Example usage for org.dom4j Element elementIterator

Introduction

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

Prototype

Iterator<Element> elementIterator();

Source Link

Document

Returns an iterator over all this elements child elements.

Usage

From source file:au.gov.ansto.bragg.process.parse.Parse.java

License:Open Source License

protected static List<OutConfiguration> getOutConfigurationList(final Element element, final String parentName)
        throws DocumentException {
    //      List<?> list = element.selectNodes("*");
    List<OutConfiguration> portList = new LinkedList<OutConfiguration>();
    for (Iterator<?> iter = element.elementIterator(); iter.hasNext();) {
        Element item = (Element) iter.next();
        portList.add((OutConfiguration) getPortConfiguration(item, "out", parentName));
    }/*  w ww  .  j  a  va 2 s  .co m*/
    return portList;
}

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From source file:au.gov.ansto.bragg.process.parse.Parse.java

License:Open Source License

protected static List<VarConfiguration> getVarConfigurationList(final Element element, final String parentName)
        throws DocumentException {
    List<VarConfiguration> portList = new LinkedList<VarConfiguration>();
    for (Iterator<?> iter = element.elementIterator(); iter.hasNext();) {
        Element item = (Element) iter.next();
        portList.add((VarConfiguration) getPortConfiguration(item, "var", parentName));
    }/*from   w  w w .  j a va2  s  .  c om*/
    return portList;
}

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From source file:au.gov.ansto.bragg.process.parse.Parse.java

License:Open Source License

protected static List<ConnectorConfiguration> getConnectorConfigurationList(final Element element,
        final String parentName) throws DocumentException {
    List<ConnectorConfiguration> connectorList = new LinkedList<ConnectorConfiguration>();
    for (Iterator<?> iter = element.elementIterator(); iter.hasNext();) {
        Element item = (Element) iter.next();
        connectorList.add((ConnectorConfiguration) getConnectorConfiguration(item, parentName));
    }/*  ww  w. j ava2  s  .co m*/
    return connectorList;
}

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From source file:au.gov.ansto.bragg.process.parse.Parse.java

License:Open Source License

protected static List<AgentConfiguration> getAgentConfigurationList(final Element element) {
    List<AgentConfiguration> agentConfigurationList = new ArrayList<AgentConfiguration>();
    for (Iterator<?> iter = element.elementIterator(); iter.hasNext();) {
        Element item = (Element) iter.next();
        agentConfigurationList.add((AgentConfiguration) getAgentConfiguration(item));
    }/*from  ww  w  .  j a  v a  2s .c o m*/
    return agentConfigurationList;
}

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From source file:bio.pih.genoogle.io.XMLConfigurationReader.java

/**
 * @return {@link List} of {@link AbstractSequenceDataBank} that are
 *         configured in the XML file./*w w w  .j a  v a2  s .  c  o  m*/
 */
@SuppressWarnings("unchecked")
public static List<AbstractSequenceDataBank> getDataBanks() throws IOException, InvalidConfigurationException {
    Element rootElement = doc.getRootElement();
    Element databanks = rootElement.element("databanks");

    if (databanks == null) {
        return null;
    }

    List<AbstractSequenceDataBank> sequenceDataBanks = Lists.newLinkedList();
    Iterator<AbstractSimpleSequenceDataBank> databankIterator = databanks.elementIterator();
    while (databankIterator.hasNext()) {
        AbstractSequenceDataBank databank = getDatabank((Element) databankIterator.next(), null);
        if (databank == null) {
            return null;
        }
        sequenceDataBanks.add(databank);
    }

    return sequenceDataBanks;
}

---

From source file:bio.pih.genoogle.io.XMLConfigurationReader.java

private static AbstractSequenceDataBank getDatabank(Element e,
        AbstractDatabankCollection<? extends AbstractSimpleSequenceDataBank> parent)
        throws IOException, InvalidConfigurationException {
    String name = e.attributeValue("name");
    String path = readPath(e.attributeValue("path"));
    String mask = e.attributeValue("mask");
    String lowComplexityFilterString = e.attributeValue("low-complexity-filter");
    String type = e.attributeValue("type");
    String remoteSimilarity = e.attributeValue("remoteSimilarity");

    boolean remoteSimilarityDatabank = false;
    if (remoteSimilarity != null) {
        remoteSimilarityDatabank = Boolean.parseBoolean(remoteSimilarity);
    }//from w w  w.  j  a va 2 s.c o m

    String subSequenceLengthString = e.attributeValue("sub-sequence-length");
    int subSequenceLength;
    if (parent != null) {
        subSequenceLength = parent.getSubSequenceLength();
    } else {
        subSequenceLength = Integer.parseInt(subSequenceLengthString);
    }

    if (name == null) {
        throw new InvalidConfigurationException("Missing attribute name in element " + e.getName());
    }

    if (path == null) {
        throw new InvalidConfigurationException("Missing attribute path in element " + e.getName());
    }

    if (path.equals(name)) {
        throw new InvalidConfigurationException("It is not possible to have a FASTA file (" + path
                + ") with the same name (" + name + ") of the data base.");
    }

    if ((parent != null) && path.equals(parent.getName())) {
        throw new InvalidConfigurationException("It is not possible to have a FASTA (" + path
                + ") file with the same name (" + parent.getName() + ") of the its parent data bank.");
    }

    int lowComplexityFilter = -1;
    if (lowComplexityFilterString != null) {
        lowComplexityFilter = Integer.parseInt(lowComplexityFilterString);
    }

    Alphabet alphabet = DNAAlphabet.SINGLETON;
    if (type != null) {
        if (type.toLowerCase().equals("dna")) {
            alphabet = DNAAlphabet.SINGLETON;
        } else if (type.toLowerCase().equals("rna")) {
            alphabet = RNAAlphabet.SINGLETON;
        } else if (type.toLowerCase().equals("protein")) {
            alphabet = AminoAcidAlphabet.SINGLETON;
        } else {
            throw new InvalidConfigurationException("Sequences type: " + type + " is invalid.");
        }
    } else {
        if (parent != null) {
            alphabet = parent.getAlphabet();
        }
    }

    if (e.getName().trim().equals("split-databanks")) {
        String numberOfSubDatabanksAttr = e.attributeValue("number-of-sub-databanks");
        if (numberOfSubDatabanksAttr == null) {
            throw new RuntimeException("Missing atribute 'number-of-sub-databanks' in the databank " + name);
        }
        int size = Integer.parseInt(numberOfSubDatabanksAttr);

        SplittedDatabankCollection splittedSequenceDatabank = new SplittedDatabankCollection(name, alphabet,
                new File(Genoogle.getHome(), path), subSequenceLength, size, mask);
        splittedSequenceDatabank.setLowComplexityFilter(lowComplexityFilter);

        Iterator databankIterator = e.elementIterator();
        while (databankIterator.hasNext()) {
            try {
                IndexedSequenceDataBank databank = (IndexedSequenceDataBank) getDatabank(
                        (Element) databankIterator.next(), splittedSequenceDatabank);
                if (databank == null) {
                    return null;
                }
                splittedSequenceDatabank.addDatabank(databank);
            } catch (DuplicateDatabankException e1) {
                logger.fatal("Duplicate databanks named " + e1.getDatabankName() + " defined in "
                        + e1.getDatabankName(), e1);
                return null;
            }
        }
        return splittedSequenceDatabank;

    } else if (e.getName().trim().equals("databank")) {
        File file = new File(path);
        try {
            if (remoteSimilarityDatabank == false) {
                return new IndexedSequenceDataBank(name, alphabet, subSequenceLength, mask, file, parent);
            } else {
                return new RemoteSimilaritySequenceDataBank(name, alphabet, subSequenceLength, file, parent);
            }
        } catch (ValueOutOfBoundsException e1) {
            logger.fatal("Error creating IndexedDNASequenceDataBank.", e1);
        }
        return null;

    }
    logger.error("Unknow element name " + e.getName());
    return null;
}

---

From source file:br.com.atus.util.CEPWebService.java

@SuppressWarnings("rawtypes")
public CEPWebService(String cep) {
    try {/*from   w  w  w  .  ja va2 s.c  o m*/
        URL url = new URL("http://cep.republicavirtual.com.br/web_cep.php?cep=" + cep + "&formato=xml");

        Document document = getDocumento(url);

        Element root = document.getRootElement();

        for (Iterator i = root.elementIterator(); i.hasNext();) {
            Element element = (Element) i.next();

            if (element.getQualifiedName().equals("uf"))
                setEstado(element.getText());

            if (element.getQualifiedName().equals("cidade"))
                setCidade(element.getText());

            if (element.getQualifiedName().equals("bairro"))
                setBairro(element.getText());

            if (element.getQualifiedName().equals("tipo_logradouro"))
                setTipoLogradouro(element.getText());

            if (element.getQualifiedName().equals("logradouro"))
                setLogradouro(element.getText());

            if (element.getQualifiedName().equals("resultado"))
                setResultado(Integer.parseInt(element.getText()));
        }
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

---

From source file:br.com.cgcop.utilitarios.CEPWebService.java

public void consultar(String cep) throws MalformedURLException, DocumentException {

    URL url = new URL("http://cep.republicavirtual.com.br/web_cep.php?cep=" + cep + "&formato=xml");

    Document document = getDocumento(url);

    Element root = document.getRootElement();

    for (Iterator i = root.elementIterator(); i.hasNext();) {
        Element element = (Element) i.next();

        if (element.getQualifiedName().equals("uf")) {
            setEstado(element.getText());
        }/*from   w  ww.jav  a2s  .co  m*/

        if (element.getQualifiedName().equals("cidade")) {
            setCidade(element.getText());
        }

        if (element.getQualifiedName().equals("bairro")) {
            setBairro(element.getText());
        }

        if (element.getQualifiedName().equals("tipo_logradouro")) {
            setTipoLogradouro(element.getText());
        }

        if (element.getQualifiedName().equals("logradouro")) {
            setLogradouro(element.getText());
        }

        if (element.getQualifiedName().equals("resultado")) {
            setResultado(Integer.parseInt(element.getText()));
        }
    }
}

---

From source file:br.com.sistemapetshop.util.CepWebService.java

@SuppressWarnings("rawtypes")
public CepWebService(String cep) {

    try {//from  w ww  .  ja  v  a  2 s  .c  o  m
        URL url = new URL("http://cep.republicavirtual.com.br/web_cep.php?cep=" + cep + "&formato=xml");

        Document document = getDocumento(url);
        Element root = document.getRootElement();

        for (Iterator i = root.elementIterator(); i.hasNext();) {
            Element element = (Element) i.next();

            if (element.getQualifiedName().equals("uf")) {
                setEstado(element.getText());
            }

            if (element.getQualifiedName().equals("cidade")) {
                setCidade(element.getText());
            }

            if (element.getQualifiedName().equals("bairro")) {
                setBairro(element.getText());
            }

            if (element.getQualifiedName().equals("tipo_logradouro")) {
                setTipoLogradouro(element.getText());
            }

            if (element.getQualifiedName().equals("logradouro")) {
                setLogradouro(element.getText());
            }

            if (element.getQualifiedName().equals("resultado")) {
                setResultado(Integer.parseInt(element.getText()));
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

---

From source file:br.com.ufra.cep.service.CepWebService.java

public CepWebService(String cep) {

    try {//ww  w  .j  a v a  2s.co  m
        URL url = new URL("http://cep.republicavirtual.com.br/web_cep.php?cep=" + cep + "&formato=xml");

        Document document = getDocumento(url);

        Element root = document.getRootElement();

        for (Iterator i = root.elementIterator(); i.hasNext();) {
            Element element = (Element) i.next();

            if (element.getQualifiedName().equals("estado")) {
                setEstado(element.getText());
            }

            if (element.getQualifiedName().equals("cidade")) {
                setCidade(element.getText());
            }

            if (element.getQualifiedName().equals("bairro")) {
                setBairro(element.getText());
            }

            if (element.getQualifiedName().equals("tipo_logradouro")) {
                setTipo_logradouro(element.getText());
            }

            if (element.getQualifiedName().equals("logradouro")) {
                setLogradouro(element.getText());
            }

            if (element.getQualifiedName().equals("resultado")) {
                setResultado(Integer.parseInt(element.getText()));
            }

            if (element.getQualifiedName().equals("resultado_txt")) {
                setResultado_txt(element.getText());
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

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