Examples with XMLOutputter org.jdom.output.XMLOutputter used on opensource projects

Example 56 with XMLOutputter

use of org.jdom.output.XMLOutputter in project beast-mcmc by beast-dev.

the class AntigenicPlotter method writeKML.

/**
     * Discrete KML
     * @param fileName
     * @param labels
     * @param data
     * @param clusterIndices
     * @param clusterSizes
     */
private void writeKML(String fileName, String[] labels, double[][][] data, int[][] clusterIndices, int[][] clusterSizes) {
    int[] traceOrder = sortTraces(labels);
    Element traceSchema = new Element("Schema");
    traceSchema.setAttribute("id", "Cluster_Schema");
    traceSchema.addContent(new Element("SimpleField").setAttribute("name", "Label").setAttribute("type", "string").addContent(new Element("displayName").addContent("Label")));
    traceSchema.addContent(new Element("SimpleField").setAttribute("name", "Number").setAttribute("type", "double").addContent(new Element("displayName").addContent("Number")));
    traceSchema.addContent(new Element("SimpleField").setAttribute("name", "Year").setAttribute("type", "double").addContent(new Element("displayName").addContent("Year")));
    traceSchema.addContent(new Element("SimpleField").setAttribute("name", "State").setAttribute("type", "double").addContent(new Element("displayName").addContent("State")));
    Element virusSchema = new Element("Schema");
    virusSchema.setAttribute("id", "Virus_Schema");
    virusSchema.addContent(new Element("SimpleField").setAttribute("name", "Label").setAttribute("type", "string").addContent(new Element("displayName").addContent("Label")));
    virusSchema.addContent(new Element("SimpleField").setAttribute("name", "Year").setAttribute("type", "double").addContent(new Element("displayName").addContent("Year")));
    virusSchema.addContent(new Element("SimpleField").setAttribute("name", "Trace").setAttribute("type", "double").addContent(new Element("displayName").addContent("Trace")));
    //        final Element contourFolderElement = new Element("Folder");
    //        Element contourFolderNameElement = new Element("name");
    //        contourFolderNameElement.addContent("HPDs");
    //        contourFolderElement.addContent(contourFolderNameElement);
    final Element traceFolderElement = new Element("Folder");
    Element traceFolderNameElement = new Element("name");
    traceFolderNameElement.addContent("traces");
    traceFolderElement.addContent(traceFolderNameElement);
    final Element clustersFolderElement = new Element("Folder");
    Element clustersFolderNameElement = new Element("name");
    clustersFolderNameElement.addContent("clusters");
    clustersFolderElement.addContent(clustersFolderNameElement);
    Element documentNameElement = new Element("name");
    String documentName = fileName;
    if (documentName.endsWith(".kml"))
        documentName = documentName.replace(".kml", "");
    documentNameElement.addContent(documentName);
    final Element documentElement = new Element("Document");
    documentElement.addContent(documentNameElement);
    documentElement.addContent(traceSchema);
    documentElement.addContent(virusSchema);
    //        documentElement.addContent(hpdSchema);
    documentElement.addContent(clustersFolderElement);
    documentElement.addContent(traceFolderElement);
    //        documentElement.addContent(contourFolderElement);
    final Element rootElement = new Element("kml");
    rootElement.addContent(documentElement);
    Element traceElement = generateTraceElement(labels, data, traceOrder);
    traceFolderElement.addContent(traceElement);
    Element clustersElement = generateClusterElement(labels, data, clusterIndices, clusterSizes, traceOrder);
    clustersFolderElement.addContent(clustersElement);
    //        Element contourElement = generateKDEElement(0.95, labels, data, traceOrder);
    //        contourFolderElement.addContent(contourElement);
    PrintStream resultsStream;
    try {
        resultsStream = new PrintStream(new File(fileName));
        XMLOutputter xmlOutputter = new XMLOutputter(Format.getPrettyFormat().setTextMode(Format.TextMode.PRESERVE));
        xmlOutputter.output(rootElement, resultsStream);
    } catch (IOException e) {
        System.err.println("Error opening file: " + fileName);
        System.exit(-1);
    }
}

Example 57 with XMLOutputter

use of org.jdom.output.XMLOutputter in project beast-mcmc by beast-dev.

the class TreeKMLGenerator method main.

public static void main(String[] args) {
    String inputTreeFile = args[0];
    RootedTree tree = null;
    try {
        TreeImporter importer = new NexusImporter(new FileReader(inputTreeFile));
        tree = (RootedTree) importer.importNextTree();
    } catch (ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    TreeKMLGenerator generator = new TreeKMLGenerator(tree);
    Settings settings = new Settings(AnalysisType.CONTINUOUS);
    //        settings.getAltitudeTreeSettings().setTreeType(TreeType.ARC_TREE);
    //        settings.getAltitudeTreeSettings().getBranchStyle().setColorProperty("height");
    settings.getGroundTreeSettings().setTreeType(TreeType.SURFACE_TREE);
    settings.getGroundTreeSettings().getBranchStyle().setColorProperty("height");
    settings.setPlotAltitude(0);
    settings.setMostRecentDate(2003);
    //settings.setAgeCutOff(1995);
    settings.setTimeDivisionCount(0);
    settings.setTraitName("antigenic");
    settings.setLatitudeName("antigenic1");
    settings.setLongitudeName("antigenic2");
    try {
        BufferedWriter out = new BufferedWriter(new FileWriter(args[0] + ".kml"));
        Document doc = new Document(generator.generate(args[0], settings));
        try {
            XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
            outputter.output(doc, out);
        } catch (IOException e) {
            System.err.println(e);
        }
        out.close();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}

Example 58 with XMLOutputter

use of org.jdom.output.XMLOutputter in project cas by apereo.

the class AbstractSamlObjectBuilder method toDom.

/**
 * Convert the received jdom doc to a Document element.
 *
 * @param doc the doc
 * @return the org.w3c.dom. document
 */
private static org.w3c.dom.Document toDom(final Document doc) {
    try {
        final XMLOutputter xmlOutputter = new XMLOutputter();
        final StringWriter elemStrWriter = new StringWriter();
        xmlOutputter.output(doc, elemStrWriter);
        final byte[] xmlBytes = elemStrWriter.toString().getBytes(Charset.defaultCharset());
        final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        dbf.setNamespaceAware(true);
        dbf.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
        dbf.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
        dbf.setFeature("http://apache.org/xml/features/validation/schema/normalized-value", false);
        dbf.setFeature("http://javax.xml.XMLConstants/feature/secure-processing", true);
        dbf.setFeature("http://xml.org/sax/features/external-general-entities", false);
        dbf.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
        return dbf.newDocumentBuilder().parse(new ByteArrayInputStream(xmlBytes));
    } catch (final Exception e) {
        LOGGER.trace(e.getMessage(), e);
        return null;
    }
}

Example 59 with XMLOutputter

use of org.jdom.output.XMLOutputter in project cas by apereo.

the class AbstractSamlObjectBuilder method signSamlResponse.

/**
 * Sign SAML response.
 *
 * @param samlResponse the SAML response
 * @param privateKey   the private key
 * @param publicKey    the public key
 * @return the response
 */
public static String signSamlResponse(final String samlResponse, final PrivateKey privateKey, final PublicKey publicKey) {
    final Document doc = constructDocumentFromXml(samlResponse);
    if (doc != null) {
        final org.jdom.Element signedElement = signSamlElement(doc.getRootElement(), privateKey, publicKey);
        doc.setRootElement((org.jdom.Element) signedElement.detach());
        return new XMLOutputter().outputString(doc);
    }
    throw new IllegalArgumentException("Error signing SAML Response: Null document");
}

Example 60 with XMLOutputter

use of org.jdom.output.XMLOutputter in project vcell by virtualcell.

the class XmlUtil method writeXml.

/**
 * @param doc non-null
 * @param writer non-null
 * @param bTrimAllWhiteSpace remove whitespace from output
 * @throws IOException
 */
public static void writeXml(Document doc, Writer writer, boolean bTrimAllWhiteSpace) throws IOException {
    Objects.requireNonNull(doc);
    Objects.requireNonNull(writer);
    XMLOutputter xmlOut = new XMLOutputter();
    Format f = Format.getPrettyFormat();
    if (bTrimAllWhiteSpace) {
        f.setTextMode(Format.TextMode.TRIM_FULL_WHITE);
    }
    xmlOut.setFormat(f);
    xmlOut.output(doc, writer);
}