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

Example 6 with XMLParser

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

the class ExampleXmlParsingTest method test_ThatXmlExamplesParse.

public void test_ThatXmlExamplesParse(String dir) {
    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) {
            System.out.println("Processing " + fileName);
            XMLParser parser = new XMLParser();
            try {
                parser.parseFile(new File(dir + "/" + fileName));
            } 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_ThatXmlExamplesParse::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\ntest_ThatXmlExamplesParse::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 7 with XMLParser

use of beast.util.XMLParser 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 8 with XMLParser

use of beast.util.XMLParser in project bacter by tgvaughan.

the class AddRemoveDetourTest method test5Taxon.

@Test
public void test5Taxon() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/addRemoveDetourTests/addRemoveDetourTest5taxon.xml"));
    disableScreenLog(runnable);
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.606, 0.2));
    expectations.add(new Expectation("acg.CFlength", 4.181, 0.5));
    expectations.add(new Expectation("acg.nConv", 21.0, 0.5));
    LogAnalyser logAnalyser = new LogAnalyser("addRemoveDetourTest5taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon_trimmed.trees"));
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("addRemoveDetourTest5taxon.xml.state"));
}

Example 9 with XMLParser

use of beast.util.XMLParser in project bacter by tgvaughan.

the class AllOperatorTest method testMultiLocus.

@Test
public void testMultiLocus() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/allOperatorTests/allOperatorTestSSMultiLocus.xml"));
    disableScreenLog(runnable);
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.909, 0.2));
    expectations.add(new Expectation("acg.CFlength", 4.655, 0.5));
    expectations.add(new Expectation("acg.nConv", 23.381, 0.5));
    LogAnalyser logAnalyser = new LogAnalyser("allOperatorTestSSMultiLocus.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("allOperatorTestSSMultiLocus.stats"));
    Files.deleteIfExists(Paths.get("allOperatorTestSSMultiLocus.converted"));
    Files.deleteIfExists(Paths.get("allOperatorTestSSMultiLocus.trees"));
    Files.deleteIfExists(Paths.get("allOperatorTestSSMultiLocus.cf"));
    Files.deleteIfExists(Paths.get("allOperatorTestSSMultiLocus.xml.state"));
}

Example 10 with XMLParser

use of beast.util.XMLParser in project bacter by tgvaughan.

the class CFOperatorTest method testCFUniform.

@Test
public void testCFUniform() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/CFOperatorTests/CFUniformTest5taxon.xml"));
    disableScreenLog(runnable);
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.606, 0.2));
    expectations.add(new Expectation("acg.CFlength", 4.181, 0.5));
    expectations.add(new Expectation("acg.nConv", 21.0, 0.5));
    new LogAnalyser("CFUniformTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("CFUniformTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("CFUniformTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("CFUniformTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("CFUniformTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("CFUniformTest5taxon.xml.state"));
}