Examples with DTDResolver ffx.ui.commands.DTDResolver used on opensource projects

Example 1 with DTDResolver

use of ffx.ui.commands.DTDResolver in project ffx by mjschnie.

the class ModelingPanel method initialize.

private void initialize() {
    // Command Description
    descriptTextArea = new JTextArea();
    descriptTextArea.setEditable(false);
    descriptTextArea.setLineWrap(true);
    descriptTextArea.setWrapStyleWord(true);
    descriptTextArea.setDoubleBuffered(true);
    Insets insets = descriptTextArea.getInsets();
    insets.set(5, 5, 5, 5);
    descriptTextArea.setMargin(insets);
    descriptScrollPane = new JScrollPane(descriptTextArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    descriptScrollPane.setBorder(etchedBorder);
    // Command Input
    commandTextArea = new JTextArea();
    commandTextArea.setEditable(false);
    commandTextArea.setLineWrap(true);
    commandTextArea.setWrapStyleWord(true);
    commandTextArea.setDoubleBuffered(true);
    commandTextArea.setMargin(insets);
    // Command Options
    optionsTabbedPane = new JTabbedPane();
    statusLabel = new JLabel();
    statusLabel.setBorder(etchedBorder);
    statusLabel.setToolTipText("  Modeling command that will be executed");
    commandPanel = new JPanel(flowLayout);
    commandPanel.add(optionsTabbedPane);
    splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, commandPanel, descriptScrollPane);
    splitPane.setContinuousLayout(true);
    splitPane.setResizeWeight(1.0d);
    splitPane.setOneTouchExpandable(true);
    setLayout(new BorderLayout());
    add(splitPane, BorderLayout.CENTER);
    add(statusLabel, BorderLayout.SOUTH);
    // Initialize the Amino/Nucleic Acid ComboBox.
    acidComboBox.setEditable(false);
    acidComboBox.setMaximumSize(sizer.getPreferredSize());
    acidComboBox.setPreferredSize(sizer.getPreferredSize());
    acidComboBox.setMinimumSize(sizer.getPreferredSize());
    acidComboBox.setFont(Font.decode("Monospaced"));
    acidTextField.setMaximumSize(sizer.getPreferredSize());
    acidTextField.setMinimumSize(sizer.getPreferredSize());
    acidTextField.setPreferredSize(sizer.getPreferredSize());
    acidTextArea.setEditable(false);
    acidTextArea.setWrapStyleWord(true);
    acidTextArea.setLineWrap(true);
    acidTextArea.setFont(Font.decode("Monospaced"));
    acidScrollPane = new JScrollPane(acidTextArea);
    Dimension d = new Dimension(300, 400);
    acidScrollPane.setPreferredSize(d);
    acidScrollPane.setMaximumSize(d);
    acidScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    // Load the FFX commands.xml file that defines FFX commands.
    try {
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        db.setEntityResolver(new DTDResolver());
        URL comURL = getClass().getClassLoader().getResource("ffx/ui/commands/commands.xml");
        Document doc = db.parse(comURL.openStream());
        NodeList nodelist = doc.getChildNodes();
        Node commandroot = null;
        for (int i = 0; i < nodelist.getLength(); i++) {
            commandroot = nodelist.item(i);
            if (commandroot.getNodeName().equals("FFXCommands") && commandroot instanceof Element) {
                break;
            }
        }
        if (commandroot == null || !(commandroot instanceof Element)) {
            commandList = null;
        }
        commandList = ((Element) commandroot).getElementsByTagName("Command");
    } catch (ParserConfigurationException | SAXException | IOException e) {
        System.err.println(e);
    } finally {
        if (commandList == null) {
            System.out.println("Force Field X commands.xml could not be parsed.");
            logger.severe("Force Field X will exit.");
            System.exit(-1);
        }
    }
    // Create a ComboBox with commands specific to each type of coordinate
    // file.
    xyzCommands = new JComboBox<>();
    intCommands = new JComboBox<>();
    arcCommands = new JComboBox<>();
    pdbCommands = new JComboBox<>();
    anyCommands = new JComboBox<>();
    Element command;
    String name;
    int numcommands = commandList.getLength();
    for (int i = 0; i < numcommands; i++) {
        command = (Element) commandList.item(i);
        name = command.getAttribute("name");
        String temp = command.getAttribute("fileType");
        if (temp.contains("ANY")) {
            temp = "XYZ INT ARC PDB";
            anyCommands.addItem(name);
        }
        String[] types = temp.split(" +");
        for (String type : types) {
            if (type.contains("XYZ")) {
                xyzCommands.addItem(name);
            }
            if (type.contains("INT")) {
                intCommands.addItem(name);
            }
            if (type.contains("ARC")) {
                arcCommands.addItem(name);
            }
            if (type.contains("PDB")) {
                pdbCommands.addItem(name);
            }
        }
    }
    initCommandComboBox(xyzCommands);
    initCommandComboBox(intCommands);
    initCommandComboBox(arcCommands);
    initCommandComboBox(pdbCommands);
    initCommandComboBox(anyCommands);
    currentCommandBox = anyCommands;
    activeCommand = (String) anyCommands.getSelectedItem();
    // Load the default Command.
    loadCommand();
    // Load the default Log File Settings.
    logSettings.setActionCommand("LogSettings");
    loadLogSettings();
    // Create the Toolbar.
    toolBar = new JToolBar("Modeling Commands", JToolBar.HORIZONTAL);
    toolBar.setLayout(new FlowLayout(FlowLayout.LEFT));
    jbLaunch = new JButton(new ImageIcon(getClass().getClassLoader().getResource("ffx/ui/icons/cog_go.png")));
    jbLaunch.setActionCommand("Launch");
    jbLaunch.setToolTipText("Launch the Force Field X Command");
    jbLaunch.addActionListener(this);
    insets.set(2, 2, 2, 2);
    jbLaunch.setMargin(insets);
    toolBar.add(jbLaunch);
    jbStop = new JButton(new ImageIcon(getClass().getClassLoader().getResource("ffx/ui/icons/stop.png")));
    jbStop.setActionCommand("End");
    jbStop.setToolTipText("Terminate the Current Force Field X Command");
    jbStop.addActionListener(this);
    jbStop.setMargin(insets);
    jbStop.setEnabled(false);
    toolBar.add(jbStop);
    toolBar.addSeparator();
    toolBar.add(anyCommands);
    currentCommandBox = anyCommands;
    toolBar.addSeparator();
    /*
         toolBar.add(logSettings);
         JButton jbdelete = new JButton(new ImageIcon(getClass().getClassLoader().getResource("ffx/ui/icons/page_delete.png")));
         jbdelete.setActionCommand("Delete");
         jbdelete.setToolTipText("Delete Log Files");
         jbdelete.addActionListener(this);
         jbdelete.setMargin(insets);
         toolBar.add(jbdelete);
         toolBar.addSeparator();
         */
    ImageIcon icinfo = new ImageIcon(getClass().getClassLoader().getResource("ffx/ui/icons/information.png"));
    descriptCheckBox = new JCheckBoxMenuItem(icinfo);
    descriptCheckBox.addActionListener(this);
    descriptCheckBox.setActionCommand("Description");
    descriptCheckBox.setToolTipText("Show/Hide Modeling Command Descriptions");
    descriptCheckBox.setMargin(insets);
    toolBar.add(descriptCheckBox);
    toolBar.add(new JLabel(""));
    toolBar.setBorderPainted(false);
    toolBar.setFloatable(false);
    toolBar.setRollover(true);
    add(toolBar, BorderLayout.NORTH);
    // Load ModelingPanel preferences.
    Preferences prefs = Preferences.userNodeForPackage(ffx.ui.ModelingPanel.class);
    descriptCheckBox.setSelected(!prefs.getBoolean("JobPanel_description", true));
    descriptCheckBox.doClick();
}

Example 2 with DTDResolver

use of ffx.ui.commands.DTDResolver in project ffx by mjschnie.

the class KeywordPanel method loadXML.

/**
 * Load up the Force Field X Keyword Definitions
 */
private void loadXML() {
    NodeList groups, keywords, values;
    Element group, keyword, value;
    String groupName;
    String keywordName, keywordDescription, keywordGUI;
    groups = null;
    try {
        // Build the Document from the keywords.xml file
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        db.setEntityResolver(new DTDResolver());
        URL keyURL = getClass().getClassLoader().getResource("ffx/ui/commands/keywords.xml");
        Document doc = db.parse(keyURL.openStream());
        Element document = doc.getDocumentElement();
        Element body = (Element) document.getElementsByTagName("body").item(0);
        groups = body.getElementsByTagName("section");
    } catch (ParserConfigurationException | SAXException | IOException e) {
        logger.warning(e.toString());
    }
    keywordHashMap = new LinkedHashMap<>();
    groupHashMap = new LinkedHashMap<>();
    groupHashMap.put("ACTIVE KEYWORDS", "Active Keywords");
    groupHashMap.put("FLAT FILE VIEW", "Flat File View");
    groupComboBox = new JComboBox<>();
    groupComboBox.addItem("Active Keywords");
    groupComboBox.addItem("Flat File View");
    descriptTextArea = new JTextArea();
    descriptTextArea.setLineWrap(true);
    descriptTextArea.setWrapStyleWord(true);
    Insets insets = descriptTextArea.getInsets();
    insets.set(5, 5, 5, 5);
    descriptTextArea.setMargin(insets);
    int length = groups.getLength();
    // Iterate through the Keyword Groups
    for (int i = 0; i < length; i++) {
        group = (Element) groups.item(i);
        groupName = group.getAttribute("name");
        groupComboBox.addItem(groupName);
        keywords = group.getElementsByTagName("subsection");
        int klength = keywords.getLength();
        for (int j = 0; j < klength; j++) {
            keyword = (Element) keywords.item(j);
            keywordName = keyword.getAttribute("name");
            Node text = keyword.getFirstChild();
            keywordDescription = text.getNodeValue().replace('\n', ' ');
            keywordDescription = keywordDescription.replaceAll("  +", " ");
            keywordGUI = keyword.getAttribute("rep");
            KeywordComponent.SwingRepresentation type;
            try {
                type = KeywordComponent.SwingRepresentation.valueOf(keywordGUI.toUpperCase());
            } catch (Exception e) {
                type = null;
                logger.log(Level.WARNING, "{0}: Unknown GUI Component - {1}", new Object[] { keywordName, type });
                System.exit(-1);
            }
            KeywordComponent key;
            if (type == KeywordComponent.SwingRepresentation.CHECKBOXES || type == KeywordComponent.SwingRepresentation.COMBOBOX) {
                values = keyword.getElementsByTagName("Value");
                String[] labels = new String[values.getLength()];
                for (int k = 0; k < values.getLength(); k++) {
                    value = (Element) values.item(k);
                    labels[k] = value.getAttribute("name");
                }
                key = new KeywordComponent(keywordName, groupName, type, keywordDescription, descriptTextArea, labels);
            } else {
                key = new KeywordComponent(keywordName, groupName, type, keywordDescription, descriptTextArea);
            }
            keywordHashMap.put(keywordName.toUpperCase(), key);
            groupHashMap.put(groupName.toUpperCase(), groupName);
        }
    }
    groupComboBox.setSelectedIndex(0);
}