Package org.openscience.jmol.app.nbo

Class NBODialogRun

  • All Implemented Interfaces:
    java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants
    Direct Known Subclasses:
    NBODialogView
    abstract class NBODialogRun
extends NBODialogModel

    • Nested Class Summary

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

        javax.swing.JDialog.AccessibleJDialog

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

        java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

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

        java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

      • 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 
      Modifier Constructor Description
      protected NBODialogRun​(javax.swing.JFrame f)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void addBond​(java.lang.String[] atoms, java.lang.String key)  
      (package private) void addChooseKeylist()
      Builds the choose key list interface
      protected void addDelFieldEl​(javax.swing.JPanel b, javax.swing.JButton btn, javax.swing.JScrollPane p, java.lang.String s1, java.lang.String s2, java.util.List<java.lang.String> deleteElements, int val)  
      private void addDelKeylist()
      Builds the deletion key list interface
      protected void addManualEditor()  
      protected void addNBOKeylist()  
      protected void buildRun​(java.awt.Container p)  
      private javax.swing.Box chooseBox​(java.lang.Object[] list, java.lang.String title, javax.swing.SpinnerModel model, java.util.Hashtable<java.lang.String,​java.lang.String> table, int num)
      Box for editing the $Choose list in input file
      private java.lang.String cleanNBOKeylist​(java.lang.String params)  
      protected void deleteBlocks​(javax.swing.JButton btn, javax.swing.Box container, java.util.ArrayList<java.lang.String> deleteBlocks, int val)  
      protected void editOpChanged​(java.lang.String item)  
      protected void essChanged​(java.lang.String item, javax.swing.DefaultComboBoxModel<java.lang.String> editModel)  
      protected boolean getChooseList()
      gets a valid $CHOOSE list from nbo file if it exists and corrects the bonds in the jmol model
      protected java.lang.String getCurrentChooseList()  
      protected java.lang.String getDelList()  
      protected java.lang.String getFileContents()  
      protected void goRunClicked​(java.lang.String keywords, java.lang.String ess, java.io.File inputFile, java.lang.Runnable whenDone)  
      protected void readInputFile​(java.io.File inputFile)  
      protected void removeListParams​(java.util.List<java.lang.String> list, javax.swing.DefaultListModel<java.lang.String> listModel)  
      protected void resetBadChooseList()  
      protected void resetRunFile()  
      private void runJob​(java.lang.String keywords, java.io.File inputFile, java.lang.String ess, java.lang.Runnable whenDone)  
      protected javax.swing.JPanel runS()  
      protected void setBonds​(java.lang.String[] atoms, java.lang.String key)  
      private void setChooseList​(java.lang.String data, boolean isValid)  
      protected int showConfDialog()  
      protected java.lang.String showInputDialog()  

      • Methods inherited from class javax.swing.JDialog

        addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

      • Methods inherited from class java.awt.Dialog

        addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

      • Methods inherited from class java.awt.Window

        addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

      • Methods inherited from class java.awt.Container

        add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, 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

      • keywordList

        protected static final java.lang.String[] keywordList

      • CHOOSE_DESCRIPTION

        private static final java.lang.String CHOOSE_DESCRIPTION
        See Also:
        Constant Field Values

      • runFrame

        private javax.swing.JFrame runFrame

      • validBonds

        protected java.lang.String validBonds

      • validLP

        protected java.lang.String validLP

      • valid3C

        protected java.lang.String valid3C

      • delOrbs

        protected java.lang.String delOrbs

      • delOrbsL

        protected java.lang.String delOrbsL

      • deleteElements

        protected java.util.ArrayList<java.lang.String> deleteElements

      • deleteBlocks

        protected java.util.ArrayList<java.lang.String> deleteBlocks

      • deleteAtomBlocks

        protected java.util.ArrayList<java.lang.String> deleteAtomBlocks

      • delDeloc

        protected java.util.ArrayList<java.lang.String> delDeloc

      • deleteLewisOrbs

        protected boolean deleteLewisOrbs

      • deleteVicinal

        protected boolean deleteVicinal

      • deleteGeminal

        protected boolean deleteGeminal

      • fileData

        java.lang.String fileData

      • fileData2

        java.lang.String fileData2

      • nboKeywords

        java.lang.String nboKeywords

      • plotFileName

        protected javax.swing.JTextField plotFileName

      • chooseBonds

        java.util.Hashtable<java.lang.String,​java.lang.String> chooseBonds

      • choose3C

        java.util.Hashtable<java.lang.String,​java.lang.String> choose3C

      • lastEss

        int lastEss

      • editOps

        protected javax.swing.JComboBox<java.lang.String> editOps

      • keywordButtons

        protected javax.swing.JRadioButton[] keywordButtons

    • Constructor Detail

      • NBODialogRun

        protected NBODialogRun​(javax.swing.JFrame f)

    • Method Detail

      • buildRun

        protected void buildRun​(java.awt.Container p)

      • runS

        protected javax.swing.JPanel runS()

      • showConfDialog

        protected int showConfDialog()

      • showInputDialog

        protected java.lang.String showInputDialog()

      • addManualEditor

        protected void addManualEditor()

      • getFileContents

        protected java.lang.String getFileContents()

      • getCurrentChooseList

        protected java.lang.String getCurrentChooseList()

      • essChanged

        protected void essChanged​(java.lang.String item,
                          javax.swing.DefaultComboBoxModel<java.lang.String> editModel)

      • editOpChanged

        protected void editOpChanged​(java.lang.String item)

      • getChooseList

        protected boolean getChooseList()
        gets a valid $CHOOSE list from nbo file if it exists and corrects the bonds in the jmol model
        Returns:
        false if output contains error

      • setChooseList

        private void setChooseList​(java.lang.String data,
                           boolean isValid)

      • resetBadChooseList

        protected void resetBadChooseList()

      • setBonds

        protected void setBonds​(java.lang.String[] atoms,
                        java.lang.String key)
        Specified by:
        setBonds in class NBODialogConfig

      • addBond

        protected void addBond​(java.lang.String[] atoms,
                       java.lang.String key)

      • cleanNBOKeylist

        private java.lang.String cleanNBOKeylist​(java.lang.String params)

      • addNBOKeylist

        protected void addNBOKeylist()

      • addChooseKeylist

        void addChooseKeylist()
        Builds the choose key list interface

      • chooseBox

        private javax.swing.Box chooseBox​(java.lang.Object[] list,
                                  java.lang.String title,
                                  javax.swing.SpinnerModel model,
                                  java.util.Hashtable<java.lang.String,​java.lang.String> table,
                                  int num)
        Box for editing the $Choose list in input file
        Parameters:
        list -
        title -
        model -
        table -
        num -
        Returns:
        choose box

      • addDelKeylist

        private void addDelKeylist()
        Builds the deletion key list interface

      • addDelFieldEl

        protected void addDelFieldEl​(javax.swing.JPanel b,
                             javax.swing.JButton btn,
                             javax.swing.JScrollPane p,
                             java.lang.String s1,
                             java.lang.String s2,
                             java.util.List<java.lang.String> deleteElements,
                             int val)

      • deleteBlocks

        protected void deleteBlocks​(javax.swing.JButton btn,
                            javax.swing.Box container,
                            java.util.ArrayList<java.lang.String> deleteBlocks,
                            int val)

      • getDelList

        protected java.lang.String getDelList()

      • resetRunFile

        protected void resetRunFile()

      • removeListParams

        protected void removeListParams​(java.util.List<java.lang.String> list,
                                javax.swing.DefaultListModel<java.lang.String> listModel)

      • goRunClicked

        protected void goRunClicked​(java.lang.String keywords,
                            java.lang.String ess,
                            java.io.File inputFile,
                            java.lang.Runnable whenDone)
        Specified by:
        goRunClicked in class NBODialogConfig

      • runJob

        private void runJob​(java.lang.String keywords,
                    java.io.File inputFile,
                    java.lang.String ess,
                    java.lang.Runnable whenDone)