Examples with Xref org.vcell.pathway.Xref used on opensource projects

Example 11 with Xref

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

the class PathwayProducerBiopax3 method addContentXref.

private Element addContentXref(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    Xref ob = (Xref) bpObject;
    Element tmpElement = null;
    if (ob.getDb() != null && ob.getDb().length() > 0) {
        tmpElement = new Element("db", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getDb());
        element.addContent(tmpElement);
    }
    if (ob.getDbVersion() != null && ob.getDbVersion().length() > 0) {
        tmpElement = new Element("dbVersion", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getDbVersion());
        element.addContent(tmpElement);
    }
    if (ob.getId() != null && ob.getId().length() > 0) {
        tmpElement = new Element("id", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getId());
        element.addContent(tmpElement);
    }
    if (ob.getIdVersion() != null && ob.getIdVersion().length() > 0) {
        tmpElement = new Element("idVersion", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getIdVersion());
        element.addContent(tmpElement);
    }
    return element;
}

Example 12 with Xref

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

the class PathwayProducerBiopax3 method addContentBioSource.

// tissue 		TissueVocabulary 	single
// cellType 	CellVocabulary 		single
// name 		String 				multiple
// xref 		Xref 				multiple
private Element addContentBioSource(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    BioSource ob = (BioSource) bpObject;
    Element tmpElement = null;
    if (ob.getTissue() != null) {
        tmpElement = new Element("tissue", bp);
        addIDToProperty(tmpElement, ob.getTissue());
        mustPrintObject(ob.getTissue());
        element.addContent(tmpElement);
    }
    if (ob.getCellType() != null) {
        tmpElement = new Element("cellType", bp);
        addIDToProperty(tmpElement, ob.getCellType());
        mustPrintObject(ob.getCellType());
        element.addContent(tmpElement);
    }
    if (ob.getName() != null && ob.getName().size() > 0) {
        List<String> list = ob.getName();
        for (String item : list) {
            tmpElement = new Element("name", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        List<Xref> list = ob.getxRef();
        for (Xref item : list) {
            tmpElement = new Element("xref", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 13 with Xref

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

the class PathwayProducerBiopax3 method addContentProvenance.

// name 	String 	multiple
// xref 	Xref 	multiple
private Element addContentProvenance(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    Provenance ob = (Provenance) bpObject;
    Element tmpElement = null;
    if (ob.getName() != null && ob.getName().size() > 0) {
        List<String> list = ob.getName();
        for (String item : list) {
            tmpElement = new Element("name", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        List<Xref> list = ob.getxRef();
        for (Xref item : list) {
            tmpElement = new Element("xref", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 14 with Xref

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

the class SBPAXSBOExtractor method extractSBOTerms.

public static Set<SBOTerm> extractSBOTerms(SBVocabulary sbTerm) {
    Set<SBOTerm> sboTerms = new HashSet<SBOTerm>();
    for (Xref xref : sbTerm.getxRef()) {
        String db = xref.getDb().trim();
        String id = xref.getId().trim();
        if (db != null && id != null) {
            if (db.equalsIgnoreCase("sbo") || db.equalsIgnoreCase("systems biology ontology")) {
                SBOTerm sboTerm = SBOList.getTermFromIndex(SBOUtil.getIndexFromId(id));
                if (sboTerm != null) {
                    sboTerms.add(sboTerm);
                }
            }
        }
    }
    return sboTerms;
}

Example 15 with Xref

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

the class PathwayReader method addObjectXRef.

private Xref addObjectXRef(Element element) {
    Xref xRef = new Xref();
    addAttributes(xRef, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentXref(xRef, element, childElement)) {
                showUnexpected(childElement, xRef);
            }
        }
    }
    pathwayModel.add(xRef);
    return xRef;
}