Example usage for org.dom4j.io SAXReader read

Introduction

In this page you can find the example usage for org.dom4j.io SAXReader read.

Prototype

public Document read(InputSource in) throws DocumentException

Source Link

Document

Reads a Document from the given InputSource using SAX

Usage

From source file:com.github.autoprimer3.AutoPrimer3Config.java

License:Open Source License

public LinkedHashSet<String> readTableFile(File xml) throws DocumentException {
    SAXReader reader = new SAXReader();
    Document dasXml = reader.read(xml);
    return readTableFile(dasXml);
}

From source file:com.github.autoprimer3.AutoPrimer3Config.java

License:Open Source License

public LinkedHashSet<String> readTableFile(File xml, String category)
        throws DocumentException, MalformedURLException {
    SAXReader reader = new SAXReader();
    Document dasXml = reader.read(xml);
    return readTableFile(dasXml, category);
}

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

License:Open Source License

public void connectToUcsc() throws DocumentException, MalformedURLException {
    SAXReader reader = new SAXReader();
    URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");
    //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");
    dasGenomeXml = reader.read(url);
    readDasGenomeXmlDocument();//from   w ww  .  j a  v a 2 s  .  c om
}

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

License:Open Source License

public Document getTableXmlDocument(String build) throws DocumentException, MalformedURLException {
    SAXReader reader = new SAXReader();
    URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/" + build + "/types");
    Document dasXml;/*from   w w w. ja v  a 2 s  . c o  m*/
    dasXml = reader.read(url);
    return dasXml;
}

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();
    }/* ww w .  j  a  va 2s .c  o  m*/
    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  ww w.j  a v a 2  s. com
        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 {/* ww  w .  jav  a 2 s . c  o m*/
        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.github.cutstock.utils.ResourceUtil.java

License:Apache License

private ResourceUtil() {
    SAXReader reader = new SAXReader();
    InputStream is = CutStockPlugin.class.getClassLoader().getResourceAsStream(DEF_RESOURCE);

    try {/* w  w  w .j av a 2  s  .  com*/
        if (is != null) {
            document = reader.read(is);
        } else {
            throw new Exception("resource not found");
        }
    } catch (DocumentException e) {
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:com.github.ipaas.ifw.util.XmlUtil.java

License:Apache License

/**
 * xml??map//w w w  .  j  a v a 2 s.c o  m
 * 
 * @param in
 *            -- xml?
 * @return -- map
 */
public static Map toMap(InputStream in) {

    try {
        SAXReader reader = new SAXReader();
        Document doc = reader.read(in);
        return toMap(doc.getRootElement());
    } catch (Exception ex) {
        throw new RuntimeException("?xml?map", ex);
    }
}

From source file:com.github.megatronking.svg.applet.graphics.VdParser.java

License:Apache License

VdTree parse(InputStream is, StringBuilder vdErrorLog) {
    final VdTree tree = new VdTree();
    try {/*from w ww . ja va  2s. c  o m*/
        SAXReader reader = new SAXReader();
        reader.setEntityResolver(new IgnoreDTDEntityResolver());
        tree.parse(reader.read(is));
    } catch (Exception e) {
        vdErrorLog.append(e.getMessage());
    }
    return tree;
}