Example usage for javax.xml.stream XMLStreamWriter writeStartDocument

List of usage examples for javax.xml.stream XMLStreamWriter writeStartDocument

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Introduction

In this page you can find the example usage for javax.xml.stream XMLStreamWriter writeStartDocument.

Prototype

public void writeStartDocument(String encoding, String version) throws XMLStreamException;

Source Link

Document

Write the XML Declaration.

Usage

From source file:XmlReaderToWriter.java

public static void write(XMLStreamReader xmlr, XMLStreamWriter writer) throws XMLStreamException {
    switch (xmlr.getEventType()) {
    case XMLEvent.START_ELEMENT:
        final String localName = xmlr.getLocalName();
        final String namespaceURI = xmlr.getNamespaceURI();
        if (namespaceURI != null && namespaceURI.length() > 0) {
            final String prefix = xmlr.getPrefix();
            if (prefix != null)
                writer.writeStartElement(prefix, localName, namespaceURI);
            else/*from   w  w w .  j a v  a  2 s .co m*/
                writer.writeStartElement(namespaceURI, localName);
        } else {
            writer.writeStartElement(localName);
        }

        for (int i = 0, len = xmlr.getNamespaceCount(); i < len; i++) {
            writer.writeNamespace(xmlr.getNamespacePrefix(i), xmlr.getNamespaceURI(i));
        }

        for (int i = 0, len = xmlr.getAttributeCount(); i < len; i++) {
            String attUri = xmlr.getAttributeNamespace(i);
            if (attUri != null)
                writer.writeAttribute(attUri, xmlr.getAttributeLocalName(i), xmlr.getAttributeValue(i));
            else
                writer.writeAttribute(xmlr.getAttributeLocalName(i), xmlr.getAttributeValue(i));
        }
        break;
    case XMLEvent.END_ELEMENT:
        writer.writeEndElement();
        break;
    case XMLEvent.SPACE:
    case XMLEvent.CHARACTERS:
        writer.writeCharacters(xmlr.getTextCharacters(), xmlr.getTextStart(), xmlr.getTextLength());
        break;
    case XMLEvent.PROCESSING_INSTRUCTION:
        writer.writeProcessingInstruction(xmlr.getPITarget(), xmlr.getPIData());
        break;
    case XMLEvent.CDATA:
        writer.writeCData(xmlr.getText());
        break;

    case XMLEvent.COMMENT:
        writer.writeComment(xmlr.getText());
        break;
    case XMLEvent.ENTITY_REFERENCE:
        writer.writeEntityRef(xmlr.getLocalName());
        break;
    case XMLEvent.START_DOCUMENT:
        String encoding = xmlr.getCharacterEncodingScheme();
        String version = xmlr.getVersion();

        if (encoding != null && version != null)
            writer.writeStartDocument(encoding, version);
        else if (version != null)
            writer.writeStartDocument(xmlr.getVersion());
        break;
    case XMLEvent.END_DOCUMENT:
        writer.writeEndDocument();
        break;
    case XMLEvent.DTD:
        writer.writeDTD(xmlr.getText());
        break;
    }
}

From source file:de.uni_koblenz.jgralab.utilities.rsa2tg.SchemaGraph2XMI.java

/**
 * This method creates the XMI file. Created content is:<br/>
 * <code>&lt;?xml version="{@link XMIConstants4SchemaGraph2XMI#XML_VERSION}" encoding="{@link XMIConstants4SchemaGraph2XMI#XML_ENCODING}"?&gt;<br/>
 * &lt;!-- content created by {@link SchemaGraph2XMI#createRootElement(XMLStreamWriter, SchemaGraph)} --&gt;
 * </code>/*from w  w w .  j a v  a2  s .c  o m*/
 * 
 * @param xmiName
 *            {@link String} the path of the XMI file
 * @param schemaGraph
 *            {@link SchemaGraph} to be converted into an XMI
 * @throws XMLStreamException
 * @throws IOException
 */
private void createXMI(String xmiName, SchemaGraph schemaGraph) throws XMLStreamException, IOException {
    Writer out = null;
    XMLStreamWriter writer = null;
    try {
        // create the XMLStreamWriter which creates the current xmi-file.
        out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(xmiName), "UTF-8"));
        XMLOutputFactory factory = XMLOutputFactory.newInstance();
        factory.setProperty("javax.xml.stream.isRepairingNamespaces", Boolean.TRUE);
        writer = factory.createXMLStreamWriter(out);

        // write the first line
        writer.writeStartDocument(XMIConstants4SchemaGraph2XMI.XML_ENCODING,
                XMIConstants4SchemaGraph2XMI.XML_VERSION);
        createRootElement(writer, schemaGraph);
        // write the end of the document
        writer.writeEndDocument();

        // close the XMLStreamWriter
        writer.flush();
        out.flush();
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        // no handling of exceptions, because they are throw as mentioned in
        // the declaration.
        if (writer != null) {
            writer.close();
        }
        if (out != null) {
            out.close();
        }
    }
}

From source file:Main.java

/**
 * Borrowed from org.apache.xml.security.test.stax.utils.XmlReaderToWriter
 *//*  ww  w . jav  a 2  s  .  c  o  m*/
public static void write(XMLStreamReader xmlr, XMLStreamWriter writer) throws XMLStreamException {
    switch (xmlr.getEventType()) {
    case XMLEvent.START_ELEMENT:
        final String localName = xmlr.getLocalName();
        final String namespaceURI = xmlr.getNamespaceURI();
        if (namespaceURI != null && namespaceURI.length() > 0) {
            final String prefix = xmlr.getPrefix();
            if (prefix != null) {
                writer.writeStartElement(prefix, localName, namespaceURI);
            } else {
                writer.writeStartElement(namespaceURI, localName);
            }
        } else {
            writer.writeStartElement(localName);
        }

        for (int i = 0, len = xmlr.getNamespaceCount(); i < len; i++) {
            String prefix = xmlr.getNamespacePrefix(i);
            if (prefix == null) {
                writer.writeDefaultNamespace(xmlr.getNamespaceURI(i));
            } else {
                writer.writeNamespace(prefix, xmlr.getNamespaceURI(i));
            }
        }

        for (int i = 0, len = xmlr.getAttributeCount(); i < len; i++) {
            final String attUri = xmlr.getAttributeNamespace(i);

            if (attUri != null && attUri.length() > 0) {
                final String prefix = xmlr.getAttributePrefix(i);
                if (prefix != null) {
                    writer.writeAttribute(prefix, attUri, xmlr.getAttributeLocalName(i),
                            xmlr.getAttributeValue(i));
                } else {
                    writer.writeAttribute(attUri, xmlr.getAttributeLocalName(i), xmlr.getAttributeValue(i));
                }
            } else {
                writer.writeAttribute(xmlr.getAttributeLocalName(i), xmlr.getAttributeValue(i));
            }

        }
        break;
    case XMLEvent.END_ELEMENT:
        writer.writeEndElement();
        break;
    case XMLEvent.SPACE:
    case XMLEvent.CHARACTERS:
        char[] text = new char[xmlr.getTextLength()];
        xmlr.getTextCharacters(0, text, 0, xmlr.getTextLength());
        writer.writeCharacters(text, 0, text.length);
        break;
    case XMLEvent.PROCESSING_INSTRUCTION:
        writer.writeProcessingInstruction(xmlr.getPITarget(), xmlr.getPIData());
        break;
    case XMLEvent.CDATA:
        writer.writeCData(xmlr.getText());
        break;
    case XMLEvent.COMMENT:
        writer.writeComment(xmlr.getText());
        break;
    case XMLEvent.ENTITY_REFERENCE:
        writer.writeEntityRef(xmlr.getLocalName());
        break;
    case XMLEvent.START_DOCUMENT:
        String encoding = xmlr.getCharacterEncodingScheme();
        String version = xmlr.getVersion();

        if (encoding != null && version != null) {
            writer.writeStartDocument(encoding, version);
        } else if (version != null) {
            writer.writeStartDocument(xmlr.getVersion());
        }
        break;
    case XMLEvent.END_DOCUMENT:
        writer.writeEndDocument();
        break;
    case XMLEvent.DTD:
        writer.writeDTD(xmlr.getText());
        break;
    }
}

From source file:jp.zippyzip.impl.GeneratorServiceImpl.java

/**
 * XML ??//from  www  .j a va2 s .co m
 * 
 * @param name "area" / "corp"
 * @param suffix "" / "c"
 */
void storeXml(String name, String suffix) {

    long timestamp = getLzhDao().getZipInfo().getTimestamp().getTime();
    Collection<City> cities = getCities();
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    ZipOutputStream zos = new ZipOutputStream(baos);
    ZipEntry entry = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_" + name + "_utf8.xml");
    entry.setTime(timestamp);
    int cnt = 0;

    try {

        zos.putNextEntry(entry);

        OutputStreamWriter writer = new OutputStreamWriter(zos, "UTF-8");
        XMLStreamWriter xwriter = XMLOutputFactory.newInstance().createXMLStreamWriter(writer);

        xwriter.writeStartDocument("UTF-8", "1.0");
        xwriter.writeStartElement("zips");
        xwriter.writeAttribute("type", name);

        for (City city : cities) {

            ParentChild pc = getParentChildDao().get(city.getCode() + suffix);

            if (pc == null) {
                continue;
            }

            for (String json : pc.getChildren()) {

                Zip zip = Zip.fromJson(json);

                xwriter.writeStartElement("zip");
                xwriter.writeAttribute("zip", zip.getCode());
                xwriter.writeAttribute("x0402", zip.getX0402());
                xwriter.writeAttribute("add1", zip.getAdd1());
                xwriter.writeAttribute("add2", zip.getAdd2());
                xwriter.writeAttribute("corp", zip.getCorp());
                xwriter.writeAttribute("add1Yomi", zip.getAdd1Yomi());
                xwriter.writeAttribute("add2Yomi", zip.getAdd2Yomi());
                xwriter.writeAttribute("corpYomi", zip.getCorpYomi());
                xwriter.writeAttribute("note", zip.getNote());
                xwriter.writeEndElement();
                ++cnt;
            }
        }

        xwriter.writeEndElement();
        xwriter.writeEndDocument();
        xwriter.flush();
        zos.closeEntry();
        zos.finish();
        getRawDao().store(baos.toByteArray(), name + "_utf8_xml.zip");
        log.info("count: " + cnt);

    } catch (XMLStreamException e) {
        log.log(Level.WARNING, "", e);
    } catch (FactoryConfigurationError e) {
        log.log(Level.WARNING, "", e);
    } catch (IOException e) {
        log.log(Level.WARNING, "", e);
    }
}

From source file:jp.zippyzip.impl.GeneratorServiceImpl.java

public void storeX0401Zip() {

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    long timestamp = getLzhDao().getZipInfo().getTimestamp().getTime();
    ZipOutputStream out = new ZipOutputStream(baos);
    Collection<Pref> prefs = getPrefs();
    ZipEntry tsv = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0401_utf8.txt");
    ZipEntry csv = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0401_sjis.csv");
    ZipEntry json = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0401_utf8.json");
    ZipEntry xml = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0401_utf8.xml");

    tsv.setTime(timestamp);//from  www  .j  a v a 2s .c  o m
    csv.setTime(timestamp);
    json.setTime(timestamp);
    xml.setTime(timestamp);

    try {

        out.putNextEntry(tsv);

        for (Pref pref : prefs) {

            out.write(new String(pref.getCode() + "\t" + pref.getName() + "\t" + pref.getYomi() + CRLF)
                    .getBytes("UTF-8"));
        }

        out.closeEntry();
        out.putNextEntry(csv);

        for (Pref pref : prefs) {

            out.write(new String(pref.getCode() + "," + pref.getName() + "," + pref.getYomi() + CRLF)
                    .getBytes("MS932"));
        }

        out.closeEntry();
        out.putNextEntry(json);

        OutputStreamWriter writer = new OutputStreamWriter(out, "UTF-8");
        JSONWriter jwriter = new JSONWriter(writer);

        jwriter.array();

        for (Pref pref : prefs) {

            jwriter.object().key("code").value(pref.getCode()).key("name").value(pref.getName()).key("yomi")
                    .value(pref.getYomi()).endObject();
        }

        jwriter.endArray();
        writer.flush();
        out.closeEntry();
        out.putNextEntry(xml);

        XMLStreamWriter xwriter = XMLOutputFactory.newInstance()
                .createXMLStreamWriter(new OutputStreamWriter(out, "UTF-8"));

        xwriter.writeStartDocument("UTF-8", "1.0");
        xwriter.writeStartElement("x0401s");

        for (Pref pref : prefs) {

            xwriter.writeStartElement("x0401");
            xwriter.writeAttribute("code", pref.getCode());
            xwriter.writeAttribute("name", pref.getName());
            xwriter.writeAttribute("yomi", pref.getYomi());
            xwriter.writeEndElement();
        }

        xwriter.writeEndElement();
        xwriter.writeEndDocument();
        xwriter.flush();
        out.closeEntry();
        out.finish();
        baos.flush();
        getRawDao().store(baos.toByteArray(), "x0401.zip");
        log.info("prefs: " + prefs.size());

    } catch (JSONException e) {
        log.log(Level.WARNING, "", e);
    } catch (XMLStreamException e) {
        log.log(Level.WARNING, "", e);
    } catch (FactoryConfigurationError e) {
        log.log(Level.WARNING, "", e);
    } catch (IOException e) {
        log.log(Level.WARNING, "", e);
    }
}

From source file:jp.zippyzip.impl.GeneratorServiceImpl.java

public void storeX0402Zip() {

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    long timestamp = getLzhDao().getZipInfo().getTimestamp().getTime();
    ZipOutputStream out = new ZipOutputStream(baos);
    Collection<City> cities = getCities();
    ZipEntry tsv = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0402_utf8.txt");
    ZipEntry csv = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0402_sjis.csv");
    ZipEntry json = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0402_utf8.json");
    ZipEntry xml = new ZipEntry(FILENAME_DATE_FORMAT.format(new Date(timestamp)) + "_x0402_utf8.xml");

    tsv.setTime(timestamp);/*from   www.j  a  v a  2s .c om*/
    csv.setTime(timestamp);
    json.setTime(timestamp);
    xml.setTime(timestamp);

    try {

        out.putNextEntry(tsv);

        for (City city : cities) {

            out.write(new String(city.getCode() + "\t" + city.getName() + "\t" + city.getYomi() + "\t"
                    + ((city.getExpiration().getTime() < new Date().getTime()) ? "" : "") + CRLF)
                            .getBytes("UTF-8"));
        }

        out.closeEntry();
        out.putNextEntry(csv);

        for (City city : cities) {

            out.write(new String(city.getCode() + "," + city.getName() + "," + city.getYomi() + ","
                    + ((city.getExpiration().getTime() < new Date().getTime()) ? "" : "") + CRLF)
                            .getBytes("MS932"));
        }

        out.closeEntry();
        out.putNextEntry(json);

        OutputStreamWriter writer = new OutputStreamWriter(out, "UTF-8");
        JSONWriter jwriter = new JSONWriter(writer);

        jwriter.array();

        for (City city : cities) {

            jwriter.object().key("code").value(city.getCode()).key("name").value(city.getName()).key("yomi")
                    .value(city.getYomi()).key("expired")
                    .value((city.getExpiration().getTime() < new Date().getTime()) ? "true" : "false")
                    .endObject();
        }

        jwriter.endArray();
        writer.flush();
        out.closeEntry();
        out.putNextEntry(xml);

        XMLStreamWriter xwriter = XMLOutputFactory.newInstance()
                .createXMLStreamWriter(new OutputStreamWriter(out, "UTF-8"));

        xwriter.writeStartDocument("UTF-8", "1.0");
        xwriter.writeStartElement("x0402s");

        for (City city : cities) {

            xwriter.writeStartElement("x0402");
            xwriter.writeAttribute("code", city.getCode());
            xwriter.writeAttribute("name", city.getName());
            xwriter.writeAttribute("yomi", city.getYomi());
            xwriter.writeAttribute("expired",
                    (city.getExpiration().getTime() < new Date().getTime()) ? "true" : "false");
            xwriter.writeEndElement();
        }

        xwriter.writeEndElement();
        xwriter.writeEndDocument();
        xwriter.flush();
        out.closeEntry();
        out.finish();
        baos.flush();
        getRawDao().store(baos.toByteArray(), "x0402.zip");
        log.info("cities: " + cities.size());

    } catch (JSONException e) {
        log.log(Level.WARNING, "", e);
    } catch (XMLStreamException e) {
        log.log(Level.WARNING, "", e);
    } catch (FactoryConfigurationError e) {
        log.log(Level.WARNING, "", e);
    } catch (IOException e) {
        log.log(Level.WARNING, "", e);
    }
}

From source file:com.github.lindenb.jvarkit.tools.vcfcmp.VcfCompareCallers.java

@Override
public Collection<Throwable> call() throws Exception {
    htsjdk.samtools.util.IntervalTreeMap<Boolean> capture = null;
    PrintWriter exampleWriter = null;
    XMLStreamWriter exampleOut = null;
    PrintStream pw = null;// ww w. j  ava 2s.co  m
    VcfIterator vcfInputs[] = new VcfIterator[] { null, null };
    VCFHeader headers[] = new VCFHeader[] { null, null };
    final List<String> args = getInputFiles();
    try {
        if (args.size() == 1) {
            LOG.info("Reading from stdin and " + args.get(0));
            vcfInputs[0] = VCFUtils.createVcfIteratorStdin();
            vcfInputs[1] = VCFUtils.createVcfIterator(args.get(0));
        } else if (args.size() == 2) {
            LOG.info("Reading from stdin and " + args.get(0) + " and " + args.get(1));
            vcfInputs[0] = VCFUtils.createVcfIterator(args.get(0));
            vcfInputs[1] = VCFUtils.createVcfIterator(args.get(1));
        } else {
            return wrapException(getMessageBundle("illegal.number.of.arguments"));
        }

        if (super.captureFile != null) {
            LOG.info("Reading " + super.captureFile);
            capture = super.readBedFileAsBooleanIntervalTreeMap(super.captureFile);
        }

        for (int i = 0; i < vcfInputs.length; ++i) {
            headers[i] = vcfInputs[i].getHeader();
        }
        /* dicts */
        final SAMSequenceDictionary dict0 = headers[0].getSequenceDictionary();
        final SAMSequenceDictionary dict1 = headers[1].getSequenceDictionary();
        final Comparator<VariantContext> ctxComparator;
        if (dict0 == null && dict1 == null) {
            ctxComparator = VCFUtils.createChromPosRefComparator();
        } else if (dict0 != null && dict1 != null) {
            if (!SequenceUtil.areSequenceDictionariesEqual(dict0, dict1)) {
                return wrapException(getMessageBundle("not.the.same.sequence.dictionaries"));
            }
            ctxComparator = VCFUtils.createTidPosRefComparator(dict0);
        } else {
            return wrapException(getMessageBundle("not.the.same.sequence.dictionaries"));
        }
        /* samples */
        Set<String> samples0 = new HashSet<>(headers[0].getSampleNamesInOrder());
        Set<String> samples1 = new HashSet<>(headers[1].getSampleNamesInOrder());
        Set<String> samples = new TreeSet<>(samples0);
        samples.retainAll(samples1);

        if (samples.size() != samples0.size() || samples.size() != samples1.size()) {
            LOG.warn("Warning: Not the same samples set. Using intersection of both lists.");
        }
        if (samples.isEmpty()) {
            return wrapException("No common samples");
        }

        Map<String, Counter<Category>> sample2info = new HashMap<String, Counter<Category>>(samples.size());
        for (String sampleName : samples) {
            sample2info.put(sampleName, new Counter<Category>());
        }

        if (super.exampleFile != null) {
            exampleWriter = new PrintWriter(exampleFile, "UTF-8");
            XMLOutputFactory xof = XMLOutputFactory.newFactory();
            exampleOut = xof.createXMLStreamWriter(exampleWriter);
            exampleOut.writeStartDocument("UTF-8", "1.0");
            exampleOut.writeStartElement("compare-callers");
        }

        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict0);
        VariantContext buffer[] = new VariantContext[vcfInputs.length];
        VariantContext prev[] = new VariantContext[vcfInputs.length];
        for (;;) {
            VariantContext smallest = null;
            //refill buffer
            for (int i = 0; i < vcfInputs.length; ++i) {
                if (buffer[i] == null && vcfInputs[i] != null) {
                    if (vcfInputs[i].hasNext()) {
                        buffer[i] = vcfInputs[i].peek();
                        /* check data are sorted */
                        if (prev[i] != null && ctxComparator.compare(prev[i], buffer[i]) > 0) {
                            return wrapException("Input " + (i + 1) + "/2 is not sorted"
                                    + (((i == 0 && dict0 == null) || (i == 1 && dict1 == null))
                                            ? "on chrom/pos/ref"
                                            : "on sequence dictionary")
                                    + ". got\n" + buffer[i] + "\nafter\n" + prev[i]);
                        }
                    } else {
                        vcfInputs[i].close();
                        vcfInputs[i] = null;
                    }
                }

                if (buffer[i] != null) {
                    if (smallest == null || ctxComparator.compare(buffer[i], smallest) < 0) {
                        smallest = buffer[i];
                    }
                }
            }

            if (smallest == null)
                break;

            VariantContext ctx0 = null;
            VariantContext ctx1 = null;
            Interval interval = null;

            if (buffer[0] != null && ctxComparator.compare(buffer[0], smallest) == 0) {
                prev[0] = progress.watch(vcfInputs[0].next());
                ctx0 = prev[0];
                buffer[0] = null;
                interval = new Interval(ctx0.getContig(), ctx0.getStart(), ctx0.getEnd());
            }
            if (buffer[1] != null && ctxComparator.compare(buffer[1], smallest) == 0) {
                prev[1] = progress.watch(vcfInputs[1].next());
                ctx1 = prev[1];
                buffer[1] = null;
                interval = new Interval(ctx1.getContig(), ctx1.getStart(), ctx1.getEnd());
            }
            boolean in_capture = true;
            if (capture != null && interval != null) {
                in_capture = capture.containsOverlapping(interval);
            }

            for (final String sampleName : sample2info.keySet()) {
                final Counter<Category> sampleInfo = sample2info.get(sampleName);
                Genotype g0 = (ctx0 == null ? null : ctx0.getGenotype(sampleName));
                Genotype g1 = (ctx1 == null ? null : ctx1.getGenotype(sampleName));
                if (g0 != null && (g0.isNoCall() || !g0.isAvailable()))
                    g0 = null;
                if (g1 != null && (g1.isNoCall() || !g1.isAvailable()))
                    g1 = null;

                if (g0 == null && g1 == null) {
                    watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.both_missing);
                    continue;
                } else if (g0 != null && g1 == null) {
                    if (!in_capture) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.off_target_only_1);
                        continue;
                    }
                    watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.unique_to_file_1);

                    if (ctx0.isIndel()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.unique_to_file_1_indel);
                    } else if (ctx0.isSNP()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.unique_to_file_1_snp);
                    }
                    continue;
                } else if (g0 == null && g1 != null) {
                    if (!in_capture) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.off_target_only_2);
                        continue;
                    }
                    watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.unique_to_file_2);
                    if (ctx1.isIndel()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.unique_to_file_2_indel);
                    } else if (ctx1.isSNP()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.unique_to_file_2_snp);
                    }
                    continue;
                } else {
                    if (!in_capture) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.off_target_both);
                        continue;
                    }
                    watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.common_context);
                    if (ctx0.isIndel() && ctx1.isIndel()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.common_context_indel);
                    } else if (ctx0.isSNP() && ctx1.isSNP()) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.common_context_snp);
                    }

                    if ((ctx0.hasID() && !ctx1.hasID()) || (!ctx0.hasID() && ctx1.hasID())
                            || (ctx0.hasID() && ctx1.hasID() && !ctx0.getID().equals(ctx1.getID()))) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.common_context_discordant_id);
                    }

                    if (g0.sameGenotype(g1)) {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo, Category.called_and_same);

                        if (g0.isHomRef()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_and_same_hom_ref);
                        }
                        if (g0.isHomVar()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_and_same_hom_var);
                        } else if (g0.isHet()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_and_same_het);
                        }
                    } else {
                        watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                Category.called_but_discordant);

                        if (g0.isHom() && g1.isHet()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_but_discordant_hom1_het2);
                        } else if (g0.isHet() && g1.isHom()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_but_discordant_het1_hom2);
                        } else if (g0.isHom() && g1.isHom()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_but_discordant_hom1_hom2);
                        } else if (g0.isHet() && g1.isHet()) {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_but_discordant_het1_het2);
                        } else {
                            watch(exampleOut, ctx0, ctx1, g0, g1, sampleName, sampleInfo,
                                    Category.called_but_discordant_others);
                        }
                    }

                }
            }
        }
        progress.finish();

        pw = openFileOrStdoutAsPrintStream();
        pw.print("#Sample");
        for (Category c : Category.values()) {
            pw.print('\t');
            pw.print(c.name());
        }
        pw.println();
        for (String sample : sample2info.keySet()) {
            Counter<Category> count = sample2info.get(sample);
            pw.print(sample);
            for (Category c : Category.values()) {
                pw.print('\t');
                pw.print(count.count(c));
            }
            pw.println();
            if (pw.checkError())
                break;
        }
        pw.flush();

        if (exampleOut != null) {
            exampleOut.writeEndElement();
            exampleOut.writeEndDocument();
            exampleOut.flush();
            exampleOut.close();
        }
        return RETURN_OK;
    } catch (Exception err) {
        return wrapException(err);
    } finally {
        if (getOutputFile() != null)
            CloserUtil.close(pw);
        CloserUtil.close(exampleWriter);
    }

}

From source file:nl.nn.adapterframework.soap.Wsdl.java

/**
 * Writes the WSDL to an output stream//from  w w w .  j  a v a  2  s.co  m
 * @param out
 * @param servlet  The servlet what is used as the web service (because this needs to be present in the WSDL)
 * @throws XMLStreamException
 * @throws IOException
 */
public void wsdl(OutputStream out, String servlet)
        throws XMLStreamException, IOException, ConfigurationException, NamingException {
    XMLStreamWriter w = WsdlUtils.getWriter(out, isIndent());

    w.writeStartDocument(XmlUtils.STREAM_FACTORY_ENCODING, "1.0");
    w.setPrefix(WSDL_NAMESPACE_PREFIX, WSDL_NAMESPACE);
    w.setPrefix(XSD_NAMESPACE_PREFIX, XSD_NAMESPACE);
    w.setPrefix(soapPrefix, soapNamespace);
    if (jmsActive) {
        if (esbSoap) {
            w.setPrefix(SOAP_JMS_NAMESPACE_PREFIX, ESB_SOAP_JMS_NAMESPACE);
            w.setPrefix(ESB_SOAP_JNDI_NAMESPACE_PREFIX, ESB_SOAP_JNDI_NAMESPACE);
        } else {
            w.setPrefix(SOAP_JMS_NAMESPACE_PREFIX, SOAP_JMS_NAMESPACE);
        }
    }
    w.setPrefix(getTargetNamespacePrefix(), getTargetNamespace());
    for (String prefix : namespaceByPrefix.keySet()) {
        w.setPrefix(prefix, namespaceByPrefix.get(prefix));
    }
    w.writeStartElement(WSDL_NAMESPACE, "definitions");
    {
        w.writeNamespace(WSDL_NAMESPACE_PREFIX, WSDL_NAMESPACE);
        w.writeNamespace(XSD_NAMESPACE_PREFIX, XSD_NAMESPACE);
        w.writeNamespace(soapPrefix, soapNamespace);
        if (esbSoap) {
            w.writeNamespace(ESB_SOAP_JNDI_NAMESPACE_PREFIX, ESB_SOAP_JNDI_NAMESPACE);
        }
        w.writeNamespace(getTargetNamespacePrefix(), getTargetNamespace());
        for (String prefix : namespaceByPrefix.keySet()) {
            w.writeNamespace(prefix, namespaceByPrefix.get(prefix));
        }
        w.writeAttribute("targetNamespace", getTargetNamespace());

        documentation(w);
        types(w);
        messages(w);
        portType(w);
        binding(w);
        service(w, servlet);
    }
    w.writeEndDocument();
    warnings(w);
    w.close();
}

From source file:nz.co.jsrsolutions.ds3.test.RetrieveTestData.java

public static void main(String[] args) {

    logger.info("Starting application [ rtd ] ...");

    try {//from  w w w. j  a v a  2 s  .  c  o m

        config.addConfiguration(
                new XMLConfiguration(RetrieveTestData.class.getClassLoader().getResource(CONFIG_FILENAME)));

        HierarchicalConfiguration appConfig = config.configurationAt(APPLICATION_CONFIG_ROOT);

        EodDataProvider eodDataProvider = null;

        OutputStream out = new FileOutputStream(OUTPUT_FILENAME);
        XMLOutputFactory factory = XMLOutputFactory.newInstance();
        XMLStreamWriter writer = factory.createXMLStreamWriter(out);

        eodDataProvider = EodDataProviderFactory.create(appConfig, EODDATA_PROVIDER_NAME);

        writer.writeStartDocument("utf-8", "1.0");
        writer.writeCharacters(NEWLINE);
        writer.writeComment("Test data for running DataScraper unit tests against");
        writer.writeCharacters(NEWLINE);

        writer.setPrefix(XML_PREFIX, XML_NAMESPACE_URI);

        writer.writeStartElement(XML_NAMESPACE_URI, TESTDATA_LOCALNAME);
        writer.writeNamespace(XML_PREFIX, XML_NAMESPACE_URI);
        writer.writeCharacters(NEWLINE);

        serializeExchanges(eodDataProvider, writer);
        serializeSymbols(eodDataProvider, writer);
        serializeQuotes(eodDataProvider, writer);

        writer.writeEndElement();
        writer.writeCharacters(NEWLINE);
        writer.writeEndDocument();
        writer.flush();
        writer.close();

    } catch (ConfigurationException ce) {

        logger.error(ce.toString());
        ce.printStackTrace();

    } catch (Exception e) {

        logger.error(e.toString());
        logger.error(e);

    }

    logger.info("Exiting application [ rtd ] ...");

}

From source file:org.activiti.bpmn.converter.export.DefinitionsRootExport.java

@SuppressWarnings("unchecked")
public static void writeRootElement(BpmnModel model, XMLStreamWriter xtw, String encoding) throws Exception {
    xtw.writeStartDocument(encoding, "1.0");

    // start definitions root element
    xtw.writeStartElement(ELEMENT_DEFINITIONS);
    xtw.setDefaultNamespace(BPMN2_NAMESPACE);
    xtw.writeDefaultNamespace(BPMN2_NAMESPACE);
    xtw.writeNamespace(XSI_PREFIX, XSI_NAMESPACE);
    xtw.writeNamespace(XSD_PREFIX, SCHEMA_NAMESPACE);
    xtw.writeNamespace(ACTIVITI_EXTENSIONS_PREFIX, ACTIVITI_EXTENSIONS_NAMESPACE);
    xtw.writeNamespace(BPMNDI_PREFIX, BPMNDI_NAMESPACE);
    xtw.writeNamespace(OMGDC_PREFIX, OMGDC_NAMESPACE);
    xtw.writeNamespace(OMGDI_PREFIX, OMGDI_NAMESPACE);
    for (String prefix : model.getNamespaces().keySet()) {
        if (!defaultNamespaces.contains(prefix) && StringUtils.isNotEmpty(prefix))
            xtw.writeNamespace(prefix, model.getNamespaces().get(prefix));
    }//  w w  w .ja  v  a 2s.  com
    xtw.writeAttribute(TYPE_LANGUAGE_ATTRIBUTE, SCHEMA_NAMESPACE);
    xtw.writeAttribute(EXPRESSION_LANGUAGE_ATTRIBUTE, XPATH_NAMESPACE);
    if (StringUtils.isNotEmpty(model.getTargetNamespace())) {
        xtw.writeAttribute(TARGET_NAMESPACE_ATTRIBUTE, model.getTargetNamespace());
    } else {
        xtw.writeAttribute(TARGET_NAMESPACE_ATTRIBUTE, PROCESS_NAMESPACE);
    }

    BpmnXMLUtil.writeCustomAttributes(model.getDefinitionsAttributes().values(), xtw, model.getNamespaces(),
            defaultAttributes);
}