Example usage for org.dom4j Element attributeValue

Introduction

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

Prototype

String attributeValue(QName qName);

Source Link

Document

This returns the attribute value for the attribute with the given fully qualified name or null if there is no such attribute or the empty string if the attribute value is empty.

Usage

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   ww w . jav a  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:bixo.examples.webmining.AnalyzeHtml.java

License:Apache License

private String getAttributeFromNode(Node node, String attribute) {
    String attributeValue = null;
    if (node.getNodeType() == Node.ELEMENT_NODE) {
        Element e = (Element) node;
        attributeValue = e.attributeValue(attribute);
    }//from   ww w  . j  av  a 2 s  . com
    return (attributeValue == null ? "" : attributeValue);
}

---

From source file:ca.upei.roblib.fedora.servletfilter.DrupalAuthModule.java

License:Apache License

protected Map<String, String> parseConnectionElement(Element connection) {
    Map<String, String> toReturn = new HashMap<String, String>();
    toReturn.put("server", connection.attributeValue("server"));
    toReturn.put("database", connection.attributeValue("dbname"));
    toReturn.put("user", connection.attributeValue("user"));
    toReturn.put("pass", connection.attributeValue("password"));
    toReturn.put("port", connection.attributeValue("port"));
    toReturn.put("jdbcDriverClass", connection.attributeValue("jdbcDriverClass"));
    toReturn.put("jdbcURLProtocol", connection.attributeValue("jdbcURLProtocol"));
    Element sqlElement = connection.element("sql");
    toReturn.put("sql", sqlElement.getTextTrim());

    return toReturn;
}

---

From source file:cc.warlock.core.client.logging.LoggingConfiguration.java

License:Open Source License

public void parseElement(Element element) {
    if (element.getName().equals("logging")) {
        enableLogging = Boolean.parseBoolean(element.attributeValue("enabled"));
        logFormat = element.attributeValue("format");

        Element dir = element.element("dir");
        if (dir != null) {
            logDirectory = new File(dir.getTextTrim());
        }//from   w  w  w.  ja v a  2  s.  c o m
    }
}

---

From source file:cc.warlock.core.client.settings.internal.ClientConfigurationProvider.java

License:Open Source License

protected WarlockFont elementToFont(Element element) {
    if (element == null)
        return WarlockFont.DEFAULT_FONT;
    if (element.attributeValue("family").equals("default"))
        return WarlockFont.DEFAULT_FONT;

    WarlockFont font = new WarlockFont();
    font.setFamilyName(element.attributeValue("family"));
    font.setSize(Integer.parseInt(element.attributeValue("size")));
    return font;// w  ww  .j  a  va 2 s. c  o  m
}

---

From source file:cc.warlock.core.client.settings.internal.ClientSettings.java

License:Open Source License

@Override
public boolean supportsElement(Element element) {
    if (element.getName().equals("client-settings") && client.getClientId() != null) {
        String clientId = element.attributeValue("client-id");
        if (clientId.equals(client.getClientId())) {
            return true;
        }/* www. j a va  2  s  . co m*/
    }
    return false;
}

---

From source file:cc.warlock.core.client.settings.internal.HighlightConfigurationProvider.java

License:Open Source License

protected IWarlockStyle createStyle(Element sElement) {
    WarlockStyle style = new WarlockStyle();
    style.setBackgroundColor(colorValue(sElement, "background"));
    style.setForegroundColor(colorValue(sElement, "foreground"));

    if (sElement.attributeValue("name") != null) {
        style.setName(stringValue(sElement, "name"));
    }//from www. j  a v  a2 s  .c om

    for (Element typeElement : (List<Element>) sElement.elements()) {
        String text = typeElement.getTextTrim();
        style.addStyleType(IWarlockStyle.StyleType.valueOf(text));
    }

    style.setFullLine(booleanValue(sElement, "full-line"));
    //System.out.println("Setting style sound to " + sElement.attributeValue("sound"));
    style.setSound(sElement.attributeValue("sound"));

    return style;
}

---

From source file:cc.warlock.core.client.settings.internal.PatternConfigurationProvider.java

License:Open Source License

protected void fillSetting(IPatternSetting setting, Element element) {
    String pattern = stringValue(element, "pattern");
    boolean literal = booleanValue(element, "literal");
    boolean caseSensitive = booleanValue(element, "caseSensitive");
    boolean fullWordMatch = true;
    if (element.attributeValue("fullWordMatch") == null) {
        fullWordMatch = true;/*  www.ja  v  a 2 s.c  o m*/
    } else {
        fullWordMatch = booleanValue(element, "fullWordMatch");
    }

    setting.setLiteral(literal);
    setting.setCaseSensitive(caseSensitive);
    setting.setFullWordMatch(fullWordMatch);
    setting.setText(pattern);
}

---

From source file:cc.warlock.core.client.settings.internal.VariableConfigurationProvider.java

License:Open Source License

@Override
protected void parseChild(Element child) {
    if (child.getName().equals("variable")) {
        String name = child.attributeValue("id");
        String value = child.getStringValue();

        Variable variable = new Variable(this, name, value);
        variables.put(name, variable);/*from  ww w .  ja v  a  2  s.c o  m*/
    }
}

---

From source file:cc.warlock.core.client.settings.internal.WindowSettingsConfigurationProvider.java

License:Open Source License

@Override
protected void parseChild(Element child) {
    if (child.getName().equals("window")) {
        WindowSettings settings = (WindowSettings) getWindowSettings(child.attributeValue("id"));
        boolean add = false;
        if (settings == null) {
            settings = new WindowSettings(this);
            add = true;/*from   w w w.ja v a  2  s  . c  o m*/
        }

        settings.setBackgroundColor(colorValue(child, "background"));
        settings.setForegroundColor(colorValue(child, "foreground"));
        settings.setFont(elementToFont(child.element("font")));
        settings.setColumnFont(elementToFont(child.element("columnFont")));
        settings.setId(child.attributeValue("id"));

        if (add) {
            windowSettings.add(settings);
        }
    }
}

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