AtomSetChooser

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Frame
      - javax.swing.JFrame
        
        org.openscience.jmol.app.jmolpanel.AtomSetChooser

All Implemented Interfaces:

ActionListener, ImageObserver, MenuContainer, PropertyChangeListener, Serializable, Runnable, EventListener, Accessible, ChangeListener, TreeSelectionListener, RootPaneContainer, WindowConstants
```
public class AtomSetChooser
extends JFrame
implements TreeSelectionListener, PropertyChangeListener, ActionListener, ChangeListener, Runnable
```
A JFrame that allows for choosing an Atomset to view.

Author:

René Kanters, University of Richmond

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

private static class AtomSetChooser.AtomSet
Objects in the AtomSetChooser tree
- Nested classes/interfaces inherited from class javax.swing.JFrame
  JFrame.AccessibleJFrame
- Nested classes/interfaces inherited from class java.awt.Frame
  Frame.AccessibleAWTFrame
- Nested classes/interfaces inherited from class java.awt.Window
  Window.AccessibleAWTWindow, Window.Type
- 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
Modifier and Type	Class and Description
`private static class`	`AtomSetChooser.AtomSet` Objects in the AtomSetChooser tree

Field Summary

Fields
Modifier and Type	Field and Description
`private static float`	`AMPLITUDE_MAX` Maximum value for vibration scale.
`private static float`	`AMPLITUDE_PRECISION` Precision of the vibration scale slider
`private static float`	`AMPLITUDE_VALUE` Initial value of vibration scale.
`private JSlider`	`amplitudeSlider`
`private Thread`	`animThread`
`(package private) static String`	`COLLECTION` String for prefix/resource identifier for the collection area.
`private int`	`currentIndex`
`(package private) static String`	`FF`
`private static int`	`FPS_MAX` Maximum value for the fps slider.
`private JSlider`	`fpsSlider`
`private int[]`	`indexes` Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
`private JLabel`	`infoLabel`
`(package private) static String`	`NEXT`
`(package private) static String`	`PAUSE`
`private static float`	`PERIOD_MAX` Maximum value for the vibration period in seconds.
`private static float`	`PERIOD_PRECISION` Precision of the vibration period slider in seconds.
`private static float`	`PERIOD_VALUE` Initial value for the vibration period in seconds.
`private JSlider`	`periodSlider`
`(package private) static String`	`PLAY`
`(package private) static String`	`PREVIOUS`
`private JTextArea`	`propertiesTextArea`
`private static int`	`RADIUS_MAX` Maximum value for vector radius.
`private static int`	`RADIUS_VALUE` Initial value of vector radius.
`private JSlider`	`radiusSlider`
`private int`	`radiusValue`
`private JCheckBox`	`repeatCheckBox`
`(package private) static String`	`REWIND`
`(package private) static String`	`SAVE`
`private JFileChooser`	`saveChooser`
`private static float`	`SCALE_MAX` Maximum value for vector scale.
`private static float`	`SCALE_PRECISION` Precision of the vector scale slider
`private static float`	`SCALE_VALUE` Initial value of vector scale.
`private JSlider`	`scaleSlider`
`private JSlider`	`selectSlider`
`private JTree`	`tree`
`private DefaultTreeModel`	`treeModel`
`(package private) static String`	`VECTOR` String for prefix/resource identifier for the vector area.
`private Viewer`	`vwr`

Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

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, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description

AtomSetChooser(Viewer vwr, JFrame frame)

Constructors
Constructor and Description
`AtomSetChooser(Viewer vwr, JFrame frame)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`actionPerformed(ActionEvent e)`
`private void`	`createTreeModel()` Creates the treeModel of the AtomSets available in the JmolViewer
`private JPanel`	`createVCRController(String section)` Creates a VCR type set of controller inside a JPanel.
`void`	`findFrequency(int index, int increment)` Have the vwr show a particular frame with frequencies if it can be found.
`private void`	`layoutWindow(Container container)`
`void`	`propertyChange(PropertyChangeEvent propertyChangeEvent)`
`void`	`run()`
`void`	`saveXYZCollection()` Saves the currently active collection as a multistep XYZ file.
`private void`	`script(String cmd)`
`protected void`	`setIndexes(DefaultMutableTreeNode node)` Sets the indexes to the atomSetIndex values of each leaf of the node.
`protected void`	`showAtomSetIndex(int index, boolean bSetSelectSlider)` Show an atom set from the indexes array
`protected void`	`showAuxiliaryInfo(Map<String,Object> auxiliaryInfo)` Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
`protected void`	`showProperties(Properties properties)` Shows the properties in the propertiesPane of the AtomSetChooser window
`void`	`stateChanged(ChangeEvent e)`
`void`	`valueChanged(TreeSelectionEvent e)`

Methods inherited from class java.awt.Frame
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, 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, 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

Methods inherited from interface java.awt.MenuContainer
getFont, postEvent

- Field Detail
  - animThread
```
private Thread animThread
```
  - propertiesTextArea
```
private JTextArea propertiesTextArea
```
  - tree
```
private JTree tree
```
  - treeModel
```
private DefaultTreeModel treeModel
```
  - vwr
```
private Viewer vwr
```
  - repeatCheckBox
```
private JCheckBox repeatCheckBox
```
  - selectSlider
```
private JSlider selectSlider
```
  - infoLabel
```
private JLabel infoLabel
```
  - fpsSlider
```
private JSlider fpsSlider
```
  - amplitudeSlider
```
private JSlider amplitudeSlider
```
  - periodSlider
```
private JSlider periodSlider
```
  - scaleSlider
```
private JSlider scaleSlider
```
  - radiusSlider
```
private JSlider radiusSlider
```
  - saveChooser
```
private JFileChooser saveChooser
```
  - REWIND
```
static final String REWIND
```
    See Also:
    
    Constant Field Values
  - PREVIOUS
```
static final String PREVIOUS
```
    See Also:
    
    Constant Field Values
  - PLAY
```
static final String PLAY
```
    See Also:
    
    Constant Field Values
  - PAUSE
```
static final String PAUSE
```
    See Also:
    
    Constant Field Values
  - NEXT
```
static final String NEXT
```
    See Also:
    
    Constant Field Values
  - FF
```
static final String FF
```
    See Also:
    
    Constant Field Values
  - SAVE
```
static final String SAVE
```
    See Also:
    
    Constant Field Values
  - COLLECTION
```
static final String COLLECTION
```
    String for prefix/resource identifier for the collection area. This value is used in the Jmol properties files.
    
    See Also:
    
    Constant Field Values
  - VECTOR
```
static final String VECTOR
```
    String for prefix/resource identifier for the vector area. This value is used in the Jmol properties files.
    
    See Also:
    
    Constant Field Values
  - indexes
```
private int[] indexes
```
    Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
  - currentIndex
```
private int currentIndex
```
  - FPS_MAX
```
private static final int FPS_MAX
```
    Maximum value for the fps slider.
    
    See Also:
    
    Constant Field Values
  - AMPLITUDE_PRECISION
```
private static final float AMPLITUDE_PRECISION
```
    Precision of the vibration scale slider
    
    See Also:
    
    Constant Field Values
  - AMPLITUDE_MAX
```
private static final float AMPLITUDE_MAX
```
    Maximum value for vibration scale. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - AMPLITUDE_VALUE
```
private static final float AMPLITUDE_VALUE
```
    Initial value of vibration scale. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - PERIOD_PRECISION
```
private static final float PERIOD_PRECISION
```
    Precision of the vibration period slider in seconds.
    
    See Also:
    
    Constant Field Values
  - PERIOD_MAX
```
private static final float PERIOD_MAX
```
    Maximum value for the vibration period in seconds. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - PERIOD_VALUE
```
private static final float PERIOD_VALUE
```
    Initial value for the vibration period in seconds. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - RADIUS_MAX
```
private static final int RADIUS_MAX
```
    Maximum value for vector radius.
    
    See Also:
    
    Constant Field Values
  - RADIUS_VALUE
```
private static final int RADIUS_VALUE
```
    Initial value of vector radius. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - SCALE_PRECISION
```
private static final float SCALE_PRECISION
```
    Precision of the vector scale slider
    
    See Also:
    
    Constant Field Values
  - SCALE_MAX
```
private static final float SCALE_MAX
```
    Maximum value for vector scale. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - SCALE_VALUE
```
private static final float SCALE_VALUE
```
    Initial value of vector scale. Should be in preferences?
    
    See Also:
    
    Constant Field Values
  - radiusValue
```
private int radiusValue
```
- Constructor Detail
  - AtomSetChooser
```
public AtomSetChooser(Viewer vwr,
                      JFrame frame)
```
- Method Detail
  - layoutWindow
```
private void layoutWindow(Container container)
```
  - createVCRController
```
private JPanel createVCRController(String section)
```
    Creates a VCR type set of controller inside a JPanel.
    Uses the JmolResourceHandler to get the label for the panel, the images for the buttons, and the tooltips. The button names are rewind, prev, play, pause, next, and ff.
    The handler for the buttons should determine from the getActionCommand which button in which section triggered the actionEvent, which is identified by {section}.{name}.
    
    Parameters:
    
    section - String of the section that the controller belongs to.
    
    Returns:
    
    The JPanel
  - valueChanged
```
public void valueChanged(TreeSelectionEvent e)
```
    Specified by:
    
    valueChanged in interface TreeSelectionListener
  - showAtomSetIndex
```
protected void showAtomSetIndex(int index,
                                boolean bSetSelectSlider)
```
    Show an atom set from the indexes array
    
    Parameters:
    
    index - The index in the index array
    
    bSetSelectSlider - If true, updates the selectSlider
  - setIndexes
```
protected void setIndexes(DefaultMutableTreeNode node)
```
    Sets the indexes to the atomSetIndex values of each leaf of the node.
    
    Parameters:
    
    node - The node whose leaf's atomSetIndex values should be used
  - actionPerformed
```
public void actionPerformed(ActionEvent e)
```
    Specified by:
    
    actionPerformed in interface ActionListener
  - saveXYZCollection
```
public void saveXYZCollection()
```
    Saves the currently active collection as a multistep XYZ file.
  - findFrequency
```
public void findFrequency(int index,
                          int increment)
```
    Have the vwr show a particular frame with frequencies if it can be found.
    
    Parameters:
    
    index - Starting index where to start looking for frequencies
    
    increment - Increment value for how to go through the list
  - stateChanged
```
public void stateChanged(ChangeEvent e)
```
    Specified by:
    
    stateChanged in interface ChangeListener
  - script
```
private void script(String cmd)
```
  - showProperties
```
protected void showProperties(Properties properties)
```
    Shows the properties in the propertiesPane of the AtomSetChooser window
    
    Parameters:
    
    properties - Properties to be shown.
  - showAuxiliaryInfo
```
protected void showAuxiliaryInfo(Map<String,Object> auxiliaryInfo)
```
    Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
    
    Parameters:
    
    auxiliaryInfo - Hashtable to be shown.
  - createTreeModel
```
private void createTreeModel()
```
    Creates the treeModel of the AtomSets available in the JmolViewer
  - propertyChange
```
public void propertyChange(PropertyChangeEvent propertyChangeEvent)
```
    Specified by:
    
    propertyChange in interface PropertyChangeListener
  - run
```
public void run()
```
    Specified by:
    
    run in interface Runnable

Class AtomSetChooser

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

Nested classes/interfaces inherited from class java.awt.Frame

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

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

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

Field Summary

Fields inherited from class javax.swing.JFrame

Fields inherited from class java.awt.Frame

Fields inherited from class java.awt.Component

Fields inherited from interface javax.swing.WindowConstants

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JFrame

Methods inherited from class java.awt.Frame

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface java.awt.MenuContainer

Field Detail

animThread

propertiesTextArea

tree

treeModel

vwr

repeatCheckBox

selectSlider

infoLabel

fpsSlider

amplitudeSlider

periodSlider

scaleSlider

radiusSlider

saveChooser

REWIND

PREVIOUS

PLAY

PAUSE

NEXT

FF

SAVE

COLLECTION

VECTOR

indexes

currentIndex

FPS_MAX

AMPLITUDE_PRECISION

AMPLITUDE_MAX

AMPLITUDE_VALUE

PERIOD_PRECISION

PERIOD_MAX

PERIOD_VALUE

RADIUS_MAX

RADIUS_VALUE

SCALE_PRECISION

SCALE_MAX

SCALE_VALUE

radiusValue

Constructor Detail

AtomSetChooser

Method Detail

layoutWindow

createVCRController

valueChanged

showAtomSetIndex

setIndexes

actionPerformed

saveXYZCollection

findFrequency

stateChanged

script

showProperties

showAuxiliaryInfo

createTreeModel

propertyChange

run