c)

      • setNoesy

        public void setNoesy​(boolean b)

      • setlrefSingle

        public void setlrefSingle​(boolean l)

      • getCorrelationTime

        public double getCorrelationTime()
        get the correlation time in seconds
        Returns:
        the correlation time in seconds

      • getMixingTime

        public double getMixingTime()
        get the mixing time
        Returns:
        the mixing time in seconds

      • getNMRfreq

        public double getNMRfreq()
        gets the NMR frequency
        Returns:
        the NMR frequency in MHz

      • getCutoff

        public double getCutoff()
        get the cutoff distance
        Returns:
        the cutoff in Angstroms

      • getRhoStar

        public double getRhoStar()

      • getNoesy

        public boolean getNoesy()

      • setRedValue

        public void setRedValue​(double value)

      • setYellowValue

        public void setYellowValue​(double value)

      • getRedValue

        public double getRedValue()

      • getYellowValue

        public double getYellowValue()

      • getnoeNPrefIndices

        public int[] getnoeNPrefIndices()

      • setNoeNPrefIndices

        public void setNoeNPrefIndices​(int[] noeNPrefIndices)

      • getNoeExprefValue

        public double getNoeExprefValue()

      • setNoeExprefValue

        public void setNoeExprefValue​(double value)

      • setFrameDeltaDisplay

        public void setFrameDeltaDisplay​(FrameDeltaDisplay frameDeltaDisplay)

      • getlexpNoes

        public boolean getlexpNoes()