Examples with Namespace org.jdom.Namespace used on opensource projects

Example 21 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToMathModel.

static MathModel XMLToMathModel(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    MathModel mathModel = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element mathRoot = root.getChild(XMLTags.MathModelTag, ns);
        if (mathRoot == null) {
            mathRoot = root.getChild(XMLTags.MathModelTag);
            // mathRoot was null, so obtained the <Mathmodel> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = mathRoot;
    }
    // else - root is assumed to be old-style vcml with <Mathmodel> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (mathmodel is root)
    // If namespace is null, xml is the old-style xml with mathmodel as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    mathModel = reader.getMathModel(root);
    mathModel.refreshDependencies();
    return mathModel;
}

Example 22 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToGeometry.

static Geometry XMLToGeometry(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    Geometry geometry = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element geoRoot = root.getChild(XMLTags.GeometryTag, ns);
        if (geoRoot == null) {
            geoRoot = root.getChild(XMLTags.GeometryTag);
            // geoRoot was null, so obtained the <Geometry> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = geoRoot;
    }
    // else - root is assumed to be old-style vcml with <Geometry> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (geometry is root)
    // If namespace is null, xml is the old-style xml with geometry as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    geometry = reader.getGeometry(root);
    geometry.refreshDependencies();
    return geometry;
}

Example 23 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class MicroscopyXmlReader method getPrimaryROIs.

/**
 * This method is only called by DataSymbolsPanel to get the primary ROIs
 */
public ROI[] getPrimaryROIs(Element param, /*root, frapstudy element*/
ClientTaskStatusSupport progressListener) throws XmlParseException {
    // get frapData element
    Element frapDataElement = param.getChild(MicroscopyXMLTags.FRAPDataTag);
    Namespace ns = param.getNamespace();
    List<Element> roiList = frapDataElement.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = null;
    int numROIs = 3;
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            if (roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_BLEACHED.name()) || roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()) || roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_CELL.name())) {
                rois[index++] = getROI(roiElement);
                if (index == 3) {
                    break;
                }
            }
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    return reorderedROIs;
}

Example 24 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XMLDict method getMatchingElement.

private static Element getMatchingElement(Element root, String reName, String attName, String attValue) {
    String path;
    // accomodate math models.
    if (!root.getName().equals(XMLTags.MathModelTag)) {
        path = (String) reHashBio.get(reName);
    } else {
        path = (String) reHashMath.get(reName);
    }
    if (path == null) {
        System.err.println("The xpath of the element to resolve is not available: " + reName);
        return getMatchingElementGeneric(root, reName, attName, attValue);
    }
    java.util.StringTokenizer tokenizer = new java.util.StringTokenizer(path, XMLDict.XPATH_SEP);
    // System.out.println(root.getName() + " " + reName + " " + attName + " " + attValue + " " + path + " " + tokenizer.countTokens());
    if (tokenizer.countTokens() < 2) {
        // the element to resolve is the root. Should not happen.
        System.err.println("No tokens found for element: " + reName);
        return null;
    }
    while (tokenizer.hasMoreTokens()) {
        // start at the parent of interest, which can be a shorter path than the one saved.
        String curToken = tokenizer.nextToken();
        if (root.getName().equals(curToken)) {
            break;
        }
    }
    Namespace ns = root.getNamespace();
    for (int i = 0; i < tokenizer.countTokens() - 1; i++) {
        // break when reaching the direct parent.
        String elementName = tokenizer.nextToken();
        // System.out.println("Current Token: " + elementName);
        root = root.getChild(elementName, ns);
    }
    String resElementName = tokenizer.nextToken();
    // System.out.println(resElementName);
    @SuppressWarnings("unchecked") Iterator<Element> // last 2 tokens (direct parent, and element to resolve)
    iterator = root.getChildren(resElementName, ns).iterator();
    Element temp = null;
    while (iterator.hasNext()) {
        temp = iterator.next();
        if (attValue.equals(temp.getAttributeValue(attName))) {
            break;
        } else {
            temp = null;
        }
    }
    return temp;
}

Example 25 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class AnatomicalStructure method getCompartmentGoTerms.

public static HashMap<String, AnatomicalStructure> getCompartmentGoTerms(String sbmlText) {
    HashMap<String, AnatomicalStructure> compartmentAnatomyMap = new HashMap<String, AnatomicalStructure>();
    Namespace sbmlNamespace = Namespace.getNamespace("http://www.sbml.org/sbml/level2");
    Namespace rdfNamespace = Namespace.getNamespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
    Namespace bioqualifierNamespace = Namespace.getNamespace("http://biomodels.net/biology-qualifiers/");
    Element rootSBML = (XmlUtil.stringToXML(sbmlText, null)).getRootElement();
    Element sbmlModelElement = rootSBML.getChild("model", sbmlNamespace);
    Element listOfCompartments = sbmlModelElement.getChild("listOfCompartments", sbmlNamespace);
    List<Element> compartmentElementList = listOfCompartments.getChildren("compartment", sbmlNamespace);
    for (Element compartmentElement : compartmentElementList) {
        AnatomicalStructure anatomicalStructure = null;
        String compartmentID = compartmentElement.getAttributeValue("id");
        String goPrefix = "http://www.geneontology.org/#GO:";
        String compartmentOutside = compartmentElement.getAttributeValue("outside");
        Element annotationElement = compartmentElement.getChild("annotation", sbmlNamespace);
        if (annotationElement != null) {
            Element rdfElement = annotationElement.getChild("RDF", rdfNamespace);
            Element descriptionElement = rdfElement.getChild("Description", rdfNamespace);
            Element isElement = descriptionElement.getChild("is", bioqualifierNamespace);
            if (isElement == null) {
                isElement = descriptionElement.getChild("isVersionOf", bioqualifierNamespace);
            }
            if (isElement != null) {
                Element bagElement = isElement.getChild("Bag", rdfNamespace);
                Element liElement = bagElement.getChild("li", rdfNamespace);
                String compartmentRdfResource = liElement.getAttributeValue("resource", rdfNamespace);
                if (compartmentRdfResource.startsWith(goPrefix)) {
                    String GoTerm = compartmentRdfResource.substring(goPrefix.length(), compartmentRdfResource.length());
                    anatomicalStructure = AnatomicalStructure.fromGOTerm(GoTerm);
                }
                if (compartmentOutside != null) {
                    System.out.println(compartmentOutside + "," + compartmentID);
                }
            }
            compartmentAnatomyMap.put(compartmentID, anatomicalStructure);
        }
    }
    return compartmentAnatomyMap;
}