Examples with Annotation org.sbml.jsbml.Annotation used on opensource projects

Example 1 with Annotation

use of org.sbml.jsbml.Annotation in project vcell by virtualcell.

the class SBMLAnnotationUtil method readVCellSpecificAnnotation.

/**
 * readVCellSpecificAnnotation : separate method to handle only the VCellRelatedInfo annotation stored in VCellInfo element of
 * 				SBML <annotation>. This is currently used only for species and reactions, since the information stored in these
 * 				elements in the SBML annotation is required for building the corresponding VCell element.
 * @param sBase - the corresponding SBML element
 * @return - the <VcellRelatedInfo> element
 * @throws XMLStreamException
 */
public Element readVCellSpecificAnnotation(SBase sBase) throws XMLStreamException {
    Element vcellSpecificElement = null;
    Annotation annotation = sBase.getAnnotation();
    XMLNode annotationRoot = annotation.getXMLNode();
    if (annotationRoot != null) {
        long childCount = annotationRoot.getNumChildren();
        for (int i = 0; i < childCount; ++i) {
            XMLNode annotationBranch = annotationRoot.getChild(i);
            String namespace = annotationBranch.getNamespaceURI(annotationBranch.getPrefix());
            if ((namespace != null) && (namespace.equals(tripleVCellInfo.getURI()) || namespace.equals(XMLTags.VCML_NS_OLD) || namespace.equals(XMLTags.VCML_NS))) {
                int numChildren = (int) annotationBranch.getNumChildren();
                for (int j = 0; j < numChildren; j++) {
                    XMLNode child = annotationBranch.getChild(j);
                    if (!child.isElement()) {
                        continue;
                    }
                    // if this child has a prefix, but no explicit namespace (it is defined in its parent); try getting prefix from parent
                    String childPrefix = child.getPrefix();
                    if (childPrefix != null) {
                        String childNamespaceURI = child.getNamespaceURI(childPrefix);
                        if (childNamespaceURI == null || childNamespaceURI.length() == 0) {
                            childNamespaceURI = annotationBranch.getNamespaceURI(childPrefix);
                            child.addNamespace(childNamespaceURI, childPrefix);
                        }
                    }
                    if (child.getName().equals(XMLTags.VCellRelatedInfoTag)) {
                        // new style VCellInfo element (with <FreeText> and <SbmlImportRelated> subelements
                        vcellSpecificElement = xmlNodeToElement(child);
                    } else {
                        // check if 'child' is oldStyle VCellInfo element.
                        vcellSpecificElement = processOldStyleVCellInfo(child);
                        if (vcellSpecificElement == null) {
                            System.out.println("Unknown VCellInfo annotation type : '" + child.getName());
                        }
                    }
                // if - else (child is VCellRelatedInfoTag)
                }
            // for - numChildren
            }
        // nameSpace != null & equals VCell_NS
        }
    // for - childCount
    }
    // annotationRoot != null
    return vcellSpecificElement;
}