Examples with XMLProducer beast.util.XMLProducer used on opensource projects

Example 1 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class BeautiDoc method toXML.

public String toXML() {
    Set<BEASTInterface> beastObjects = new HashSet<>();
    // for (BEASTObject beastObject : pluginmap.values()) {
    // String name = beastObject.getClass().getName();
    // if (!name.startsWith("beast.app.beauti")) {
    // beastObjects.add(beastObject);
    // }
    // }
    String xml = new XMLProducer().toXML(mcmc.get(), beastObjects);
    xml = xml.replaceFirst("<beast ", "<beast beautitemplate='" + templateName + "' beautistatus='" + getBeautiStatus() + "' ");
    return xml + "\n";
}

Example 2 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class XMLProducerTest method test_ThatNexusExamplesProduces.

// @Test
// public void test_ThatXmlExamplesProduces() {
// System.setProperty("java.only", "true");
// String dir = System.getProperty("user.dir") + "/examples";
// //String dir = "/tmp";
// List<String> exceptions = new ArrayList<String>();
// exceptions.add("testExponentialGrowth.xml");
// test_ThatXmlExamplesProduces(dir, exceptions);
// }
@Test
public void test_ThatNexusExamplesProduces() {
    try {
        String dirName = System.getProperty("user.dir") + "/examples/nexus";
        System.out.println("Test Nexus Examples in " + dirName);
        File exampleDir = new File(dirName);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".nex") || name.endsWith(".nxs");
            }
        });
        List<String> failedFiles = new ArrayList<>();
        for (String fileName : exampleFiles) {
            System.out.println("Processing " + fileName);
            NexusParser parser = new NexusParser();
            try {
                parser.parseFile(new File(dirName + "/" + fileName));
            } catch (Exception e) {
                System.out.println("ExampleNexusParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            XMLProducer producer = new XMLProducer();
            BEASTInterface o = parser.m_alignment;
            if (o != null) {
                String xml = producer.toXML(o);
                // FileWriter outfile = new FileWriter(new File("/tmp/XMLProducerTest.xml"));
                // outfile.write(xml);
                // outfile.close();
                XMLParser parser2 = new XMLParser();
                try {
                    BEASTInterface o2 = parser2.parseFragment(xml, false);
                    System.out.println(o2);
                } catch (Exception e) {
                    System.out.println("test_ThatNexusExamplesProduces::Failed for " + fileName + ": " + e.getMessage());
                    failedFiles.add(fileName);
                }
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\test_ThatNexusExamplesProduces::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\test_ThatNexusExamplesProduces::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 3 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class BEASTObjectDialog method main.

/**
 * rudimentary test *
 */
public static void main(String[] args) {
    BEASTObjectDialog dlg = null;
    try {
        if (args.length == 0) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel(new MCMC(), Runnable.class, null), null);
        } else if (args[0].equals("-x")) {
            StringBuilder text = new StringBuilder();
            String NL = System.getProperty("line.separator");
            Scanner scanner = new Scanner(new File(args[1]));
            try {
                while (scanner.hasNextLine()) {
                    text.append(scanner.nextLine() + NL);
                }
            } finally {
                scanner.close();
            }
            BEASTInterface beastObject = new beast.util.XMLParser().parseBareFragment(text.toString(), false);
            dlg = new BEASTObjectDialog(new BEASTObjectPanel(beastObject, beastObject.getClass(), null), null);
        } else if (args.length == 1) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[0]), null), null);
        } else if (args.length == 2) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[1]), null), null);
        } else {
            throw new IllegalArgumentException("Incorrect number of arguments");
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Usage: " + BEASTObjectDialog.class.getName() + " [-x file ] [class [type]]\n" + "where [class] (optional, default MCMC) is a BEASTObject to edit\n" + "and [type] (optional only if class is specified, default Runnable) the type of the BEASTObject.\n" + "for example\n" + "");
        System.exit(1);
    }
    dlg.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
    if (dlg.showDialog()) {
        BEASTInterface beastObject = dlg.m_panel.m_beastObject;
        String xml = new XMLProducer().modelToXML(beastObject);
        System.out.println(xml);
    }
}

Example 4 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class BEASTObjectPanel method main.

/**
 * rudimentary test *
 */
public static void main(String[] args) {
    init();
    BEASTObjectPanel pluginPanel = null;
    try {
        if (args.length == 0) {
            pluginPanel = new BEASTObjectPanel(new MCMC(), Runnable.class, null);
        } else if (args[0].equals("-x")) {
            StringBuilder text = new StringBuilder();
            String NL = System.getProperty("line.separator");
            Scanner scanner = new Scanner(new File(args[1]));
            try {
                while (scanner.hasNextLine()) {
                    text.append(scanner.nextLine() + NL);
                }
            } finally {
                scanner.close();
            }
            BEASTInterface beastObject = new beast.util.XMLParser().parseBareFragment(text.toString(), false);
            pluginPanel = new BEASTObjectPanel(beastObject, beastObject.getClass(), null);
        } else if (args.length == 1) {
            pluginPanel = new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[0]), null);
        } else if (args.length == 2) {
            pluginPanel = new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[1]), null);
        } else {
            throw new IllegalArgumentException("Incorrect number of arguments");
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Usage: " + BEASTObjectPanel.class.getName() + " [-x file ] [class [type]]\n" + "where [class] (optional, default MCMC) is a BEASTObject to edit\n" + "and [type] (optional only if class is specified, default Runnable) the type of the BEASTObject.\n" + "for example\n" + "");
        System.exit(1);
    }
    pluginPanel.setVisible(true);
    if (pluginPanel.m_bOK) {
        BEASTInterface beastObject = pluginPanel.m_beastObject;
        String xml = new XMLProducer().modelToXML(beastObject);
        System.out.println(xml);
    }
}

Example 5 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class Document method toXML.

// parseNode
public String toXML() {
    XMLProducer xmlProducer = new XMLProducer();
    BEASTObjectSet pluginSet = calcPluginSet();
    if (pluginSet.m_plugins.get().size() == 1) {
        return xmlProducer.toXML(pluginSet.m_plugins.get().get(0));
    }
    return xmlProducer.toXML(pluginSet);
}