Examples with BEASTInterface beast.core.BEASTInterface used on opensource projects

Example 71 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLParser method createObject.

// checkType
BEASTInterface createObject(final Node node, final String classname) throws XMLParserException {
    // try the IDMap first
    final String id = getID(node);
    if (id != null) {
        if (IDMap.containsKey(id)) {
            final BEASTInterface beastObject = IDMap.get(id);
            if (checkType(classname, beastObject, node)) {
                return beastObject;
            }
            throw new XMLParserException(node, "id=" + id + ". Expected object of type " + classname + " instead of " + beastObject.getClass().getName(), 105);
        }
    }
    final String dRef = getIDRef(node);
    if (dRef != null) {
        // produce warning if there are other attributes than idref
        if (node.getAttributes().getLength() > 1) {
            // check if there are just 2 attributes and other attribute is 'name' and/or 'id'
            final int offset = (getAttribute(node, "id") == null ? 0 : 1) + (getAttribute(node, "name") == null ? 0 : 1);
            if (node.getAttributes().getLength() > 1 + offset) {
                Log.warning.println("Element " + node.getNodeName() + " found with idref='" + dRef + "'. All other attributes are ignored.\n");
            }
        }
        if (IDMap.containsKey(dRef)) {
            final BEASTInterface beastObject = IDMap.get(dRef);
            // this hack should stay in place, but should eventually (v2.5?) be removed.
            if (classname.equals("Alignment") || checkType(classname, beastObject, node)) {
                return beastObject;
            }
            checkType(classname, beastObject, node);
            throw new XMLParserException(node, "id=" + dRef + ". Expected object of type " + classname + " instead of " + beastObject.getClass().getName(), 106);
        } else if (IDNodeMap.containsKey(dRef)) {
            final BEASTInterface beastObject = createObject(IDNodeMap.get(dRef), classname);
            if (checkType(classname, beastObject, node)) {
                return beastObject;
            }
            throw new XMLParserException(node, "id=" + dRef + ". Expected object of type " + classname + " instead of " + beastObject.getClass().getName(), 107);
        }
        throw new XMLParserException(node, "Could not find object associated with idref " + dRef, 170);
    }
    // it's not in the ID map yet, so we have to create a new object
    String specClass = classname;
    final String elementName = node.getNodeName();
    if (element2ClassMap.containsKey(elementName)) {
        specClass = element2ClassMap.get(elementName);
    }
    final String spec = getAttribute(node, "spec");
    if (spec != null) {
        specClass = spec;
    }
    // if (specClass.indexOf("BEASTInterface") > 0) {
    // Log.info.println(specClass);
    // }
    String clazzName = null;
    // determine clazzName from specName, taking name spaces in account
    clazzName = resolveClass(specClass);
    if (clazzName == null) {
        // try to create the old-fashioned way by creating the class
        boolean isDone = false;
        for (final String nameSpace : nameSpaces) {
            try {
                if (!isDone) {
                    Class.forName(nameSpace + specClass);
                    clazzName = nameSpace + specClass;
                    isDone = true;
                }
            } catch (ClassNotFoundException e) {
            // class does not exist -- try another namespace
            }
        }
    }
    if (clazzName == null) {
        if (unavailablePacakges.length() > 2) {
            String msg = "Class " + specClass + " could not be found.\n" + (unavailablePacakges.contains(",") ? "This XML requires the following packages that are not installed: " : "This XML requires the following package that is not installed: ") + unavailablePacakges + "\n" + "See http://beast2.org/managing-packages/ for details on how to install packages.\n" + "Or perhaps there is a typo in spec and you meant " + XMLParserUtils.guessClass(specClass) + "?";
            throw new XMLParserException(node, msg, 1018);
        }
        throw new XMLParserException(node, "Class could not be found. Did you mean " + XMLParserUtils.guessClass(specClass) + "?", 1017);
    // throw new ClassNotFoundException(specClass);
    }
    // sanity check
    try {
        Class<?> clazz = Class.forName(clazzName);
        if (!BEASTInterface.class.isAssignableFrom(clazz)) {
            throw new XMLParserException(node, "Expected object to be instance of BEASTObject", 108);
        }
    } catch (ClassNotFoundException e1) {
        // should never happen since clazzName is in the list of classes collected by the PackageManager
        e1.printStackTrace();
        throw new RuntimeException(e1);
    }
    // process inputs
    List<NameValuePair> inputInfo = parseInputs(node, clazzName);
    BEASTInterface beastObject = createBeastObject(node, id, clazzName, inputInfo);
    // initialise
    if (needsInitialisation) {
        try {
            beastObject.determindClassOfInputs();
            beastObject.validateInputs();
            beastObjectsWaitingToInit.add(beastObject);
            nodesWaitingToInit.add(node);
        } catch (IllegalArgumentException e) {
            // next lines for debugging only
            // beastObject.validateInputs();
            // beastObject.initAndValidate();
            e.printStackTrace();
            throw new XMLParserException(node, "validate and intialize error: " + e.getMessage(), 110);
        }
    }
    return beastObject;
}

Example 72 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLParser method main.

/**
 * parses file and formats it using the XMLProducer *
 */
public static void main(final String[] args) {
    try {
        // redirect stdout to stderr
        final PrintStream out = System.out;
        System.setOut(System.err);
        // parse the file
        final XMLParser parser = new XMLParser();
        final BEASTInterface beastObject = parser.parseFile(new File(args[0]));
        // restore stdout
        System.setOut(out);
        System.out.println(new XMLProducer().toXML(beastObject));
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 73 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLParser method parseBareFragments.

public List<BEASTInterface> parseBareFragments(final String xml, final boolean initialise) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    needsInitialisation = initialise;
    // parse the XML fragment into a DOM document
    final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    doc = factory.newDocumentBuilder().parse(new InputSource(new StringReader(xml)));
    doc.normalize();
    processPlates(doc, PLATE_ELEMENT);
    // find top level beast element
    final NodeList nodes = doc.getElementsByTagName("*");
    if (nodes == null || nodes.getLength() == 0) {
        throw new XMLParserException("Expected top level beast element in XML");
    }
    final Node topNode = nodes.item(0);
    initIDNodeMap(topNode);
    parseNameSpaceAndMap(topNode);
    final NodeList children = topNode.getChildNodes();
    final List<BEASTInterface> beastObjects = new ArrayList<>();
    for (int i = 0; i < children.getLength(); i++) {
        if (children.item(i).getNodeType() == Node.ELEMENT_NODE) {
            final BEASTInterface beastObject = createObject(children.item(i), BEAST_INTERFACE_CLASS);
            beastObjects.add(beastObject);
        }
    }
    initBEASTObjects();
    return beastObjects;
}

Example 74 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLParser method initBEASTObjects.

// parseTemplate
private void initBEASTObjects() throws XMLParserException {
    Node node = null;
    try {
        for (int i = 0; i < beastObjectsWaitingToInit.size(); i++) {
            final BEASTInterface beastObject = beastObjectsWaitingToInit.get(i);
            node = nodesWaitingToInit.get(i);
            beastObject.initAndValidate();
        }
    } catch (Exception e) {
        // next lines for debugging only
        // beastObject.validateInputs();
        // beastObject.initAndValidate();
        e.printStackTrace();
        throw new XMLParserException(node, "validate and intialize error: " + e.getMessage(), 110);
    }
}

Example 75 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BeautiBase method assertParameterCountInPriorIs.

void assertParameterCountInPriorIs(int i) {
    // count nr of parameters in Prior objects in prior
    // including those for prior distributions (Normal, etc)
    // useful to make sure they do (or do not) get linked
    Set<Function> parameters = new LinkedHashSet<>();
    CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
    for (Distribution p : prior.pDistributions.get()) {
        if (p instanceof Prior) {
            Prior p2 = (Prior) p;
            parameters.add(p2.m_x.get());
            for (BEASTInterface o : p2.distInput.get().listActiveBEASTObjects()) {
                if (o instanceof Parameter) {
                    parameters.add((Parameter<?>) o);
                }
            }
        }
    }
    System.err.println("Number of parameters in prior = " + parameters.size());
    if (i >= 0) {
        assertThat(parameters.size()).as("Expected " + i + " parameters in prior").isEqualTo(i);
    }
}