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

Example 11 with XMLParser

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

the class CFOperatorTest method testCFCS.

@Test
public void testCFCS() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/CFOperatorTests/CFConversionSwapTest5taxon.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("CFConversionSwapTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("CFConversionSwapTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("CFConversionSwapTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("CFConversionSwapTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("CFConversionSwapTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("CFConversionSwapTest5taxon.xml.state"));
}

Example 12 with XMLParser

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

the class RegionShiftTest method testBoundaryShift.

@Test
public void testBoundaryShift() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/regionShiftTests/boundaryShiftTest5taxon.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("boundaryShiftTest5taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("boundaryShiftTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("boundaryShiftTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("boundaryShiftTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("boundaryShiftTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("boundaryShiftTest5taxon.xml.state"));
}

Example 13 with XMLParser

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

the class SimulatedACGTest method test5TaxonSerialSampling.

@Test
public void test5TaxonSerialSampling() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/ACGsimulations/simulateACGs5taxonSerialSampling.xml"));
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.909, 1e-2));
    expectations.add(new Expectation("acg.CFlength", 4.655, 1e-2));
    expectations.add(new Expectation("acg.nConv", 23.381, 5e-2));
    LogAnalyser logAnalyser = new LogAnalyser("simulateACGs5taxonSerialSampling.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("simulateACGs5taxonSerialSampling.stats"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonSerialSampling.converted"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonSerialSampling.trees"));
}

Example 14 with XMLParser

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

the class SimulatedACGTest method test5TaxonMultiLocus.

@Test
public void test5TaxonMultiLocus() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/ACGsimulations/simulateACGs5taxonMultiLocus.xml"));
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.917, 1e-2));
    expectations.add(new Expectation("acg.CFlength", 4.672, 1e-2));
    expectations.add(new Expectation("acg.nConv", 23.614, 5e-2));
    LogAnalyser logAnalyser = new LogAnalyser("simulateACGs5taxonMultiLocus.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("simulateACGs5taxonMultiLocus.stats"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonMultiLocus.converted"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonMultiLocus.trees"));
}

Example 15 with XMLParser

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

the class SimulatedACGTest method test2Taxon.

@Test
public void test2Taxon() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/ACGsimulations/simulateACGs2taxon.xml"));
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.0, 1e-2));
    expectations.add(new Expectation("acg.CFlength", 2.0, 1e-2));
    expectations.add(new Expectation("acg.nConv", 10.0, 5e-2));
    LogAnalyser logAnalyser = new LogAnalyser("simulateACGs2taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("simulateACGs2taxon.stats"));
    Files.deleteIfExists(Paths.get("simulateACGs2taxon.converted"));
    Files.deleteIfExists(Paths.get("simulateACGs2taxon.trees"));
}