Examples with Keyword ffx.utilities.Keyword used on opensource projects

Example 1 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class ModelingPanel method loadCommand.

private void loadCommand() {
    synchronized (this) {
        // Force Field X Command
        Element command;
        // Command Options
        NodeList options;
        Element option;
        // Option Values
        NodeList values;
        Element value;
        // Options may be Conditional based on previous Option values (not
        // always supplied)
        NodeList conditionalList;
        Element conditional;
        // JobPanel GUI Components that change based on command
        JPanel optionPanel;
        // Clear the previous components
        commandPanel.removeAll();
        optionsTabbedPane.removeAll();
        conditionals.clear();
        String currentCommand = (String) currentCommandBox.getSelectedItem();
        if (currentCommand == null) {
            commandPanel.validate();
            commandPanel.repaint();
            return;
        }
        command = null;
        for (int i = 0; i < commandList.getLength(); i++) {
            command = (Element) commandList.item(i);
            String name = command.getAttribute("name");
            if (name.equalsIgnoreCase(currentCommand)) {
                break;
            }
        }
        int div = splitPane.getDividerLocation();
        descriptTextArea.setText(currentCommand.toUpperCase() + ": " + command.getAttribute("description"));
        splitPane.setBottomComponent(descriptScrollPane);
        splitPane.setDividerLocation(div);
        // The "action" tells Force Field X what to do when the
        // command finishes
        commandActions = command.getAttribute("action").trim();
        // The "fileType" specifies what file types this command can execute
        // on
        String string = command.getAttribute("fileType").trim();
        String[] types = string.split(" +");
        commandFileTypes.clear();
        for (String type : types) {
            if (type.contains("XYZ")) {
                commandFileTypes.add(FileType.XYZ);
            }
            if (type.contains("INT")) {
                commandFileTypes.add(FileType.INT);
            }
            if (type.contains("ARC")) {
                commandFileTypes.add(FileType.ARC);
            }
            if (type.contains("PDB")) {
                commandFileTypes.add(FileType.PDB);
            }
            if (type.contains("ANY")) {
                commandFileTypes.add(FileType.ANY);
            }
        }
        // Determine what options are available for this command
        options = command.getElementsByTagName("Option");
        int length = options.getLength();
        for (int i = 0; i < length; i++) {
            // This Option will be enabled (isEnabled = true) unless a
            // Conditional disables it
            boolean isEnabled = true;
            option = (Element) options.item(i);
            conditionalList = option.getElementsByTagName("Conditional");
            /*
                 * Currently, there can only be 0 or 1 Conditionals per Option
                 * There are three types of Conditionals implemented. 1.)
                 * Conditional on a previous Option, this option may be
                 * available 2.) Conditional on input for this option, a
                 * sub-option may be available 3.) Conditional on the presence
                 * of keywords, this option may be available
                 */
            if (conditionalList != null) {
                conditional = (Element) conditionalList.item(0);
            } else {
                conditional = null;
            }
            // Get the command line flag
            String flag = option.getAttribute("flag").trim();
            // Get the description
            String optionDescript = option.getAttribute("description");
            JTextArea optionTextArea = new JTextArea("  " + optionDescript.trim());
            optionTextArea.setEditable(false);
            optionTextArea.setLineWrap(true);
            optionTextArea.setWrapStyleWord(true);
            optionTextArea.setBorder(etchedBorder);
            // Get the default for this Option (if one exists)
            String defaultOption = option.getAttribute("default");
            // Option Panel
            optionPanel = new JPanel(new BorderLayout());
            optionPanel.add(optionTextArea, BorderLayout.NORTH);
            String swing = option.getAttribute("gui");
            JPanel optionValuesPanel = new JPanel(new FlowLayout());
            optionValuesPanel.setBorder(etchedBorder);
            ButtonGroup bg = null;
            if (swing.equalsIgnoreCase("CHECKBOXES")) {
                // CHECKBOXES allows selection of 1 or more values from a
                // predefined set (Analyze, for example)
                values = option.getElementsByTagName("Value");
                for (int j = 0; j < values.getLength(); j++) {
                    value = (Element) values.item(j);
                    JCheckBox jcb = new JCheckBox(value.getAttribute("name"));
                    jcb.addMouseListener(this);
                    jcb.setName(flag);
                    if (defaultOption != null && jcb.getActionCommand().equalsIgnoreCase(defaultOption)) {
                        jcb.setSelected(true);
                    }
                    optionValuesPanel.add(jcb);
                }
            } else if (swing.equalsIgnoreCase("TEXTFIELD")) {
                // TEXTFIELD takes an arbitrary String as input
                JTextField jtf = new JTextField(20);
                jtf.addMouseListener(this);
                jtf.setName(flag);
                if (defaultOption != null && defaultOption.equals("ATOMS")) {
                    FFXSystem sys = mainPanel.getHierarchy().getActive();
                    if (sys != null) {
                        jtf.setText("" + sys.getAtomList().size());
                    }
                } else if (defaultOption != null) {
                    jtf.setText(defaultOption);
                }
                optionValuesPanel.add(jtf);
            } else if (swing.equalsIgnoreCase("RADIOBUTTONS")) {
                // RADIOBUTTONS allows one choice from a set of predifined
                // values
                bg = new ButtonGroup();
                values = option.getElementsByTagName("Value");
                for (int j = 0; j < values.getLength(); j++) {
                    value = (Element) values.item(j);
                    JRadioButton jrb = new JRadioButton(value.getAttribute("name"));
                    jrb.addMouseListener(this);
                    jrb.setName(flag);
                    bg.add(jrb);
                    if (defaultOption != null && jrb.getActionCommand().equalsIgnoreCase(defaultOption)) {
                        jrb.setSelected(true);
                    }
                    optionValuesPanel.add(jrb);
                }
            } else if (swing.equalsIgnoreCase("PROTEIN")) {
                // Protein allows selection of amino acids for the protein
                // builder
                optionValuesPanel.setLayout(new BoxLayout(optionValuesPanel, BoxLayout.Y_AXIS));
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                optionValuesPanel.add(getAminoAcidPanel());
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                acidComboBox.removeAllItems();
                JButton add = new JButton("Edit");
                add.setActionCommand("PROTEIN");
                add.addActionListener(this);
                add.setAlignmentX(Button.CENTER_ALIGNMENT);
                JPanel comboPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
                comboPanel.add(acidTextField);
                comboPanel.add(add);
                optionValuesPanel.add(comboPanel);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                JButton remove = new JButton("Remove");
                add.setMinimumSize(remove.getPreferredSize());
                add.setPreferredSize(remove.getPreferredSize());
                remove.setActionCommand("PROTEIN");
                remove.addActionListener(this);
                remove.setAlignmentX(Button.CENTER_ALIGNMENT);
                comboPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
                comboPanel.add(acidComboBox);
                comboPanel.add(remove);
                optionValuesPanel.add(comboPanel);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                optionValuesPanel.add(acidScrollPane);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                JButton reset = new JButton("Reset");
                reset.setActionCommand("PROTEIN");
                reset.addActionListener(this);
                reset.setAlignmentX(Button.CENTER_ALIGNMENT);
                optionValuesPanel.add(reset);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                acidTextArea.setText("");
                acidTextField.setText("");
            } else if (swing.equalsIgnoreCase("NUCLEIC")) {
                // Nucleic allows selection of nucleic acids for the nucleic
                // acid builder
                optionValuesPanel.setLayout(new BoxLayout(optionValuesPanel, BoxLayout.Y_AXIS));
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                optionValuesPanel.add(getNucleicAcidPanel());
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                acidComboBox.removeAllItems();
                JButton add = new JButton("Edit");
                add.setActionCommand("NUCLEIC");
                add.addActionListener(this);
                add.setAlignmentX(Button.CENTER_ALIGNMENT);
                JPanel comboPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
                comboPanel.add(acidTextField);
                comboPanel.add(add);
                optionValuesPanel.add(comboPanel);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                JButton remove = new JButton("Remove");
                add.setMinimumSize(remove.getPreferredSize());
                add.setPreferredSize(remove.getPreferredSize());
                remove.setActionCommand("NUCLEIC");
                remove.addActionListener(this);
                remove.setAlignmentX(Button.CENTER_ALIGNMENT);
                comboPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
                comboPanel.add(acidComboBox);
                comboPanel.add(remove);
                optionValuesPanel.add(comboPanel);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                optionValuesPanel.add(acidScrollPane);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                JButton button = new JButton("Reset");
                button.setActionCommand("NUCLEIC");
                button.addActionListener(this);
                button.setAlignmentX(Button.CENTER_ALIGNMENT);
                optionValuesPanel.add(button);
                optionValuesPanel.add(Box.createRigidArea(new Dimension(0, 5)));
                acidTextArea.setText("");
                acidTextField.setText("");
            } else if (swing.equalsIgnoreCase("SYSTEMS")) {
                // SYSTEMS allows selection of an open system
                JComboBox<FFXSystem> jcb = new JComboBox<>(mainPanel.getHierarchy().getNonActiveSystems());
                jcb.setSize(jcb.getMaximumSize());
                jcb.addActionListener(this);
                optionValuesPanel.add(jcb);
            }
            // Set up a Conditional for this Option
            if (conditional != null) {
                isEnabled = false;
                String conditionalName = conditional.getAttribute("name");
                String conditionalValues = conditional.getAttribute("value");
                String cDescription = conditional.getAttribute("description");
                String cpostProcess = conditional.getAttribute("postProcess");
                if (conditionalName.toUpperCase().startsWith("KEYWORD")) {
                    optionPanel.setName(conditionalName);
                    String[] keywords = conditionalValues.split(" +");
                    if (activeSystem != null) {
                        Hashtable<String, Keyword> systemKeywords = activeSystem.getKeywords();
                        for (String key : keywords) {
                            if (systemKeywords.containsKey(key.toUpperCase())) {
                                isEnabled = true;
                            }
                        }
                    }
                } else if (conditionalName.toUpperCase().startsWith("VALUE")) {
                    isEnabled = true;
                    // the conditional options can be disabled/enabled.
                    for (int j = 0; j < optionValuesPanel.getComponentCount(); j++) {
                        JToggleButton jtb = (JToggleButton) optionValuesPanel.getComponent(j);
                        jtb.addActionListener(this);
                        jtb.setActionCommand("Conditional");
                    }
                    JPanel condpanel = new JPanel();
                    condpanel.setBorder(etchedBorder);
                    JLabel condlabel = new JLabel(cDescription);
                    condlabel.setEnabled(false);
                    condlabel.setName(conditionalValues);
                    JTextField condtext = new JTextField(10);
                    condlabel.setLabelFor(condtext);
                    if (cpostProcess != null) {
                        condtext.setName(cpostProcess);
                    }
                    condtext.setEnabled(false);
                    condpanel.add(condlabel);
                    condpanel.add(condtext);
                    conditionals.add(condlabel);
                    optionPanel.add(condpanel, BorderLayout.SOUTH);
                } else if (conditionalName.toUpperCase().startsWith("REFLECTION")) {
                    String[] condModifiers;
                    if (conditionalValues.equalsIgnoreCase("AltLoc")) {
                        condModifiers = activeSystem.getAltLocations();
                        if (condModifiers != null && condModifiers.length > 1) {
                            isEnabled = true;
                            bg = new ButtonGroup();
                            for (int j = 0; j < condModifiers.length; j++) {
                                JRadioButton jrbmi = new JRadioButton(condModifiers[j]);
                                jrbmi.addMouseListener(this);
                                bg.add(jrbmi);
                                optionValuesPanel.add(jrbmi);
                                if (j == 0) {
                                    jrbmi.setSelected(true);
                                }
                            }
                        }
                    } else if (conditionalValues.equalsIgnoreCase("Chains")) {
                        condModifiers = activeSystem.getChainNames();
                        if (condModifiers != null && condModifiers.length > 0) {
                            isEnabled = true;
                            for (int j = 0; j < condModifiers.length; j++) {
                                JRadioButton jrbmi = new JRadioButton(condModifiers[j]);
                                jrbmi.addMouseListener(this);
                                bg.add(jrbmi);
                                optionValuesPanel.add(jrbmi, j);
                            }
                        }
                    }
                }
            }
            optionPanel.add(optionValuesPanel, BorderLayout.CENTER);
            optionPanel.setPreferredSize(optionPanel.getPreferredSize());
            optionsTabbedPane.addTab(option.getAttribute("name"), optionPanel);
            optionsTabbedPane.setEnabledAt(optionsTabbedPane.getTabCount() - 1, isEnabled);
        }
    }
    optionsTabbedPane.setPreferredSize(optionsTabbedPane.getPreferredSize());
    commandPanel.setLayout(borderLayout);
    commandPanel.add(optionsTabbedPane, BorderLayout.CENTER);
    commandPanel.validate();
    commandPanel.repaint();
    loadLogSettings();
    statusLabel.setText("  " + createCommandInput());
}

Example 2 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeywordPanel method storeActive.

/**
 * Store the KeywordPanel's current keyword content in the activeSystem.
 */
public void storeActive() {
    synchronized (this) {
        if (currentSystem == null) {
            return;
        }
        // No changes
        if (!KeywordComponent.isKeywordModified()) {
            return;
        }
        Hashtable<String, Keyword> currentKeys = currentSystem.getKeywords();
        Hashtable<String, Keyword> newKeys = new Hashtable<String, Keyword>();
        for (KeywordComponent kc : keywordHashMap.values()) {
            if (kc.isActive() == true) {
                Keyword keywordData = null;
                if (currentKeys != null) {
                    keywordData = currentKeys.get(kc.getKeyword());
                }
                if (keywordData == null) {
                    keywordData = new Keyword(kc.getKeyword());
                } else {
                    keywordData.clear();
                }
                kc.getKeywordData(keywordData);
                newKeys.put(kc.getKeyword(), keywordData);
            }
        }
        Keyword comments = new Keyword("COMMENTS", commentStringBuffer.toString());
        newKeys.put("COMMENTS", comments);
        currentSystem.setKeywords(newKeys);
    }
}

Example 3 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeywordPanel method configToKeywords.

private void configToKeywords(FFXSystem newSystem) {
    CompositeConfiguration properties = newSystem.getProperties();
    Hashtable<String, Keyword> keywordHash = new Hashtable<>();
    // Create the "Comments" property.
    Keyword keyword = new Keyword("COMMENTS");
    keywordHash.put("COMMENTS", keyword);
    // Loop over properties from the keyword file.
    Configuration config = properties.getConfiguration(0);
    if (config instanceof PropertiesConfiguration) {
        PropertiesConfiguration prop = (PropertiesConfiguration) config;
        Iterator<String> keys = prop.getKeys();
        while (keys.hasNext()) {
            String key = keys.next();
            if (keywordHash.contains(key)) {
                keyword = keywordHash.get(key);
                keyword.append(prop.getStringArray(key));
            } else {
                String[] values = prop.getStringArray(key);
                keyword = new Keyword(key, values);
                keywordHash.put(key, keyword);
            }
        }
    }
    newSystem.setKeywords(keywordHash);
}

Example 4 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeywordPanel method loadActive.

/**
 * <p>
 * loadActive</p>
 *
 * @param newSystem a {@link ffx.ui.FFXSystem} object.
 * @param newKeys a {@link java.util.Hashtable} object.
 * @param newKeyFile a {@link java.io.File} object.
 * @return a boolean.
 */
public boolean loadActive(FFXSystem newSystem, Hashtable<String, Keyword> newKeys, File newKeyFile) {
    synchronized (this) {
        // Store changes made to the current system (if any) first.
        if (currentKeys != null && KeywordComponent.isKeywordModified()) {
            if (currentSystem != null && currentSystem != newSystem) {
                storeActive();
            } else {
                saveChanges();
            }
        }
        // Clear previous values
        keyClear();
        // No keywords to load
        if (newKeys == null || newKeys.size() == 0) {
            return false;
        }
        currentSystem = newSystem;
        currentKeyFile = newKeyFile;
        currentKeys = newKeys;
        fileOpen = true;
        /*
             * Keys to remove are those entries not recognized by the FFX
             * Keyword Editor These keys are removed from the active System's
             * keyword Hashtable and appended to the generic "Comments"
             * KeywordData instance.
             */
        ArrayList<String> keysToRemove = new ArrayList<>();
        Keyword comments = currentKeys.get("COMMENTS");
        for (Keyword keyword : currentKeys.values()) {
            String label = keyword.getKeyword();
            Vector<String> data = keyword.getEntries();
            if (label.equals("COMMENTS")) {
                continue;
            }
            KeywordComponent tk = keywordHashMap.get(label.toUpperCase());
            // as a Comment
            if (tk == null) {
                keysToRemove.add(keyword.getKeyword());
                if (data.isEmpty()) {
                    comments.append(label);
                } else if (label.equalsIgnoreCase("MULTIPOLE")) {
                    int count = 5;
                    for (String entry : data) {
                        count++;
                        if (count > 5) {
                            comments.append(label + " " + entry);
                            count = 1;
                        } else {
                            comments.append(entry);
                        }
                    }
                } else if (label.equalsIgnoreCase("TORTORS")) {
                    int points = 0;
                    int count = 0;
                    for (String entry : data) {
                        count++;
                        if (count > points) {
                            String[] res = entry.split(" +");
                            int xres = Integer.parseInt(res[5]);
                            int yres = Integer.parseInt(res[5]);
                            points = xres * yres;
                            comments.append(label + " " + entry);
                            count = 0;
                        } else {
                            comments.append(entry);
                        }
                    }
                } else {
                    for (String entry : data) {
                        comments.append(label + " " + entry);
                    }
                }
                continue;
            }
            // doesn't have modifiers)
            if (data.isEmpty()) {
                tk.loadKeywordEntry(label);
            }
            // can be repeated)
            for (String s : data) {
                tk.loadKeywordEntry(s);
            }
        }
        // Load up the Comments
        Vector<String> entries = comments.getEntries();
        if (entries != null) {
            for (String s : entries) {
                if (s.length() > 1) {
                    if (!groupHashMap.containsKey(s.substring(1).toUpperCase().trim())) {
                        commentStringBuffer.append(s).append("\n");
                    }
                } else {
                    commentStringBuffer.append(s).append("\n");
                }
            }
        }
        // Keywords that aren't recognized have been turned into Comments
        for (String k : keysToRemove) {
            currentKeys.remove(k);
        }
        if (currentSystem != null) {
            currentSystem.setKeywords(currentKeys);
            currentSystem.setKeyFile(currentKeyFile);
        }
        loadKeywordGroup();
        return true;
    }
}

Example 5 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class MainPanel method createKeyFile.

/**
 * <p>
 * createKeyFile</p>
 *
 * @param system a {@link ffx.ui.FFXSystem} object.
 * @return a boolean.
 */
public boolean createKeyFile(FFXSystem system) {
    String message = new String("Please select a parameter file " + "and a TINKER Key file will be created.");
    String params = (String) JOptionPane.showInputDialog(this, message, "Parameter File", JOptionPane.QUESTION_MESSAGE, null, keywordPanel.getParamFiles(), null);
    if (params != null) {
        if (params.equalsIgnoreCase("Use an existing TINKER Key file")) {
            JFileChooser fc = resetFileChooser();
            fc.setDialogTitle("Choose a KEY File");
            fc.setCurrentDirectory(pwd);
            fc.setSelectedFile(null);
            fc.setFileFilter(keyFileFilter);
            int result = fc.showOpenDialog(this);
            if (result == JFileChooser.APPROVE_OPTION) {
                File keyfile = fc.getSelectedFile();
                if (keyfile.exists()) {
                    Hashtable<String, Keyword> keywordHash = KeyFilter.open(keyfile);
                    if (keywordHash != null) {
                        system.setKeywords(keywordHash);
                    } else {
                        return false;
                    }
                    system.setKeyFile(keyfile);
                    system.setForceField(null);
                    return true;
                }
            }
        } else {
            File tempFile = system.getFile();
            if (tempFile.getParentFile().canWrite()) {
                String path = system.getFile().getParent() + File.separatorChar;
                String keyFileName = system.getName() + ".key";
                File keyfile = new File(path + keyFileName);
                try {
                    FileWriter fw = new FileWriter(keyfile);
                    BufferedWriter bw = new BufferedWriter(fw);
                    bw.write("\n");
                    bw.write("# Force Field Selection\n");
                    String tempParm = keywordPanel.getParamPath(params);
                    if (tempParm.indexOf(" ") > 0) {
                        tempParm = "\"" + keywordPanel.getParamPath(params) + "\"";
                    }
                    bw.write("PARAMETERS        " + tempParm + "\n");
                    bw.close();
                    fw.close();
                    Hashtable<String, Keyword> keywordHash = KeyFilter.open(keyfile);
                    if (keywordHash != null) {
                        system.setKeywords(keywordHash);
                    } else {
                        return false;
                    }
                    system.setKeyFile(keyfile);
                    system.setForceField(null);
                    return true;
                } catch (Exception e) {
                    logger.warning("" + e);
                    message = new String("There was an error creating " + keyfile.getAbsolutePath());
                    JOptionPane.showMessageDialog(this, message);
                }
            } else {
                message = new String("Could not create a Key file because " + pwd.getAbsolutePath() + " is not writable");
                JOptionPane.showMessageDialog(this, message);
            }
        }
    }
    return false;
}