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

Example 26 with XMLParser

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

the class CFOperatorTest method testCFSTX.

@Test
public void testCFSTX() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/CFOperatorTests/CFSubtreeExchangeTest5taxon.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("CFSubtreeExchangeTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("CFSubtreeExchangeTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("CFSubtreeExchangeTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("CFSubtreeExchangeTest5taxon.xml.state"));
}

Example 27 with XMLParser

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

the class CFOperatorTest method testCFWB.

@Test
public void testCFWB() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/CFOperatorTests/CFWilsonBaldingTest5taxon.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("CFWilsonBaldingTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("CFWilsonBaldingTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("CFWilsonBaldingTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("CFWilsonBaldingTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("CFWilsonBaldingTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("CFWilsonBaldingTest5taxon.xml.state"));
}

Example 28 with XMLParser

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

the class CFOperatorTest method testCFSTS.

@Test
public void testCFSTS() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/CFOperatorTests/CFSubtreeSlideTest5taxon.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("CFSubtreeSlideTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("CFSubtreeSlideTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("CFSubtreeSlideTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("CFSubtreeSlideTest5taxon.xml.state"));
}

Example 29 with XMLParser

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

the class MergeSplitTest method test.

@Test
public void test() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/mergeSplitTests/mergeSplitTest5taxon.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("mergeSplitTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("mergeSplitTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("mergeSplitTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("mergeSplitTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("mergeSplitTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("mergeSplitTest5taxon.xml.state"));
}

Example 30 with XMLParser

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

the class RegionShiftTest method testRegionShift.

@Test
public void testRegionShift() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/regionShiftTests/regionShiftTest5taxon.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("regionShiftTest5taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("regionShiftTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("regionShiftTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("regionShiftTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("regionShiftTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("regionShiftTest5taxon.xml.state"));
}