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

Example 16 with XMLParser

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

the class SimulatedACGTest method test5TaxonDynamicPopSize.

@Test
public void test5TaxonDynamicPopSize() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/ACGsimulations/simulateACGs5taxonDynamicPopSize.xml"));
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 8.840, 1e-2));
    expectations.add(new Expectation("acg.CFlength", 25.312, 1e-2));
    expectations.add(new Expectation("acg.nConv", 25.464, 5e-2));
    LogAnalyser logAnalyser = new LogAnalyser("simulateACGs5taxonDynamicPopSize.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("simulateACGs5taxonDynamicPopSize.stats"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonDynamicPopSize.converted"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxonDynamicPopSize.trees"));
}

Example 17 with XMLParser

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

the class DensityCalculator method main.

public static void main(String[] args) {
    if (args.length < 2) {
        System.out.println("Usage: DensityCalculator BEAST_xml_file state_file");
        System.exit(0);
    }
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = null;
    try {
        runnable = parser.parseFile(new File(args[0]));
    } catch (Exception e) {
        System.out.println("Encountered error while loading/parsing XML file.");
        e.printStackTrace();
    }
    if (runnable == null)
        System.exit(1);
    if (!(runnable instanceof MCMC)) {
        System.out.println("XML file does not seem to describe an MCMC analysis.");
        System.exit(1);
    }
    MCMC mcmc = (MCMC) runnable;
    Distribution posterior = mcmc.posteriorInput.get();
    State state = mcmc.startStateInput.get();
    state.setStateFileName(args[1]);
    try {
        state.restoreFromFile();
    } catch (Exception e) {
        System.out.println("Error reading state from file.");
        e.printStackTrace();
        System.exit(1);
    }
    try {
        state.robustlyCalcPosterior(posterior);
    } catch (Exception e) {
        e.printStackTrace();
    }
    reportTargetDensities(posterior);
}

Example 18 with XMLParser

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

the class OperatorTester method main.

public static void main(String[] args) {
    if (args.length < 4) {
        System.out.println("Usage: OperatorTester model.xml operator_ID state_file iterations");
        System.exit(0);
    }
    String modelFileName = args[0];
    String operatorID = args[1];
    String stateFileName = args[2];
    int Niter = Integer.parseInt(args[3]);
    XMLParser xmlParser = new XMLParser();
    Runnable runnable = null;
    try {
        runnable = xmlParser.parseFile(new File(modelFileName));
    } catch (Exception e) {
        System.out.println("Error parsing model XML file.");
        e.printStackTrace();
    }
    if (runnable == null)
        System.exit(1);
    if (!(runnable instanceof MCMC)) {
        System.out.println("XML file does not describe MCMC analysis.");
        System.exit(1);
    }
    MCMC mcmc = (MCMC) runnable;
    Operator operator = null;
    for (Operator thisOperator : mcmc.operatorsInput.get()) {
        if (thisOperator.getID().equals(operatorID)) {
            operator = thisOperator;
            break;
        }
    }
    if (operator == null) {
        System.out.println("Model does not include operator with ID " + operatorID + ".");
        System.exit(1);
    }
    State state = mcmc.startStateInput.get();
    state.setStateFileName(stateFileName);
    try {
        state.restoreFromFile();
    } catch (Exception e) {
        System.out.println("Error loading state from file.");
        e.printStackTrace();
        System.exit(1);
    }
    try {
        state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    } catch (Exception e) {
        System.out.println("Failed to calculate posterior.");
        System.exit(1);
    }
    Logger.FILE_MODE = Logger.LogFileMode.overwrite;
    for (Logger logger : mcmc.loggersInput.get()) {
        try {
            logger.everyInput.setValue(1, logger);
            logger.initAndValidate();
            logger.init();
            logger.log(0);
        } catch (Exception e) {
            System.out.println("Error initializing logger.");
            System.exit(1);
        }
    }
    try {
        state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    } catch (Exception e) {
        System.out.println("Failed to calculate posterior.");
        System.exit(1);
    }
    state.storeCalculationNodes();
    for (int i = 1; i < Niter; i++) {
        state.store(i);
        // for (Logger logger : mcmc.loggersInput.get())
        // logger.log(i);
        Double hgf = operator.proposal();
        if (hgf > Double.NEGATIVE_INFINITY) {
            state.checkCalculationNodesDirtiness();
            try {
                mcmc.posteriorInput.get().calculateLogP();
            } catch (Exception e) {
                System.out.println("Failed to calculate posterior.");
                System.exit(1);
            }
            for (Logger logger : mcmc.loggersInput.get()) logger.log(i);
            state.restore();
            state.restoreCalculationNodes();
            state.setEverythingDirty(false);
        } else {
            state.restore();
        }
    }
    for (Logger logger : mcmc.loggersInput.get()) logger.close();
}

Example 19 with XMLParser

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

the class AddRemoveRedundantTest method test5Taxon.

@Test
public void test5Taxon() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/addRemoveTests/addRemoveRedundantTest5taxon.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("addRemoveRedundantTest5taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("addRemoveRedundantTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("addRemoveRedundantTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("addRemoveRedundantTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("addRemoveRedundantTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("addRemoveRedundantTest5taxon.xml.state"));
}

Example 20 with XMLParser

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

the class AddRemoveTest method test5TaxonSerialSampling.

@Test
public void test5TaxonSerialSampling() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/addRemoveTests/addRemoveSerialSamplingTest5taxon.xml"));
    disableScreenLog(runnable);
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 2.07, 0.1));
    expectations.add(new Expectation("acg.CFlength", 5.00, 0.2));
    expectations.add(new Expectation("acg.nConv", 25.190, 1.0));
    LogAnalyser logAnalyser = new LogAnalyser("addRemoveSerialSamplingTest5taxon.stats", expectations);
    for (Expectation expectation : expectations) {
        assertTrue(expectation.isValid());
        assertTrue(expectation.isPassed());
    }
    Files.deleteIfExists(Paths.get("addRemoveSerialSamplingTest5taxon.stats"));
    Files.deleteIfExists(Paths.get("addRemoveSerialSamplingTest5taxon.converted"));
    Files.deleteIfExists(Paths.get("addRemoveSerialSamplingTest5taxon.trees"));
    Files.deleteIfExists(Paths.get("addRemoveSerialSamplingTest5taxon.cf"));
    Files.deleteIfExists(Paths.get("addRemoveSerialSamplingTest5taxon.xml.state"));
}