Examples with BEASTVersion2 beast.app.BEASTVersion2 used on opensource projects

Example 1 with BEASTVersion2

use of beast.app.BEASTVersion2 in project beast2 by CompEvol.

the class JSONProducer method toJSON.

public String toJSON(BEASTInterface beastObject, Collection<BEASTInterface> others) {
    try {
        StringBuffer buf = new StringBuffer();
        // buf.append("{\"version\": \"2.0\",\n\"namespace\": \"" + DEFAULT_NAMESPACE + "\",\n\n" +
        // "\"" + JSONParser.ANALYSIS_ELEMENT + "\": [\n");
        buf.append("{version: \"" + (new BEASTVersion2()).getMajorVersion() + "\",\nnamespace: \"" + DEFAULT_NAMESPACE + "\",\n\n" + XMLParser.BEAST_ELEMENT + ": [\n");
        // buf.append("\n\n");
        isDone = new HashSet<>();
        isInputsDone = new HashMap<>();
        IDs = new HashSet<>();
        indentCount = 1;
        List<BEASTInterface> priorityBeastObjects = new ArrayList<>();
        findPriorityBeastObjects(beastObject, priorityBeastObjects);
        for (BEASTInterface beastObject2 : priorityBeastObjects) {
            if (!isDone.contains(beastObject2)) {
                // name = name.substring(name.lastIndexOf('.') + 1).toLowerCase();
                beastObjectToJSON(beastObject2, BEASTInterface.class, buf, null, true);
                buf.append(",");
            }
        }
        buf.append("\n\n");
        beastObjectToJSON(beastObject, BEASTInterface.class, buf, null, true);
        String end = "\n]\n}";
        buf.append(end);
        String JSON = buf.toString();
        String[] nameSpaces = DEFAULT_NAMESPACE.split(":");
        for (String nameSpace : nameSpaces) {
            // JSON = JSON.replaceAll("\"spec\": \"" + nameSpace + ".", "\"spec\": \"");
            JSON = JSON.replaceAll("spec: \"" + nameSpace + ".", "spec: \"");
        }
        return JSON;
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
}

Example 2 with BEASTVersion2

use of beast.app.BEASTVersion2 in project beast2 by CompEvol.

the class LogComparator method main.

/**
 * main
 */
public static void main(String[] args) {
    LogAnalyser analyser1 = null;
    LogAnalyser analyser2 = null;
    try {
        if (args.length == 0) {
            BEASTVersion2 version = new BEASTVersion2();
            File file = Utils.getLoadFile("LogComparator " + version.getVersionString() + " - Select first log file to analyse", null, "BEAST log (*.log) Files", "log", "txt");
            if (file == null) {
                return;
            }
            analyser1 = new LogAnalyser(file.getAbsolutePath());
            file = Utils.getLoadFile("LogComparator " + version.getVersionString() + " - Select second log file to analyse", null, "BEAST log (*.log) Files", "log", "txt");
            if (file == null) {
                return;
            }
            analyser2 = new LogAnalyser(file.getAbsolutePath());
        } else {
            analyser1 = new LogAnalyser(args[0]);
            analyser2 = new LogAnalyser(args[1]);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    LogComparator logComparator = new LogComparator(analyser1, analyser2);
    logComparator.print(System.out, true);
}

Example 3 with BEASTVersion2

use of beast.app.BEASTVersion2 in project beast2 by CompEvol.

the class XMLProducer method toXML.

public String toXML(BEASTInterface beastObject, Collection<BEASTInterface> others) {
    try {
        StringBuffer buf = new StringBuffer();
        Set<String> requiredPacakges = getPackagesAndVersions(beastObject);
        String required = requiredPacakges.toString();
        required = required.substring(1, required.length() - 1);
        required = required.replaceAll(", ", ":");
        buf.append("<" + XMLParser.BEAST_ELEMENT + " version='" + new BEASTVersion2().getMajorVersion() + "'" + " required='" + required + "'" + " namespace='" + DEFAULT_NAMESPACE + "'>\n");
        for (String element : element2ClassMap.keySet()) {
            if (!reservedElements.contains(element)) {
                buf.append("<map name='" + element + "'>" + element2ClassMap.get(element) + "</map>\n");
            }
        }
        buf.append("\n\n");
        isDone = new HashSet<>();
        isInputsDone = new HashMap<>();
        IDs = new HashSet<>();
        indent = 0;
        beastObjectToXML(beastObject, buf, null, true);
        String endBeastString = "</" + XMLParser.BEAST_ELEMENT + ">";
        buf.append(endBeastString);
        // return buf.toString();
        // beautify XML hierarchy
        String xml = cleanUpXML(buf.toString(), m_sXMLBeuatifyXSL);
        // TODO: fix m_sIDRefReplacementXSL script to deal with nested taxon sets
        // String xml2 = cleanUpXML(xml, m_sIDRefReplacementXSL);
        String xml2 = xml;
        xml = findPlates(xml2);
        // beatify by applying name spaces to spec attributes
        String[] nameSpaces = DEFAULT_NAMESPACE.split(":");
        for (String nameSpace : nameSpaces) {
            xml = xml.replaceAll("spec=\"" + nameSpace + ".", "spec=\"");
        }
        buf = new StringBuffer();
        if (others.size() > 0) {
            for (BEASTInterface beastObject2 : others) {
                if (!IDs.contains(beastObject2.getID())) {
                    beastObjectToXML(beastObject2, buf, null, false);
                }
            }
        }
        int endIndex = xml.indexOf(endBeastString);
        String extras = buf.toString();
        // prevent double -- inside XML comment, this can happen in sequences
        extras = extras.replaceAll("--", "- - ");
        xml = // + "\n\n<!-- " + DO_NOT_EDIT_WARNING + " \n\n" +
        xml.substring(0, endIndex) + // extras +  "\n\n-->\n\n"
        endBeastString;
        xml = xml.replaceAll("xmlns=\"http://www.w3.org/TR/xhtml1/strict\"", "");
        xml = dedupName(xml);
        xml = sortTags(xml);
        // return buf2.toString();
        return xml;
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
}

Example 4 with BEASTVersion2

use of beast.app.BEASTVersion2 in project beast2 by CompEvol.

the class Beauti method main2.

public static Beauti main2(String[] args) {
    Utils6.startSplashScreen();
    Utils6.logToSplashScreen("Initialising BEAUti");
    try {
        ByteArrayOutputStream baos = null;
        for (String arg : args) {
            if (arg.equals("-v") || arg.equals("-version")) {
                System.out.println((new BEASTVersion2()).getVersionString());
                System.exit(0);
            }
            if (arg.equals("-h") || arg.equals("-help")) {
                System.out.println(usage());
                System.exit(0);
            }
            if (arg.equals("-capture")) {
                final PrintStream beautiLog = System.err;
                baos = new ByteArrayOutputStream() {

                    @Override
                    public synchronized void write(byte[] b, int off, int len) {
                        super.write(b, off, len);
                        beautiLog.write(b, off, len);
                    }

                    @Override
                    public synchronized void write(int b) {
                        super.write(b);
                        beautiLog.write(b);
                    }

                    @Override
                    public void write(byte[] b) throws java.io.IOException {
                        super.write(b);
                        beautiLog.write(b);
                    }

                    @Override
                    public void flush() throws java.io.IOException {
                        super.flush();
                        beautiLog.flush();
                    }

                    @Override
                    public void close() throws IOException {
                        super.close();
                        beautiLog.close();
                    }
                };
                PrintStream p = new PrintStream(baos);
                System.setOut(p);
                System.setErr(p);
                Log.err = p;
                Log.warning = p;
                Log.info = p;
                Log.debug = p;
                Log.trace = p;
            }
        }
        PackageManager.loadExternalJars();
        // if (!Utils.isMac()) {
        Utils.loadUIManager();
        // }
        BEASTObjectPanel.init();
        BeautiDoc doc = new BeautiDoc();
        BeautiDoc.baos = baos;
        if (doc.parseArgs(args) == ActionOnExit.WRITE_XML) {
            return null;
        }
        final Beauti beauti = new Beauti(doc);
        if (Utils.isMac() && Utils6.getMajorJavaVersion() == 8) {
            // Mac-only stuff
            try {
                URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
                Icon icon = null;
                if (url != null) {
                    icon = new ImageIcon(url);
                } else {
                    Log.warning.println("Unable to find image: " + ModelBuilder.ICONPATH + "beauti.png");
                }
                jam.framework.Application application = new jam.framework.MultiDocApplication(null, "BEAUti", "about", icon) {

                    @Override
                    protected JFrame getDefaultFrame() {
                        return null;
                    }

                    @Override
                    public void doQuit() {
                        beauti.a_quit.actionPerformed(null);
                    }

                    @Override
                    public void doAbout() {
                        beauti.a_about.actionPerformed(null);
                    }

                    @Override
                    public DocumentFrame doOpenFile(File file) {
                        return null;
                    }

                    @Override
                    public DocumentFrame doNew() {
                        return null;
                    }
                };
                jam.mac.Utils.macOSXRegistration(application);
            } catch (Exception e) {
            // ignore
            }
            try {
                Class<?> class_ = Class.forName("jam.maconly.OSXAdapter");
                Method method = class_.getMethod("enablePrefs", boolean.class);
                method.invoke(null, false);
            } catch (java.lang.NoSuchMethodException e) {
            // ignore
            }
        }
        beauti.setUpPanels();
        beauti.currentTab = beauti.panels[0];
        beauti.hidePanels();
        beauti.addChangeListener(new ChangeListener() {

            @Override
            public void stateChanged(ChangeEvent e) {
                if (beauti.currentTab == null) {
                    beauti.currentTab = beauti.panels[0];
                }
                if (beauti.currentTab != null) {
                    if (!beauti.isInitialising) {
                        beauti.currentTab.config.sync(beauti.currentTab.partitionIndex);
                    }
                    BeautiPanel panel = (BeautiPanel) beauti.getSelectedComponent();
                    beauti.currentTab = panel;
                    beauti.refreshPanel();
                }
            }
        });
        beauti.setVisible(true);
        beauti.refreshPanel();
        JFrame frame = new JFrame("BEAUti 2: " + doc.getTemplateName() + " " + doc.getFileName());
        beauti.frame = frame;
        ImageIcon icon = Utils.getIcon(BEAUTI_ICON);
        if (icon != null) {
            frame.setIconImage(icon.getImage());
        }
        JMenuBar menuBar = beauti.makeMenuBar();
        frame.setJMenuBar(menuBar);
        if (doc.getFileName() != null || doc.alignments.size() > 0) {
            beauti.a_save.setEnabled(true);
            beauti.a_saveas.setEnabled(true);
        }
        frame.add(beauti);
        int size = UIManager.getFont("Label.font").getSize();
        frame.setSize(1024 * size / 13, 768 * size / 13);
        frame.setLocation(BEAUtiIntances * 10, BEAUtiIntances * 10);
        frame.setVisible(true);
        // check file needs to be save on closing main frame
        frame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
        BEAUtiIntances++;
        frame.addWindowListener(new WindowAdapter() {

            @Override
            public void windowClosing(WindowEvent e) {
                if (!beauti.quit()) {
                    return;
                }
                JFrame frame = (JFrame) e.getSource();
                frame.dispose();
                BEAUtiIntances--;
                if (BEAUtiIntances == 0) {
                    System.exit(0);
                }
            }
        });
        // Toolkit toolkit = Toolkit.getDefaultToolkit();
        // // PropertyChangeListener plistener = new
        // PropertyChangeListener() {
        // // @Override
        // // public void propertyChange(PropertyChangeEvent event) {
        // // Object o = event.getSource();
        // // Object o2 = event.getNewValue();
        // // event.getPropertyName();
        // // System.err.println(">>> " + event.getPropertyName() + " " +
        // o.getClass().getName() + "\n" + o2.getClass().getName());
        // // }
        // // };
        // AWTEventListener listener = new AWTEventListener() {
        // @Override
        // public void eventDispatched(AWTEvent event) {
        // Object o = event.getSource();
        // String label = "";
        // try {
        // Method method = o.getClass().getMethod("getText", Object.class);
        // label = (String) method.invoke(o);
        // } catch (Exception e) {
        // // TODO: handle exception
        // }
        // if (event.paramString().matches(".*\\([0-9]*,[0-9]*\\).*")) {
        // String s = event.paramString();
        // String sx = s.substring(s.indexOf('(') + 1);
        // String sy = sx;
        // sx = sx.substring(0, sx.indexOf(','));
        // sy = sy.substring(sy.indexOf(',') + 1, sy.indexOf(')'));
        // int x = Integer.parseInt(sx);
        // int y = Integer.parseInt(sy);
        // Component c = beauti.findComponentAt(x, y);
        // if (c != null) {
        // System.err.println(c.getClass().getName());
        // }
        // }
        // 
        // System.err.println(label + " " + event.paramString() + " " +
        // o.getClass().getName());
        // 
        // }
        // };
        // toolkit.addAWTEventListener(listener,
        // AWTEvent.ACTION_EVENT_MASK|AWTEvent.ITEM_EVENT_MASK|AWTEvent.MOUSE_EVENT_MASK);
        // // beauti.addPropertyChangeListener(plistener);
        Utils6.endSplashScreen();
        return beauti;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}

Example 5 with BEASTVersion2

use of beast.app.BEASTVersion2 in project beast2 by CompEvol.

the class EBSPAnalyser method main.

/**
 * @param args
 */
public static void main(String[] args) {
    BEASTVersion2 version = new BEASTVersion2();
    final String versionString = version.getVersionString();
    String nameString = "EBSP Analyser " + versionString;
    String aboutString = "<html><center><p>" + versionString + ", " + version.getDateString() + "</p>" + "<p>by<br>" + "<p>Joseph Heled and Remco Bouckaert</p>" + "<p>Department of Computer Science, University of Auckland<br>" + "<a href=\"mailto:jheled@gmail.com\">jheled@gmail.com</a></p>" + "<a href=\"mailto:remco@cs.auckland.ac.nz\">remco@cs.auckland.ac.nz</a></p>" + "<p>Part of the BEAST 2 package:<br>" + "<a href=\"http://beast2.cs.auckland.ac.nz/\">http://beast2.cs.auckland.ac.nz/</a></p>" + "</center></html>";
    try {
        EBSPAnalyser analyser = new EBSPAnalyser();
        if (args.length == 0) {
            Utils.loadUIManager();
            System.setProperty("com.apple.macos.useScreenMenuBar", "true");
            System.setProperty("apple.laf.useScreenMenuBar", "true");
            System.setProperty("apple.awt.showGrowBox", "true");
            // TODO: set up ICON
            java.net.URL url = EBSPAnalyser.class.getResource("images/EBSPAnalyser.png");
            javax.swing.Icon icon = null;
            if (url != null) {
                icon = new javax.swing.ImageIcon(url);
            }
            // ConsoleApplication consoleApp =
            new ConsoleApplication(nameString, aboutString, icon, true);
            analyser.printTitle(aboutString);
            String titleString = "<html><center><p>EBSPAnalyser<br>" + "Version " + version.getVersionString() + ", " + version.getDateString() + "</p></center></html>";
            EBSPAnalyserDialog dialog = analyser.new EBSPAnalyserDialog(new JFrame(), titleString, icon);
            if (!dialog.showDialog(nameString)) {
                return;
            }
            String[] args2 = dialog.getArgs();
            try {
                analyser.parseArgs(args2);
                analyser.run();
            } catch (Exception ex) {
                Log.err.println("Exception: " + ex.getMessage());
                ex.printStackTrace();
            }
            System.out.println("Finished - Quit program to exit.");
            while (true) {
                try {
                    Thread.sleep(1000);
                } catch (InterruptedException e) {
                    e.printStackTrace();
                }
            }
        } else {
            analyser.printTitle(aboutString);
            analyser.parseArgs(args);
            analyser.run();
        }
    } catch (Exception e) {
        System.out.println(getUsage());
        e.printStackTrace();
    }
}