org.openscience.jmol.app.nbo

Class NBODialogRun

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

org.openscience.jmol.app.nbo.NBODialogConfig

org.openscience.jmol.app.nbo.NBODialogModel

org.openscience.jmol.app.nbo.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 org.openscience.jmol.app.nbo.NBODialogConfig

NBODialogConfig.StyledComboBoxUI

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

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	CHOOSE_DESCRIPTION
(package private) java.util.Hashtable<java.lang.String,java.lang.String>	choose3C
(package private) java.util.Hashtable<java.lang.String,java.lang.String>	chooseBonds
protected java.util.ArrayList<java.lang.String>	delDeloc
protected java.util.ArrayList<java.lang.String>	deleteAtomBlocks
protected java.util.ArrayList<java.lang.String>	deleteBlocks
protected java.util.ArrayList<java.lang.String>	deleteElements
protected boolean	deleteGeminal
protected boolean	deleteLewisOrbs
protected boolean	deleteVicinal
protected java.lang.String	delOrbs
protected java.lang.String	delOrbsL
protected javax.swing.JComboBox<java.lang.String>	editOps
(package private) java.lang.String	fileData
(package private) java.lang.String	fileData2
protected javax.swing.JRadioButton[]	keywordButtons
protected static java.lang.String[]	keywordList
(package private) int	lastEss
(package private) java.lang.String	nboKeywords
protected javax.swing.JTextField	plotFileName
private javax.swing.JFrame	runFrame
protected java.lang.String	valid3C
protected java.lang.String	validBonds
protected java.lang.String	validLP

Fields inherited from class org.openscience.jmol.app.nbo.NBODialogModel

atomNumBox, CONFIRM_SAVE, CONFIRM_VIEWOUTPUT, currVal, editAction, editBox, editMode, jbEdit, jtJmolInput, jtLineInput, jtSelectAtoms, savePath, selected, tfExtS, tfFolderS, tfNameS, titleColor, titleFont, usePath, valLab, VALUE

Fields inherited from class org.openscience.jmol.app.nbo.NBODialogConfig

alterHelp, bodyText, browse, chbHelp, clipHelp, DEFAULT_PARAMS, DIALOG_CONFIG, DIALOG_LIST, DIALOG_MODEL, DIALOG_RUN, DIALOG_SEARCH, DIALOG_VIEW, dialogMode, fuseHelp, haveService, helpBtn, helpConfig, helpModel, icon, inputFile, isJmolNBO, jCheckAtomNum, jCheckNboView, jmolAtomCount, jobStem, jpNboOutput, linkHelp, lonePairs, mainButtons, modelButton, mutateHelp, nboFont, nboService, nboView, rebondHelp, reqInfo, runButton, saveHelp, searchButton, searchHelp, sep, serverPathLabel, showHelp, showRunDone, showWorkPathDone, statusLab, statusPanel, switchHelp, symHelp, tfExt, tfFolder, tfName, topPanel, twistHelp, unifyHelp, useHelp, viewButton, vwr, workingPath

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and 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 org.openscience.jmol.app.nbo.NBODialogModel

actionSelected, buildModel, clearModel, clearSelected, clip, editModel, getModel, getSymmetry, getValue, helpDialogM, loadModel, modelCmd, modelOut, nboResetV, notifyCallbackM, notifyLoadModel, rawInputM, saveHistoryM, saveModel, showConfirmationDialog, showSaveDialog, showWorkpathDialogM

Methods inherited from class org.openscience.jmol.app.nbo.NBODialogConfig

appendOutput, appendOutputWithCaret, appendToFile, buildConfig, buildTopPanel, centerDialog, checkJmolNBO, clearInputFile, clearOutput, connect, enableComponentsR, folderBox, getExt, getHelp, getJobStem, nboReset, newNBOFile, placeNBODialog, rawCmd, resetColorScheme, saveHistory, saveWorkHistory, setComponents, setInputFile, setNBOColorScheme, setVisible, showAtomNums, showNboOutput, showNBOPathDialog, showSelected, showWorkpathDialog

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, getPeer, 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, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, 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)

readInputFile

protected void readInputFile(java.io.File inputFile)

Specified by:

readInputFile in class NBODialogConfig

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)