Package org.openscience.jmol.app.jmolpanel

Class AtomSetChooser

    • Field Detail

      • animThread

        private Thread animThread

      • propertiesTextArea

        private JTextArea propertiesTextArea

      • tree

        private JTree tree

      • 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

      • 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

      • 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

      • 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

      • 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

      • run

        public void run()
        Specified by:
        run in interface Runnable