Example usage for org.dom4j Element getTextTrim

List of usage examples for org.dom4j Element getTextTrim

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

Prototype

String getTextTrim();

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Usage

From source file:eu.planets_project.pp.plato.util.XMLCompare.java

License:Open Source License

private boolean compareTrees(Element node1, Document doc2, boolean ignoreEmptyNodes,
        boolean ignoreEmptyAttributes) {
    boolean isValid = true;

    Element root2 = doc2.getRootElement();

    String path = node1.getUniquePath();

    Element elementDoc2 = (Element) doc2.selectSingleNode(path);

    // the node doesn't exist in doc2
    if (elementDoc2 == null && node1.elements().size() == 0 && "".equals(node1.getTextTrim())) {
        if (ignoreEmptyNodes == false) {
            errorMessages//from  w  ww.  j  av a 2s.  co  m
                    .append("The following empty node doesnt exist in xml file #2: " + node1.getUniquePath())
                    .append(System.getProperty("line.separator"));
            isValid = false;
        }
    } else if (elementDoc2 == null && (node1.elements().size() > 0 || !"".equals(node1.getTextTrim()))) {
        errorMessages.append("The following node (which is not empty) doesn't exist in xml file #2: "
                + node1.getUniquePath() + System.getProperty("line.separator"));
        errorMessages.append("File #1: " + node1.getTextTrim() + System.getProperty("line.separator"));
        errorMessages
                .append("File #2: " + ((elementDoc2 == null) ? "<not existent>" : elementDoc2.getTextTrim())
                        + System.getProperty("line.separator"));

        isValid = false;
    } else if (elementDoc2 == null || !elementDoc2.getTextTrim().equals(node1.getTextTrim())) {
        errorMessages.append("Text of following nodes not equal in both xmls: " + node1.getUniquePath()
                + System.getProperty("line.separator"));
        errorMessages.append("File #1: " + node1.getTextTrim() + System.getProperty("line.separator"));
        errorMessages
                .append("File #2: " + ((elementDoc2 == null) ? "<not existent>" : elementDoc2.getTextTrim())
                        + System.getProperty("line.separator"));

        isValid = false;
    }

    //
    // compare attributes
    //
    List<Attribute> attributes = node1.attributes();

    for (Attribute a : attributes) {

        String attributePath = a.getUniquePath();

        org.dom4j.Node node = root2.selectSingleNode(attributePath);

        if (node == null && "".equals(a.getValue().trim())) {
            // document 1 has an empty attribute (sting length = 0) which
            // does not exist in document 2

            if (ignoreEmptyAttributes == false) {
                errorMessages.append(
                        "Attribute " + a.getName() + " doesn't exist in xml file #2, node " + a.getUniquePath())
                        .append(System.getProperty("line.separator"));
                isValid = false;
            }

            continue;
        }

        if (node == null || !a.getValue().equals(node.getText())) {

            errorMessages.append("Value of following attribute not equal in both xmls: " + a.getUniquePath()
                    + System.getProperty("line.separator"));
            errorMessages.append("File #1: " + a.getValue() + System.getProperty("line.separator"));
            errorMessages.append("File #2: " + ((node != null) ? node.getText() : "<not existent>")
                    + System.getProperty("line.separator"));

            isValid = false;
        }
    }

    List<Element> elements = node1.elements();

    for (Element e : elements) {
        if (!compareTrees(e, doc2, ignoreEmptyNodes, ignoreEmptyAttributes)) {
            isValid = false;
        }
    }

    return isValid;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

private String getValue(final Element e) {

    if (e == null)
        return "";

    return getValue(e.getTextTrim());
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "sequencefilters" element of the DOM.
 * @param rootElement root element of the document
 * @return a list of SequenceFilter objects
 * @throws IOException if an error occurs while parsing
 *//*from   www  .ja  va2 s  . co  m*/
private List<SequenceFilter> parseSequenceFilters(final Element rootElement) throws IOException {

    List<SequenceFilter> list = new ArrayList<SequenceFilter>();

    for (Iterator i = rootElement.elementIterator("sequencefilters"); i.hasNext();) {
        final Element filters = (Element) i.next();

        for (Iterator i2 = filters.elementIterator("sequencefilter"); i2.hasNext();) {
            final Element filter = (Element) i2.next();

            String filterName = null;

            for (Iterator i3 = filter.elementIterator("name"); i3.hasNext();) {
                final Element name = (Element) i3.next();
                filterName = name.getTextTrim();
            }

            if (filterName == null) {
                logger.warning("Filter without name.");
                continue;
            }

            // Add the sequence filter to the registery if it is a plug in
            for (Iterator i4 = filter.elementIterator("class"); i4.hasNext();) {
                final Element clazz = (Element) i4.next();
                String filterClass = clazz.getTextTrim();
                SequenceFilterRegistery.addSequenceFilterType(filterName, filterClass);
            }

            // Get the parameters of the sequenceFilter
            final Properties properties = getElementParameters(filter);
            final SequenceFilter f = SequenceFilterRegistery.getSequenceFilter(filterName);

            if (f == null)
                logger.warning("Unknown sequence filter: " + filterName);
            else {

                for (Map.Entry<Object, Object> entry : properties.entrySet())
                    // Set the initialization parameters for the sequence filter
                    f.setInitParameter((String) entry.getKey(), (String) entry.getValue());

                list.add(f);
            }
        }

    }

    // Set the defaults initialization parameters of the sequence filters
    for (SequenceFilter sq : list)
        this.design.setDefaultModuleInitParameters(sq);

    return list;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "measurements" element of the DOM.
 * @param rootElement root element of the document
 * @return a list of Measurement objects
 * @throws IOException if an error occurs while parsing
 *///  www. j  a v  a2 s. co m
private List<Measurement> parseMeasurements(final Element rootElement) throws IOException {

    final List<Measurement> list = new ArrayList<Measurement>();

    list.add(new ChromosomeMeasurement());
    list.add(new OligoStartMeasurement());
    list.add(new OligoLengthMeasurement());

    for (Iterator i = rootElement.elementIterator("measurements"); i.hasNext();) {
        final Element measurements = (Element) i.next();

        for (Iterator i2 = measurements.elementIterator("measurement"); i2.hasNext();) {
            final Element measurement = (Element) i2.next();

            String measurementName = null;

            for (Iterator i3 = measurement.elementIterator("name"); i3.hasNext();) {
                final Element name = (Element) i3.next();
                measurementName = name.getTextTrim();
            }

            if (measurementName == null) {
                logger.warning("Measurement without name.");
                continue;
            }

            // Skip if user attempt to add another Scaffold measurement
            if (ChromosomeMeasurement.MEASUREMENT_NAME.toLowerCase().equals(measurementName.toLowerCase()))
                continue;

            // Skip if user attempt to add another oligo start measurement
            if (OligoStartMeasurement.MEASUREMENT_NAME.toLowerCase().equals(measurementName.toLowerCase()))
                continue;

            // Add the measurement to registery if it is a plug in
            for (Iterator i4 = measurement.elementIterator("class"); i4.hasNext();) {
                final Element clazz = (Element) i4.next();
                String measurementClass = clazz.getTextTrim();
                MeasurementRegistery.addMeasurementType(measurementName, measurementClass);
            }

            // Get the parameters of the measurement
            final Properties properties = getElementParameters(measurement);

            final Measurement m = MeasurementRegistery.getMeasurement(measurementName);
            if (m == null)
                logger.warning("Unknown measurement: " + measurementName);
            else {

                // Set the initialization parameters for the measurement
                for (Map.Entry<Object, Object> entry : properties.entrySet())
                    m.setInitParameter((String) entry.getKey(), (String) entry.getValue());

                list.add(m);
            }
        }

    }

    // Set the default initialization parameters of the measurements
    for (Measurement m : list)
        this.design.setDefaultModuleInitParameters(m);

    return list;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "measurementfilters" element of the DOM.
 * @param rootElement root element of the document
 * @return a list of MeasurementFilter objects
 * @throws IOException if an error occurs while parsing
 *//*from ww  w  .jav  a2  s  .  com*/
private List<MeasurementFilter> parseMeasurementFilters(final Element rootElement) throws IOException {

    final List<MeasurementFilter> list = new ArrayList<MeasurementFilter>();

    for (Iterator i = rootElement.elementIterator("measurementfilters"); i.hasNext();) {
        final Element filters = (Element) i.next();

        for (Iterator i2 = filters.elementIterator("measurementfilter"); i2.hasNext();) {
            final Element filter = (Element) i2.next();

            String measurementFilterName = null;

            for (Iterator i3 = filter.elementIterator("name"); i3.hasNext();) {
                final Element name = (Element) i3.next();
                measurementFilterName = name.getTextTrim();
            }

            if (measurementFilterName == null) {
                logger.warning("Measurement filter without name.");
                continue;
            }

            // Add the measurement to registery if it is a plug in
            for (Iterator i4 = filter.elementIterator("class"); i4.hasNext();) {
                final Element clazz = (Element) i4.next();
                String measurementClass = clazz.getTextTrim();
                MeasurementFilterRegistery.addMeasurementFilterType(measurementFilterName, measurementClass);
            }

            // Get the parameters of the measurement filters
            final Properties properties = getElementParameters(filter);

            final MeasurementFilter mf = MeasurementFilterRegistery
                    .getMeasuremrentFilter(measurementFilterName);
            if (mf == null)
                logger.warning("Unknown measurement: " + measurementFilterName);
            else {

                // Set the initialization parameters for the measurement filters
                for (Map.Entry<Object, Object> entry : properties.entrySet())
                    mf.setInitParameter((String) entry.getKey(), (String) entry.getValue());

                list.add(mf);
            }
        }

    }

    // Set the defaults initialization parameters of the measurements filters
    for (MeasurementFilter mf : list)
        this.design.setDefaultModuleInitParameters(mf);

    return list;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "selector" element of the DOM.
 * @param rootElement root element of the document
 * @return a selector objects//w  w  w .ja  va  2 s .  co  m
 * @throws TeolennException if an error occurs while parsing
 */
private SequenceSelector parseSelector(final Element rootElement) throws TeolennException {

    for (Iterator i = rootElement.elementIterator("selector"); i.hasNext();) {

        final Element selector = (Element) i.next();

        String selectorName = null;

        for (Iterator i1 = selector.elementIterator("name"); i1.hasNext();) {
            final Element name = (Element) i1.next();
            selectorName = name.getTextTrim();
        }

        // Add the selector to registery if it is a plug in
        for (Iterator i2 = selector.elementIterator("class"); i2.hasNext();) {
            final Element clazz = (Element) i2.next();
            String selectorClass = clazz.getTextTrim();
            SequenceSelectorRegistery.addSequenceSelectorType(selectorName, selectorClass);
        }

        // Get the parameters of the measurement
        final Properties properties = getElementParameters(selector);

        SequenceSelector s = SequenceSelectorRegistery.getSequenceSelector(selectorName);

        if (s == null) {
            logger.warning("Unknown selector: " + selectorName);
            throw new TeolennException("Unknown selector: " + selectorName);
        }

        // Set the initialization parameters for the selector
        for (Map.Entry<Object, Object> entry : properties.entrySet())
            s.setInitParameter((String) entry.getKey(), (String) entry.getValue());

        // Set defaults parameters
        this.design.setDefaultModuleInitParameters(s);

        return s;
    }

    throw new TeolennException("No selector found.");
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "select" element of the DOM.
 * @param rootElement root element of the document
 * @return a list of weights objects/*w  w w .j a v a  2 s. c om*/
 * @throws IOException if an error occurs while parsing
 */
private WeightsSetter parseSelectWeights(final Element rootElement) throws IOException {

    // Map of weights
    final Map<String, Float> selectWeights = new HashMap<String, Float>();

    // Map of properties
    final Map<String, Properties> selectProperties = new HashMap<String, Properties>();

    for (Iterator i = rootElement.elementIterator("selector"); i.hasNext();) {
        final Element select = (Element) i.next();

        for (Iterator i2 = select.elementIterator("measurement"); i2.hasNext();) {
            final Element measurement = (Element) i2.next();

            String measurementName = null;
            String measurementWeight = null;

            for (Iterator i3 = measurement.elementIterator("name"); i3.hasNext();) {
                final Element name = (Element) i3.next();
                measurementName = name.getTextTrim();
            }

            if (measurementName == null) {
                logger.warning("Measurement without name.");
                continue;
            }

            // Get the weight for the measurement
            for (Iterator i4 = measurement.elementIterator("weight"); i4.hasNext();) {
                final Element weight = (Element) i4.next();
                measurementWeight = weight.getTextTrim();
            }

            try {
                selectWeights.put(measurementName, Float.parseFloat(measurementWeight));
            } catch (NumberFormatException e) {
                logger.warning("Invalid " + measurementName + " weight: " + measurementWeight);
            }

            // Get the properties of the measurement
            selectProperties.put(measurementName, getElementParameters(measurement));
        }
    }

    return new WeightsSetter() {

        @Override
        public void setWeights(SequenceMeasurements sm) {

            // Set the weights
            for (Map.Entry<String, Float> e : selectWeights.entrySet())
                sm.setWeight(sm.getMeasurement(e.getKey()), e.getValue());

            // Set the properties
            for (Map.Entry<String, Properties> e : selectProperties.entrySet()) {

                final String name = e.getKey();
                final Properties properties = e.getValue();

                if (!sm.isMeasurement(name)) {
                    logger.warning("Unknown measurement: " + name);
                    continue;
                }

                for (Map.Entry<Object, Object> e2 : properties.entrySet()) {

                    sm.getMeasurement(name).setProperty((String) e2.getKey(), (String) e2.getValue());

                }
            }
        }
    };

}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Parse the "output" element of the DOM.
 * @param rootElement root element of the document
 * @return a selector objects/*  w  ww . j ava2  s.com*/
 * @throws TeolennException if an error occurs while parsing
 */
private List<Output> parseOutput(final Element rootElement) throws TeolennException {

    List<Output> list = new ArrayList<Output>();

    for (Iterator i = rootElement.elementIterator("outputs"); i.hasNext();) {

        final Element outputs = (Element) i.next();

        for (Iterator i1 = outputs.elementIterator("output"); i1.hasNext();) {

            final Element output = (Element) i1.next();

            String selectorName = null;

            for (Iterator i2 = output.elementIterator("name"); i2.hasNext();) {
                final Element name = (Element) i2.next();
                selectorName = name.getTextTrim();
            }

            // Add the selector to registery if it is a plug in
            for (Iterator i3 = output.elementIterator("class"); i3.hasNext();) {
                final Element clazz = (Element) i3.next();
                String outputClass = clazz.getTextTrim();
                OutputRegistery.addOutputType(selectorName, outputClass);
            }

            // Get the parameters of the measurement
            final Properties properties = getElementParameters(output);

            Output o = OutputRegistery.getOutput(selectorName);

            if (output == null) {
                logger.warning("Unknown output: " + selectorName);
                throw new TeolennException("Unknown output: " + selectorName);
            }

            // Set the initialization parameters for the selector
            for (Map.Entry<Object, Object> entry : properties.entrySet())
                o.setInitParameter((String) entry.getKey(), (String) entry.getValue());

            list.add(o);
        }
    }

    if (list.size() == 0)
        list.add(new DefaultOutput());

    // Set the default initialization parameters of the outputs
    for (Output o : list)
        this.design.setDefaultModuleInitParameters(o);

    return list;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Get the parameter of an element// w  w  w. j a va  2  s . co m
 * @param element Element to parse
 * @return a Properties object with the name and values of the parameters
 */
private final Properties getElementParameters(final Element element) {

    final Properties result = new Properties();

    for (Iterator i4 = element.elementIterator("parameters"); i4.hasNext();) {
        final Element params = (Element) i4.next();

        for (Iterator i5 = params.elementIterator("parameter"); i5.hasNext();) {
            final Element param = (Element) i5.next();

            String pKey = null;
            String pValue = null;

            for (Iterator i6 = param.elementIterator("name"); i6.hasNext();) {
                final Element name = (Element) i6.next();
                pKey = name.getTextTrim().toLowerCase();
            }

            for (Iterator i7 = param.elementIterator("value"); i7.hasNext();) {
                final Element value = (Element) i7.next();
                pValue = getValue(value.getTextTrim());
            }

            if (pKey != null && pValue != null)
                result.setProperty(pKey, pValue);
        }

    }

    return result;
}

From source file:fr.ens.transcriptome.teolenn.DesignReader.java

License:Open Source License

/**
 * Get the constants/*from   ww  w .j  ava2 s.  c  o  m*/
 * @param element Element to parse
 * @return a Properties object with the name and values of the parameters
 */
private final Properties getElementConstants(final Element element) {

    final Properties result = new Properties();

    for (Iterator i4 = element.elementIterator("constants"); i4.hasNext();) {
        final Element params = (Element) i4.next();

        for (Iterator i5 = params.elementIterator("constant"); i5.hasNext();) {
            final Element param = (Element) i5.next();

            String pKey = null;
            String pValue = null;

            for (Iterator i6 = param.elementIterator("name"); i6.hasNext();) {
                final Element name = (Element) i6.next();
                pKey = name.getTextTrim().toLowerCase();
            }

            for (Iterator i7 = param.elementIterator("value"); i7.hasNext();) {
                final Element value = (Element) i7.next();
                pValue = value.getTextTrim();

            }

            if (pKey != null || pValue != null)
                result.setProperty(pKey, pValue);
        }

    }

    return result;
}