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

Example 36 with XMLParser

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

the class Document method reinit.

void reinit() {
    String xml = toXML();
    m_objects.clear();
    try {
        XMLParser parser = new XMLParser();
        BEASTInterface plugin0 = parser.parseBareFragment(xml, false);
        init(plugin0);
    } catch (Exception e) {
        e.printStackTrace();
    // TODO: handle exception
    }
}

Example 37 with XMLParser

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

the class Document method loadFile.

public void loadFile(String fileName) {
    m_objects.clear();
    XMLParser parser = new XMLParser();
    try {
        // fileName;
        StringBuilder xml = new StringBuilder();
        String NL = System.getProperty("line.separator");
        Scanner scanner = new Scanner(new File(fileName));
        try {
            while (scanner.hasNextLine()) {
                xml.append(scanner.nextLine() + NL);
            }
        } finally {
            scanner.close();
        }
        BEASTInterface plugin0 = parser.parseBareFragment(xml.toString(), false);
        init(plugin0);
    } catch (Exception e) {
        e.printStackTrace();
    // TODO: handle exception
    }
}

Example 38 with XMLParser

use of beast.util.XMLParser 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 39 with XMLParser

use of beast.util.XMLParser 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 40 with XMLParser

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

the class XMLElementNameTest method test_ReservedElementNames.

/**
 * test that Inputs that use reserved names have the correct type *
 */
@Test
public void test_ReservedElementNames() {
    // retrieve list of reserved names and their classes
    XMLParser parser = new XMLParser();
    HashMap<String, String> element2ClassMap = parser.getElement2ClassMap();
    // allow 'parameter' for any of the various parameter derivatives, not just RealParameter
    element2ClassMap.put("parameter", "beast.core.parameter.Parameter");
    // check each beastObject
    List<String> pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR);
    List<String> improperInputs = new ArrayList<String>();
    for (String beastObjectName : pluginNames) {
        try {
            BEASTObject beastObject = (BEASTObject) Class.forName(beastObjectName).newInstance();
            // check each input
            List<Input<?>> inputs = beastObject.listInputs();
            for (Input<?> input : inputs) {
                if (element2ClassMap.containsKey(input.getName())) {
                    if (beastObject.getClass() == null) {
                        input.determineClass(beastObject);
                    }
                    Class<?> type = input.getType();
                    String baseType = element2ClassMap.get(input.getName());
                    if (!isDerivedType(type, baseType)) {
                        improperInputs.add(beastObjectName + "." + input.getName());
                    }
                }
            }
        } catch (InstantiationException e) {
        // ignore
        } catch (Exception e) {
        // ignore
        }
    }
    if (improperInputs.size() > 0) {
        String str = improperInputs.toString();
        str = str.replaceAll(",", "\n");
        System.err.println("Reserved element names used for wrong types in:\n" + str);
    }
    // not activated till problem with naming is solved
    assertTrue("Reserved element names used for wrong types in: " + improperInputs.toString(), improperInputs.size() == 0);
}