Package org.openscience.jmol.app.nbo
Class NBODialogRun
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- java.awt.Window
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- java.awt.Dialog
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- javax.swing.JDialog
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- org.openscience.jmol.app.nbo.NBODialogConfig
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- org.openscience.jmol.app.nbo.NBODialogModel
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- org.openscience.jmol.app.nbo.NBODialogRun
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from class org.openscience.jmol.app.nbo.NBODialogConfig
NBODialogConfig.StyledComboBoxUI
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Nested classes/interfaces inherited from class javax.swing.JDialog
javax.swing.JDialog.AccessibleJDialog
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Nested classes/interfaces inherited from class java.awt.Dialog
java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType
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Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
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Field Summary
Fields Modifier and Type Field 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
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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
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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
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Fields inherited from class javax.swing.JDialog
accessibleContext, rootPane, rootPaneCheckingEnabled
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Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Constructor Summary
Constructors Modifier Constructor Description protected
NBODialogRun(javax.swing.JFrame f)
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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 interfaceprotected 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 interfaceprotected 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 fileprivate 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 modelprotected 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()
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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
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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
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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
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Methods inherited from class java.awt.Dialog
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack
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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
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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
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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, 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
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Field Detail
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keywordList
protected static final java.lang.String[] keywordList
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CHOOSE_DESCRIPTION
private static final java.lang.String CHOOSE_DESCRIPTION
- See Also:
- Constant Field Values
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runFrame
private javax.swing.JFrame runFrame
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validBonds
protected java.lang.String validBonds
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validLP
protected java.lang.String validLP
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valid3C
protected java.lang.String valid3C
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delOrbs
protected java.lang.String delOrbs
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delOrbsL
protected java.lang.String delOrbsL
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deleteElements
protected java.util.ArrayList<java.lang.String> deleteElements
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deleteBlocks
protected java.util.ArrayList<java.lang.String> deleteBlocks
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deleteAtomBlocks
protected java.util.ArrayList<java.lang.String> deleteAtomBlocks
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delDeloc
protected java.util.ArrayList<java.lang.String> delDeloc
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deleteLewisOrbs
protected boolean deleteLewisOrbs
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deleteVicinal
protected boolean deleteVicinal
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deleteGeminal
protected boolean deleteGeminal
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fileData
java.lang.String fileData
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fileData2
java.lang.String fileData2
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nboKeywords
java.lang.String nboKeywords
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plotFileName
protected javax.swing.JTextField plotFileName
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chooseBonds
java.util.Hashtable<java.lang.String,java.lang.String> chooseBonds
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choose3C
java.util.Hashtable<java.lang.String,java.lang.String> choose3C
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lastEss
int lastEss
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editOps
protected javax.swing.JComboBox<java.lang.String> editOps
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keywordButtons
protected javax.swing.JRadioButton[] keywordButtons
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Method Detail
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buildRun
protected void buildRun(java.awt.Container p)
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runS
protected javax.swing.JPanel runS()
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showConfDialog
protected int showConfDialog()
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showInputDialog
protected java.lang.String showInputDialog()
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addManualEditor
protected void addManualEditor()
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getFileContents
protected java.lang.String getFileContents()
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getCurrentChooseList
protected java.lang.String getCurrentChooseList()
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essChanged
protected void essChanged(java.lang.String item, javax.swing.DefaultComboBoxModel<java.lang.String> editModel)
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editOpChanged
protected void editOpChanged(java.lang.String item)
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readInputFile
protected void readInputFile(java.io.File inputFile)
- Specified by:
readInputFile
in classNBODialogConfig
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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
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setChooseList
private void setChooseList(java.lang.String data, boolean isValid)
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resetBadChooseList
protected void resetBadChooseList()
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setBonds
protected void setBonds(java.lang.String[] atoms, java.lang.String key)
- Specified by:
setBonds
in classNBODialogConfig
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addBond
protected void addBond(java.lang.String[] atoms, java.lang.String key)
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cleanNBOKeylist
private java.lang.String cleanNBOKeylist(java.lang.String params)
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addNBOKeylist
protected void addNBOKeylist()
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addChooseKeylist
void addChooseKeylist()
Builds the choose key list interface
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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
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addDelKeylist
private void addDelKeylist()
Builds the deletion key list interface
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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)
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deleteBlocks
protected void deleteBlocks(javax.swing.JButton btn, javax.swing.Box container, java.util.ArrayList<java.lang.String> deleteBlocks, int val)
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getDelList
protected java.lang.String getDelList()
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resetRunFile
protected void resetRunFile()
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removeListParams
protected void removeListParams(java.util.List<java.lang.String> list, javax.swing.DefaultListModel<java.lang.String> listModel)
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goRunClicked
protected void goRunClicked(java.lang.String keywords, java.lang.String ess, java.io.File inputFile, java.lang.Runnable whenDone)
- Specified by:
goRunClicked
in classNBODialogConfig
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runJob
private void runJob(java.lang.String keywords, java.io.File inputFile, java.lang.String ess, java.lang.Runnable whenDone)
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