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

Example 1 with XMLParser

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

the class BeautiDoc method processBeautiConfig.

void processBeautiConfig(Document doc) throws XMLParserException, TransformerException {
    // find configuration elements, process and remove
    NodeList nodes = doc.getElementsByTagName("beauticonfig");
    Node topNode = doc.getElementsByTagName("*").item(0);
    String nameSpaceStr = XMLParser.getAttribute(topNode, "namespace");
    for (int configElementIndex = 0; configElementIndex < nodes.getLength(); configElementIndex++) {
        Node configElement = nodes.item(configElementIndex);
        String xml = nodeToString(configElement);
        XMLParser parser = new XMLParser();
        parser.setNameSpace(nameSpaceStr);
        parser.parseBareFragment(xml, true);
        configElement.getParentNode().removeChild(configElement);
    }
}

Example 2 with XMLParser

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

the class BeautiDoc method loadTemplate.

void loadTemplate(String xml) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    // load the template and its beauti configuration parts
    XMLParser parser = new XMLParser();
    BEASTObjectPanel.init();
    List<BEASTInterface> beastObjects = parser.parseTemplate(xml, new HashMap<>(), true);
    for (BEASTInterface beastObject : beastObjects) {
        if (beastObject instanceof beast.core.Runnable) {
            mcmc.setValue(beastObject, this);
        } else if (beastObject instanceof BeautiConfig) {
            beautiConfig = (BeautiConfig) beastObject;
            beautiConfig.setDoc(this);
        } else {
            Log.warning.println("template item " + beastObject.getID() + " is ignored");
        }
        BEASTObjectPanel.addPluginToMap(beastObject, this);
    }
}

Example 3 with XMLParser

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

the class BeautiDoc method extractSequences.

void extractSequences(String xml) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    // parse the XML fragment into a DOM document
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    Document doc = factory.newDocumentBuilder().parse(new InputSource(new StringReader(xml)));
    doc.normalize();
    // find top level beast element
    NodeList nodes = doc.getElementsByTagName("*");
    Node topNode = nodes.item(0);
    String beautiTemplate = XMLParser.getAttribute(topNode, "beautitemplate");
    if (beautiTemplate == null) {
        int choice = JOptionPane.showConfirmDialog(getFrame(), "This file does not appear to be generated by BEAUti. If you load it, unexpected behaviour may follow");
        if (choice != JOptionPane.OK_OPTION) {
            return;
        }
        // load standard template
        if (beautiConfig == null) {
            String templateXML = processTemplate(STANDARD_TEMPLATE);
            loadTemplate(templateXML);
        }
    } else {
        String templateXML = processTemplate(beautiTemplate + ".xml");
        loadTemplate(templateXML);
    }
    String beautiStatus = XMLParser.getAttribute(topNode, "beautistatus");
    if (beautiStatus == null) {
        beautiStatus = "";
    }
    autoSetClockRate = !beautiStatus.contains("noAutoSetClockRate");
    beauti.autoSetClockRate.setSelected(autoSetClockRate);
    allowLinking = beautiStatus.contains("allowLinking");
    beauti.allowLinking.setSelected(allowLinking);
    autoUpdateFixMeanSubstRate = !beautiStatus.contains("noAutoUpdateFixMeanSubstRate");
    beauti.autoUpdateFixMeanSubstRate.setSelected(autoUpdateFixMeanSubstRate);
    // parse file
    XMLParser parser = new XMLParser();
    BEASTInterface MCMC = parser.parseFragment(xml, true);
    mcmc.setValue(MCMC, this);
    BEASTObjectPanel.addPluginToMap(MCMC, this);
    // reconstruct all objects from templates
    try {
        CompoundDistribution posterior = (CompoundDistribution) ((beast.core.MCMC) mcmc.get()).posteriorInput.get();
        for (Distribution distr : posterior.pDistributions.get()) {
            if (distr.getID().equals("likelihood")) {
                for (Distribution likelihood : ((CompoundDistribution) distr).pDistributions.get()) {
                    if (likelihood instanceof GenericTreeLikelihood) {
                        GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) likelihood;
                        PartitionContext context = new PartitionContext(treeLikelihood);
                        try {
                            beautiConfig.partitionTemplate.get().createSubNet(context, false);
                        } catch (Exception e) {
                        // e.printStackTrace();
                        }
                        for (BeautiSubTemplate subTemplate : beautiConfig.subTemplates) {
                            try {
                                subTemplate.createSubNet(context, false);
                            } catch (Exception e) {
                            // e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
    } catch (Exception e) {
    // e.printStackTrace();
    }
    // MCMC = parser.parseFragment(xml, true);
    // mcmc.setValue(MCMC, this);
    // PluginPanel.addPluginToMap(MCMC, this);
    // if (xml.indexOf(XMLProducer.DO_NOT_EDIT_WARNING) > 0) {
    // int start = xml.indexOf(XMLProducer.DO_NOT_EDIT_WARNING);
    // int end = xml.lastIndexOf("-->");
    // xml = xml.substring(start, end);
    // xml = xml.replaceAll(XMLProducer.DO_NOT_EDIT_WARNING, "");
    // xml = "<beast namespace='" + XMLProducer.DEFAULT_NAMESPACE + "'>" + xml + "</beast>";
    // List<BEASTObject> beastObjects = parser.parseBareFragments(xml, true);
    // for (BEASTObject beastObject : beastObjects) {
    // PluginPanel.addPluginToMap(beastObject, this);
    // }
    // }
    // extract alignments
    determinePartitions();
}

Example 4 with XMLParser

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

the class BeautiSubTemplate method createSubNet.

private BEASTInterface createSubNet(PartitionContext context, /*BeautiDoc doc,*/
HashMap<String, BEASTInterface> idMap, boolean init) {
    subNetDepth++;
    if (subNetDepth > 10) {
        // looks like we cannot find what we are looking for
        throw new IllegalArgumentException("Potential programmer error: It looks like there is a required input that was not specified in the tenmplate");
    }
    // wrap in a beast element with appropriate name spaces
    String _sXML = "<beast version='2.0' \n" + "namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'>\n" + xml + "</beast>\n";
    // resolve alignment references
    _sXML = _sXML.replaceAll("idref=[\"']data['\"]", "idref='" + context.partition + "'");
    _sXML = _sXML.replaceAll("[\"']@data['\"]", "'@" + context.partition + "'");
    // ensure uniqueness of IDs
    // _sXML.replaceAll("\\$\\(n\\)", partition);
    _sXML = BeautiDoc.translatePartitionNames(_sXML, context);
    XMLParser parser = new XMLParser();
    parser.setRequiredInputProvider(doc, context);
    List<BEASTInterface> beastObjects = null;
    try {
        beastObjects = parser.parseTemplate(_sXML, idMap, true);
        for (BEASTInterface beastObject : beastObjects) {
            doc.addPlugin(beastObject);
            try {
                Log.warning.println("Adding " + beastObject.getClass().getName() + " " + beastObject);
            } catch (Exception e) {
                Log.err.println("Adding " + beastObject.getClass().getName());
            }
        }
        for (BeautiConnector connector : connectors) {
            if (init && connector.atInitialisationOnly()) {
                // ||
                doc.connect(connector, context);
            }
            // System.out.println(connector.sourceID + " == " + connector.targetID);
            if (connector.targetID != null && connector.targetID.equals("prior")) {
                Log.warning.println(">>> No description for connector " + connector.sourceID + " == " + connector.targetID);
            }
            if (connector.getTipText() != null) {
                String ID = BeautiDoc.translatePartitionNames(connector.sourceID, context);
                String tipText = BeautiDoc.translatePartitionNames(connector.getTipText(), context).trim().replaceAll("\\s+", " ");
                // System.out.println(ID + " -> " + tipText);
                doc.tipTextMap.put(ID, tipText);
            }
        }
        if (suppressedInputs.get() != null) {
            String[] inputs = suppressedInputs.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.suppressBEASTObjects.add(input);
            }
        }
        if (inlineInput.get() != null) {
            String[] inputs = inlineInput.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.inlineBEASTObject.add(input);
            }
        }
        if (collapsedInput.get() != null) {
            String[] inputs = collapsedInput.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.collapsedBEASTObjects.add(input);
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    if (mainID.equals("[top]")) {
        subNetDepth--;
        return beastObjects.get(0);
    }
    String id = mainID;
    // id.replaceAll("\\$\\(n\\)", partition);
    id = BeautiDoc.translatePartitionNames(id, context);
    BEASTInterface beastObject = doc.pluginmap.get(id);
    if (this == doc.beautiConfig.partitionTemplate.get()) {
        // HACK: need to make sure the subst model is of the correct type
        BEASTInterface treeLikelihood = doc.pluginmap.get("treeLikelihood." + context.partition);
        if (treeLikelihood != null && ((GenericTreeLikelihood) treeLikelihood).siteModelInput.get() instanceof SiteModel.Base) {
            SiteModel.Base siteModel = (SiteModel.Base) ((GenericTreeLikelihood) treeLikelihood).siteModelInput.get();
            SubstitutionModel substModel = siteModel.substModelInput.get();
            try {
                if (!siteModel.canSetSubstModel(substModel)) {
                    setUpSubstModel(siteModel, context);
                }
            } catch (Exception e) {
                setUpSubstModel(siteModel, context);
            }
        }
        // HACK2: rename file name for trace log if it has the default value
        Logger logger = (Logger) doc.pluginmap.get("tracelog");
        if (logger != null) {
            String fileName = logger.fileNameInput.get();
            if (fileName.startsWith("beast.") && treeLikelihood != null) {
                Alignment data = ((GenericTreeLikelihood) treeLikelihood).dataInput.get();
                while (data instanceof FilteredAlignment) {
                    data = ((FilteredAlignment) data).alignmentInput.get();
                }
                fileName = data.getID() + fileName.substring(5);
                try {
                    logger.fileNameInput.setValue(fileName, logger);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    }
    subNetDepth--;
    // System.err.println(new XMLProducer().toXML(beastObject));
    return beastObject;
}

Example 5 with XMLParser

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

the class BeautiBase method makeSureXMLParses.

void makeSureXMLParses() {
    warning("Make sure that XML that BEAUti produces parses");
    File XMLFile = new File(org.fest.util.Files.temporaryFolder() + "/x.xml");
    if (XMLFile.exists()) {
        XMLFile.delete();
    }
    saveFile("" + org.fest.util.Files.temporaryFolder(), "x.xml");
    // JFileChooserFixture fileChooser = findFileChooser().using(robot());
    // fileChooser.setCurrentDirectory(org.fest.util.Files.temporaryFolder());
    // fileChooser.selectFile(new File("x.xml")).approve();
    XMLParser parser = new XMLParser();
    XMLFile = new File(org.fest.util.Files.temporaryFolder() + "/x.xml");
    try {
        parser.parseFile(XMLFile);
    } catch (Exception e) {
        e.printStackTrace();
        assertThat(0).as("Parser exception: " + e.getMessage()).isEqualTo(1);
    }
}