Example usage for org.dom4j Element getText

List of usage examples for org.dom4j Element getText

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Introduction

In this page you can find the example usage for org.dom4j Element getText.

Prototype

String getText();

Source Link

Document

Returns the text value of this element without recursing through child elements.

Usage

From source file:com.github.autoprimer3.GetUcscBuildsAndTables.java

License:Open Source License

public void readDasGenomeXmlDocument() {
    if (dasGenomeXml == null) {
        return;/*from w ww  .j ava  2s .  c om*/
    }
    Element root = dasGenomeXml.getRootElement();
    for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
        Element dsn = (Element) i.next();
        Element source = dsn.element("SOURCE");
        Attribute build = source.attribute("id");
        Element mapmaster = dsn.element("MAPMASTER");
        Element desc = dsn.element("DESCRIPTION");
        buildToMapMaster.put(build.getValue(), mapmaster.getText());
        buildToDescription.put(build.getValue(), desc.getText());
    }
}

From source file:com.github.autoprimer3.GetUcscBuildsAndTables.java

License:Open Source License

public String retrieveSequence(String build, String chrom, Integer start, Integer end)
        throws DocumentException, MalformedURLException {
    if (buildToDescription.isEmpty()) {
        this.connectToUcsc();
    }/*from w ww. j a  v a  2s  .c om*/
    if (!buildToMapMaster.containsKey(build)) {
        return null;
    } else {
        StringBuilder dna = new StringBuilder();
        URL genomeUrl = new URL(
                buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
        SAXReader reader = new SAXReader();
        Document dasXml;
        dasXml = reader.read(genomeUrl);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element seq = dsn.element("DNA");
            String text = seq.getText().replaceAll("\n", "");
            dna.append(text);
            //dna.append(seq.getText());
        }
        return dna.toString();

    }

}

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

SequenceFromDasUcsc() {//get build names and DAS urls
    try {//from  w  ww.  j  a v a 2 s.co  m
        SAXReader reader = new SAXReader();
        URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");//usa    
        //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");    
        Document dasXml;
        dasXml = reader.read(url);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element source = dsn.element("SOURCE");
            Attribute build = source.attribute("id");
            Element mapmaster = dsn.element("MAPMASTER");
            buildToMapMaster.put(build.getValue(), mapmaster.getText());
        }
    } catch (DocumentException | MalformedURLException ex) {
        //TO DO - handle (throw) this error properly
        ex.printStackTrace();
    }
}

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

public String retrieveSequence(String build, String chrom, Integer start, Integer end)
        throws DocumentException, MalformedURLException {
    if (!buildToMapMaster.containsKey(build)) {
        return null;
    } else {/*  w  w  w.  j  av  a  2  s  .  com*/
        String chromNumber = chrom.replaceFirst("chr", "");
        int length = 0;
        URL entryPointUrl = new URL(buildToMapMaster.get(build) + "/entry_points");
        Document dasXml;
        SAXReader reader = new SAXReader();
        dasXml = reader.read(entryPointUrl);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("ENTRY_POINTS"); i.hasNext();) {
            Element dsn = (Element) i.next();
            for (Iterator j = dsn.elementIterator("SEGMENT"); j.hasNext();) {
                Element seg = (Element) j.next();
                String id = seg.attributeValue("id");
                if (id != null && id.equals(chromNumber)) {
                    String stop = seg.attributeValue("stop");
                    length = Integer.valueOf(stop);
                    break;
                }
            }
        }
        if (length > 0) {
            end = end <= length ? end : length;
        }
        StringBuilder dna = new StringBuilder();
        URL genomeUrl = new URL(
                buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
        dasXml = reader.read(genomeUrl);
        root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element seq = dsn.element("DNA");
            String text = seq.getText().replaceAll("\n", "");
            dna.append(text);
            //dna.append(seq.getText());
        }
        return dna.toString();

    }

}

From source file:com.glaf.core.provider.ServiceProviderConfigReader.java

License:Apache License

private String getValue(Element parentElem, String name, boolean mandatory) {
    final Element valueElement = parentElem.element(name);
    if (mandatory) {
        Check.isNotNull(valueElement, "Element with name " + name + " not found");
    } else if (valueElement == null) {
        return null;
    }//www  . j  av  a 2 s.c  o m
    return valueElement.getText();
}

From source file:com.glaf.jbpm.util.CustomFieldInstantiator.java

License:Apache License

public static Object getValue(Class<?> type, Element propertyElement) {
    Object value = null;//ww  w . j  ava2s . c  om
    if (type == String.class) {
        value = propertyElement.getText();
    } else if ((type == Integer.class) || (type == int.class)) {
        value = Integer.parseInt(propertyElement.getTextTrim());
    } else if ((type == Long.class) || (type == long.class)) {
        value = Long.parseLong(propertyElement.getTextTrim());
    } else if ((type == Float.class) || (type == float.class)) {
        value = new Float(propertyElement.getTextTrim());
    } else if ((type == Double.class) || (type == double.class)) {
        value = Double.parseDouble(propertyElement.getTextTrim());
    } else if ((type == Boolean.class) || (type == boolean.class)) {
        value = Boolean.valueOf(propertyElement.getTextTrim());
    } else if ((type == Character.class) || (type == char.class)) {
        value = Character.valueOf(propertyElement.getTextTrim().charAt(0));
    } else if ((type == Short.class) || (type == short.class)) {
        value = Short.valueOf(propertyElement.getTextTrim());
    } else if ((type == Byte.class) || (type == byte.class)) {
        value = Byte.valueOf(propertyElement.getTextTrim());
    } else if (type.isAssignableFrom(java.util.Date.class)) {
        value = DateUtils.toDate(propertyElement.getTextTrim());
    } else if (type.isAssignableFrom(List.class)) {
        value = getCollectionValue(propertyElement, new java.util.ArrayList<Object>());
    } else if (type.isAssignableFrom(Set.class)) {
        value = getCollectionValue(propertyElement, new LinkedHashSet<Object>());
    } else if (type.isAssignableFrom(Collection.class)) {
        value = getCollectionValue(propertyElement, new java.util.ArrayList<Object>());
    } else if (type.isAssignableFrom(Map.class)) {
        value = getMapValue(propertyElement, new LinkedHashMap<Object, Object>());
    } else if (type == Element.class) {
        value = propertyElement;
    } else {
        try {
            Constructor<?> constructor = type.getConstructor(new Class[] { String.class });
            if ((propertyElement.isTextOnly()) && (constructor != null)) {
                value = constructor.newInstance(new Object[] { propertyElement.getTextTrim() });
            }
        } catch (Exception ex) {
            logger.error("couldn't parse the bean property value '" + propertyElement.asXML() + "' to a '"
                    + type.getName() + "'");
            throw new RuntimeException(ex);
        }
    }

    return value;
}

From source file:com.glaf.wechat.util.MessageUtils.java

License:Apache License

/**
 * ???XML//from  w  w  w  .  j a v a2 s  .  c  o  m
 * 
 * @param request
 * @return
 * @throws Exception
 */
@SuppressWarnings("unchecked")
public static Map<String, String> parseXml(HttpServletRequest request) {
    // ?HashMap
    Map<String, String> map = new java.util.concurrent.ConcurrentHashMap<String, String>();

    // request??
    InputStream inputStream = null;
    // ??
    SAXReader reader = new SAXReader();
    try {
        inputStream = request.getInputStream();

        Document document = reader.read(inputStream);
        // xml
        Element root = document.getRootElement();
        // ?
        List<Element> elementList = root.elements();

        // ???
        for (Element e : elementList) {
            map.put(e.getName(), e.getText());
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        throw new RuntimeException(ex);
    } finally {
        try {
            // ?
            if (inputStream != null) {
                inputStream.close();
                inputStream = null;
            }
        } catch (IOException ex) {
        }
    }

    return map;
}

From source file:com.globalsight.connector.mindtouch.util.MindTouchHelper.java

License:Apache License

/**
 * Parse tree xml from "getTreeXml(pageId)" method to form a tree.
 * //from www. j a v a  2  s.  co m
 * @param treeXml
 *            -- the tree information in XML format.
 * @return MindTouchPage
 */
@SuppressWarnings("rawtypes")
public MindTouchPage parseTreeXml(String treeXml) throws Exception {
    MindTouchPage rootMtp = null;
    Document doc = getDocument(treeXml);

    String id = null;
    String href = null;
    List pageNodes = doc.selectNodes("//page");
    List<MindTouchPage> allPages = new ArrayList<MindTouchPage>();
    Iterator it = pageNodes.iterator();
    while (it.hasNext()) {
        MindTouchPage mtp = new MindTouchPage();
        Element pageNode = (Element) it.next();
        // page id
        id = pageNode.attributeValue("id");
        mtp.setId(Long.parseLong(id));
        // href
        href = pageNode.attributeValue("href");
        mtp.setHref(href);
        // parent page id
        String parentName = null;
        if (pageNode.getParent() != null) {
            parentName = pageNode.getParent().getName();
        }
        if ("subpages".equals(parentName)) {
            String parentId = pageNode.getParent().getParent().attributeValue("id");
            mtp.setParentId(Long.parseLong(parentId));
        } else if ("pages".equals(parentName)) {
            rootMtp = mtp;
        }

        Iterator subNodeIt = pageNode.nodeIterator();
        while (subNodeIt.hasNext()) {
            Element node = (Element) subNodeIt.next();
            String name = node.getName();
            String text = node.getText();
            if ("uri.ui".equals(name)) {
                mtp.setUriUi(text);
            } else if ("title".equals(name)) {
                // title cannot have "<" and ">"
                text = text.replace("<", "&lt;").replace(">", "&gt;");
                // as json does not allow "\" and "/", remove them for displaying.
                text = text.replace("\\", "").replace("/", "");
                text = text.replace("%22", "\"");
                text = text.replace("%3F", "?");
                text = text.replace("%23", "#");
                text = text.replace("%3D", "=");
                text = text.replace("%26", "&");
                text = text.replace("%25", "%");
                mtp.setTitle(text);
            } else if ("path".equals(name)) {
                mtp.setPath(text);
            } else if ("date.created".equals(name)) {
                mtp.setDateCreated(text);
            }
        }
        allPages.add(mtp);
    }

    HashMap<Long, MindTouchPage> map = new HashMap<Long, MindTouchPage>();
    for (MindTouchPage mtp : allPages) {
        map.put(mtp.getId(), mtp);
    }

    for (MindTouchPage mtp : allPages) {
        long parentId = mtp.getParentId();
        MindTouchPage parent = map.get(parentId);
        if (parent != null) {
            parent.addSubPage(mtp);
        }
    }

    return rootMtp;
}

From source file:com.globalsight.connector.mindtouch.util.MindTouchHelper.java

License:Apache License

/**
 * Parse page info xml from "getPageInfo()" method.
 * //from   w ww  . j  av a2s  .  c  o m
 * @param pageInfoXml
 * @return MindTouchPage
 * @throws DocumentException
 */
@SuppressWarnings("rawtypes")
public MindTouchPage parsePageInfoXml(String pageInfoXml) throws DocumentException {
    MindTouchPage mtp = new MindTouchPage();
    Document doc = getDocument(pageInfoXml);

    String id = null;
    String href = null;
    List pageNodes = doc.selectNodes("//page");
    if (pageNodes != null && pageNodes.size() > 0) {
        Element pageNode = (Element) pageNodes.get(0);
        // page id
        id = pageNode.attributeValue("id");
        mtp.setId(Long.parseLong(id));
        // href
        href = pageNode.attributeValue("href");
        mtp.setHref(href);

        String name = null;
        String text = null;
        Iterator subNodeIt = pageNode.nodeIterator();
        while (subNodeIt.hasNext()) {
            Element node = (Element) subNodeIt.next();
            name = node.getName();
            text = node.getText();
            if ("uri.ui".equals(name)) {
                mtp.setUriUi(text);
            } else if ("title".equals(name)) {
                mtp.setTitle(text);
            } else if ("path".equals(name)) {
                mtp.setPath(text);
            } else if ("date.created".equals(name)) {
                mtp.setDateCreated(text);
            }
        }
    }

    return mtp;
}

From source file:com.globalsight.everest.aligner.AlignerPackageOptions.java

License:Apache License

/**
 * Initializes this object from an XML string.
 *//*from   ww w. java  2s .  c o  m*/
public void init(String p_options) throws Exception {
    XmlParser parser = null;
    Document dom = null;
    Element elem;
    List nodes;

    clearFilePairs();
    clearExtensions();

    try {
        parser = XmlParser.hire();
        dom = parser.parseXml(p_options);

        Element root = dom.getRootElement();

        m_packageName = root.elementText("packageName");

        elem = (Element) root.selectSingleNode("//extractionOptions");
        m_extractionOptions.m_formatType = elem.elementText("formatType");
        m_extractionOptions.m_rules = elem.elementText("rules");
        m_extractionOptions.m_sourceEncoding = elem.elementText("sourceEncoding");
        m_extractionOptions.m_targetEncoding = elem.elementText("targetEncoding");
        m_extractionOptions.m_sourceLocale = elem.elementText("sourceLocale");
        m_extractionOptions.m_targetLocale = elem.elementText("targetLocale");

        nodes = root.selectNodes("//extractionOptions//extension");
        for (int i = 0, max = nodes.size(); i < max; i++) {
            elem = (Element) nodes.get(i);

            String ext = elem.getText();

            addExtension(ext);
        }

        nodes = root.selectNodes("//filePair");
        for (int i = 0, max = nodes.size(); i < max; i++) {
            elem = (Element) nodes.get(i);

            FilePair pair = new FilePair(elem.elementText("source"), elem.elementText("target"));

            addFilePair(pair);
        }

        elem = (Element) root.selectSingleNode("//alignerOptions");
        m_alignerOptions.m_ignoreFormatting = elem.elementText("ignoreFormatting");
    } finally {
        XmlParser.fire(parser);
    }
}