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

Example 41 with XMLParser

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

the class LogNormalDistributionModelTest method testCalcLogP2.

@Test
public void testCalcLogP2() throws Exception {
    // does the same as testCalcLogP(), but with by constructing object through XML
    String xml = "<input spec='beast.math.distributions.LogNormalDistributionModel' " + "offset='1200' " + "M='2000' " + "S='0.6' " + "meanInRealSpace='true'/>";
    RealParameter p = new RealParameter(new Double[] { 2952.6747000000014 });
    XMLParser parser = new XMLParser();
    LogNormalDistributionModel logNormal = (LogNormalDistributionModel) parser.parseBareFragment(xml, true);
    double f0 = logNormal.calcLogP(p);
    assertEquals(-7.880210654973873, f0, 1e-10);
}

Example 42 with XMLParser

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

the class ExampleXmlParsingTest method test_ThatXmlExamplesRun.

public void test_ThatXmlExamplesRun(String dir) {
    try {
        Logger.FILE_MODE = Logger.LogFileMode.overwrite;
        System.out.println("Test that XML Examples run in " + dir);
        File exampleDir = new File(dir);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".xml");
            }
        });
        List<String> failedFiles = new ArrayList<String>();
        int seed = 127;
        for (String fileName : exampleFiles) {
            Randomizer.setSeed(seed);
            // need more than one to prevent trouble with multiMCMC logs
            seed += 10;
            System.out.println("Processing " + fileName);
            XMLParser parser = new XMLParser();
            try {
                beast.core.Runnable runable = parser.parseFile(new File(dir + "/" + fileName));
                if (runable instanceof MCMC) {
                    MCMC mcmc = (MCMC) runable;
                    mcmc.setInputValue("preBurnin", 0);
                    mcmc.setInputValue("chainLength", 1000l);
                    mcmc.run();
                }
            } catch (Exception e) {
                System.out.println("ExampleXmlParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatXmlExamplesRun::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("SUCCESS!!!");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
        ;
    }
}

Example 43 with XMLParser

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

the class ResumeTest method test_ThatXmlExampleResumes.

@Test
public void test_ThatXmlExampleResumes() throws Exception {
    Randomizer.setSeed(127);
    Logger.FILE_MODE = Logger.LogFileMode.overwrite;
    String dir = System.getProperty("user.dir") + "/examples";
    String fileName = dir + "/" + XML_FILE;
    System.out.println("Processing " + fileName);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runable = parser.parseFile(new File(fileName));
    runable.setStateFile("tmp.state", false);
    if (runable instanceof MCMC) {
        MCMC mcmc = (MCMC) runable;
        mcmc.setInputValue("preBurnin", 0);
        mcmc.setInputValue("chainLength", 1000l);
        mcmc.run();
    }
    System.out.println("Done " + fileName);
    System.out.println("Resuming " + fileName);
    Logger.FILE_MODE = Logger.LogFileMode.resume;
    parser = new XMLParser();
    runable = parser.parseFile(new File(fileName));
    runable.setStateFile("tmp.state", true);
    if (runable instanceof MCMC) {
        MCMC mcmc = (MCMC) runable;
        mcmc.setInputValue("preBurnin", 0);
        mcmc.setInputValue("chainLength", 1000l);
        mcmc.run();
    }
    System.out.println("Done " + fileName);
}

Example 44 with XMLParser

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

the class XMLProducerTest method test_ThatXmlExamplesProduces.

/**
 * parse all XML files in the given directory, then produce XML from it, and see if the produced XML still parses *
 */
public void test_ThatXmlExamplesProduces(String dir, List<String> exceptions) {
    try {
        Randomizer.setSeed(127);
        Logger.FILE_MODE = Logger.LogFileMode.overwrite;
        System.out.println("Test XML Examples in " + dir);
        File exampleDir = new File(dir);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".xml");
            }
        });
        List<String> failedFiles = new ArrayList<String>();
        for (String fileName : exampleFiles) {
            if (exceptions.contains(fileName)) {
                System.out.println("Skipping exception " + fileName);
            } else {
                System.out.println("Processing " + fileName);
                XMLProducer producer = new XMLProducer();
                BEASTInterface o = null;
                try {
                    o = producer.parseFile(new File(dir + "/" + fileName));
                } catch (Exception e) {
                    o = null;
                }
                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 {
                        parser2.parseFragment(xml, false);
                    } catch (Exception e) {
                        System.out.println("test_ThatXmlExamplesProduces::Failed for " + fileName + ": " + e.getMessage());
                        failedFiles.add(fileName);
                    }
                }
                System.out.println("Done " + fileName);
            }
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatXmlExamplesProduces::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\ntest_ThatXmlExamplesProduces::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 45 with XMLParser

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

the class XMLTest method testAnnotatedConstructor2.

@Test
public void testAnnotatedConstructor2() throws Exception {
    List<Taxon> taxa = new ArrayList<>();
    taxa.add(new Taxon("first one"));
    taxa.add(new Taxon("second one"));
    AnnotatedRunnableTestClass t = new AnnotatedRunnableTestClass(3, taxa);
    XMLProducer producer = new XMLProducer();
    String xml = producer.toXML(t);
    assertEquals(3, (int) t.getParam1());
    FileWriter outfile = new FileWriter(new File("/tmp/XMLTest.xml"));
    outfile.write(xml);
    outfile.close();
    XMLParser parser = new XMLParser();
    BEASTInterface b = parser.parseFile(new File("/tmp/XMLTest.xml"));
    assertEquals(3, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
}