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

Example 1 with ProteinReference

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

the class PathwayReaderBiopax3 method addObjectEntityReference.

private EntityReference addObjectEntityReference(Element element) {
    if (element.getChildren().size() == 0) {
        EntityReferenceProxy proxy = new EntityReferenceProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (childElement.getName().equals("DnaReference")) {
                DnaReference thingie = addObjectDnaReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("DnaRegionReference")) {
                DnaRegionReference thingie = addObjectDnaRegionReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("ProteinReference")) {
                ProteinReference thingie = addObjectProteinReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("RnaReference")) {
                RnaReference thingie = addObjectRnaReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("RnaRegionReference")) {
                RnaRegionReference thingie = addObjectRnaRegionReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("SmallMoleculeReference")) {
                SmallMoleculeReference thingie = addObjectSmallMoleculeReference(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        }
    }
    EntityReference entityReference = new EntityReference();
    addAttributes(entityReference, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentEntityReference(entityReference, element, childElement)) {
                // to self ??
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(entityReference);
    return entityReference;
}

Example 2 with ProteinReference

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

the class PathwayReader method addObjectProteinReference.

private ProteinReference addObjectProteinReference(Element element) {
    ProteinReference proteinReference = new ProteinReference();
    addAttributes(proteinReference, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentProteinReference(proteinReference, element, childElement)) {
                showUnexpected(childElement, proteinReference);
            }
        }
    }
    pathwayModel.add(proteinReference);
    return proteinReference;
}

Example 3 with ProteinReference

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

the class PathwayReaderBiopax3 method addObjectProteinReference.

private ProteinReference addObjectProteinReference(Element element) {
    ProteinReference proteinReference = new ProteinReference();
    addAttributes(proteinReference, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentProteinReference(proteinReference, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(proteinReference);
    return proteinReference;
}

Example 4 with ProteinReference

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

the class PathwayProducerBiopax3 method addContentProteinReference.

// sequence 	String 		single
// organism 	BioSource 	single
private Element addContentProteinReference(BioPaxObject bpObject, Element element) {
    element = addContentEntityReference(bpObject, element);
    ProteinReference ob = (ProteinReference) bpObject;
    Element tmpElement = null;
    if (ob.getSequence() != null && ob.getSequence().length() > 0) {
        tmpElement = new Element("sequence", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getSequence());
        element.addContent(tmpElement);
    }
    if (ob.getOrganism() != null) {
        tmpElement = new Element("organism", bp);
        addIDToProperty(tmpElement, ob.getOrganism());
        mustPrintObject(ob.getOrganism());
        element.addContent(tmpElement);
    }
    return element;
}