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Example 6 with UnificationXref

use of org.vcell.pathway.UnificationXref in project vcell by virtualcell.

the class PathwayReader method addObjectUnificationXref.

private UnificationXref addObjectUnificationXref(Element element) {
    UnificationXref unificationXref = new UnificationXref();
    addAttributes(unificationXref, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentUnificationXref(unificationXref, element, childElement)) {
                showUnexpected(childElement, unificationXref);
            }
        }
    }
    pathwayModel.add(unificationXref);
    return unificationXref;
}
Also used : UnificationXref(org.vcell.pathway.UnificationXref) Element(org.jdom.Element) BioPaxObject(org.vcell.pathway.BioPaxObject)

Aggregations

UnificationXref (org.vcell.pathway.UnificationXref)6 BioPaxObject (org.vcell.pathway.BioPaxObject)5 Element (org.jdom.Element)4 PublicationXref (org.vcell.pathway.PublicationXref)4 RelationshipXref (org.vcell.pathway.RelationshipXref)4 Xref (org.vcell.pathway.Xref)4 GroupObject (org.vcell.pathway.GroupObject)3 ArrayList (java.util.ArrayList)2 Namespace (org.jdom.Namespace)2 XrefProxy (org.vcell.pathway.persistence.BiopaxProxy.XrefProxy)2 BioModelEntityObject (cbit.vcell.model.BioModelEntityObject)1 HashSet (java.util.HashSet)1 Set (java.util.Set)1 TreeSet (java.util.TreeSet)1 CellularLocationVocabulary (org.vcell.pathway.CellularLocationVocabulary)1 Complex (org.vcell.pathway.Complex)1 Control (org.vcell.pathway.Control)1 Dna (org.vcell.pathway.Dna)1 DnaRegion (org.vcell.pathway.DnaRegion)1 Entity (org.vcell.pathway.Entity)1