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

Example 6 with XMLProducer

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

the class Logger method init.

/**
 * initialise log, open file (if necessary) and produce header of log
 */
public void init() throws IOException {
    final boolean needsHeader = openLogFile();
    if (needsHeader) {
        if (modelInput.get() != null) {
            // print model at top of log
            String xml = new XMLProducer().modelToXML(modelInput.get());
            xml = "#" + xml.replaceAll("\\n", "\n#");
            m_out.println("#\n#model:\n#");
            m_out.println(xml);
            m_out.println("#");
        }
        ByteArrayOutputStream baos = null;
        PrintStream tmp = null;
        if (m_out == System.out) {
            tmp = m_out;
            baos = new ByteArrayOutputStream();
            m_out = new PrintStream(baos);
        }
        final ByteArrayOutputStream rawbaos = new ByteArrayOutputStream();
        final PrintStream out = new PrintStream(rawbaos);
        if (mode == LOGMODE.compound) {
            out.print("Sample\t");
        }
        for (final Loggable m_logger : loggerList) {
            m_logger.init(out);
        }
        // Remove trailing tab from header
        String header = rawbaos.toString().trim();
        if (sanitiseHeadersInput.get()) {
            m_out.print(sanitiseHeader(header));
        } else {
            m_out.print(header);
        }
        if (baos != null) {
            assert tmp == System.out;
            m_out = tmp;
            try {
                String logContent = baos.toString("ASCII");
                logContent = prettifyLogLine(logContent);
                m_out.print(logContent);
            } catch (UnsupportedEncodingException e) {
                e.printStackTrace();
            }
        }
        m_out.println();
    }
}

Example 7 with XMLProducer

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

the class SequenceSimulator method main.

// printUsageAndExit
@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {
        // parse arguments
        if (args.length < 2) {
            printUsageAndExit();
        }
        String fileName = args[0];
        int replications = Integer.parseInt(args[1]);
        PrintStream out = System.out;
        if (args.length == 3) {
            File file = new File(args[2]);
            out = new PrintStream(file);
        }
        // grab the file
        String xml = "";
        BufferedReader fin = new BufferedReader(new FileReader(fileName));
        while (fin.ready()) {
            xml += fin.readLine();
        }
        fin.close();
        // parse the xml
        XMLParser parser = new XMLParser();
        BEASTInterface beastObject = parser.parseFragment(xml, true);
        // find relevant objects from the model
        TreeLikelihood treeLikelihood = getTreeLikelihood(beastObject);
        if (treeLikelihood == null) {
            throw new IllegalArgumentException("No treelikelihood found in file. Giving up now.");
        }
        Alignment data = ((Input<Alignment>) treeLikelihood.getInput("data")).get();
        Tree tree = ((Input<Tree>) treeLikelihood.getInput("tree")).get();
        SiteModel pSiteModel = ((Input<SiteModel>) treeLikelihood.getInput("siteModel")).get();
        BranchRateModel pBranchRateModel = ((Input<BranchRateModel>) treeLikelihood.getInput("branchRateModel")).get();
        // feed to sequence simulator and generate leaves
        SequenceSimulator treeSimulator = new SequenceSimulator();
        treeSimulator.init(data, tree, pSiteModel, pBranchRateModel, replications);
        XMLProducer producer = new XMLProducer();
        Alignment alignment = treeSimulator.simulate();
        xml = producer.toRawXML(alignment);
        out.println("<beast version='2.0'>");
        out.println(xml);
        out.println("</beast>");
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 8 with XMLProducer

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

the class SequenceSimulator method run.

@Override
public void run() throws IllegalArgumentException, IllegalAccessException, IOException, XMLParserException {
    for (int i = 0; i < iterationsInput.get(); i++) {
        Alignment alignment = simulate();
        // Write output to stdout or file
        PrintStream pstream;
        if (m_outputFileName == null)
            pstream = System.out;
        else
            pstream = new PrintStream(m_outputFileName);
        pstream.println(new XMLProducer().toRawXML(alignment));
        for (MergeDataWith merge : mergeListInput.get()) {
            merge.process(alignment, i);
        }
    }
}

Example 9 with XMLProducer

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

the class MergeDataWith method process.

// initAndValidate
void process(Alignment data, int iteration) throws IOException, XMLParserException, IllegalArgumentException, IllegalAccessException {
    // read template
    String templateXML = BeautiDoc.load(templateFile);
    templateXML = templateXML.replaceAll("\\$\\(n\\)", iteration + "");
    XMLParser parser = new XMLParser();
    BEASTInterface b = parser.parseBareFragment(templateXML, false);
    // repalce alignment
    Alignment a = getAlignment(b);
    List<Sequence> sequences = a.sequenceInput.get();
    sequences.clear();
    sequences.addAll(data.sequenceInput.get());
    // write file
    String outputFile = outputFileInput.get();
    outputFile = outputFile.replaceAll("\\$\\(n\\)", iteration + "");
    FileWriter outfile = new FileWriter(outputFile);
    Set<BEASTInterface> beastObjects = new HashSet<>();
    String xml = new XMLProducer().toXML(b, beastObjects);
    outfile.write(xml);
    outfile.close();
}

Example 10 with XMLProducer

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

the class SimulatedAlignment method initAndValidate.

@Override
public void initAndValidate() {
    m_tree = m_treeInput.get();
    m_siteModel = m_pSiteModelInput.get();
    m_branchRateModel = m_pBranchRateModelInput.get();
    m_sequenceLength = m_sequenceLengthInput.get();
    m_stateCount = m_data.get().getMaxStateCount();
    m_categoryCount = m_siteModel.getCategoryCount();
    m_probabilities = new double[m_categoryCount][m_stateCount * m_stateCount];
    m_outputFileName = m_outputFileNameInput.get();
    sequenceInput.get().clear();
    simulate();
    // Write simulated alignment to disk if requested:
    if (m_outputFileName != null) {
        PrintStream pstream;
        try {
            pstream = new PrintStream(m_outputFileName);
            pstream.println(new XMLProducer().toRawXML(this));
            pstream.close();
        } catch (FileNotFoundException e) {
            throw new IllegalArgumentException(e.getMessage());
        }
    }
    super.initAndValidate();
}