use of org.vcell.pathway.BindingFeature in project vcell by virtualcell.
the class PathwayProducerBiopax3 method addContentBindingFeature.
// intraMolecular Boolean single
// bindsTo BindingFeature single
private Element addContentBindingFeature(BioPaxObject bpObject, Element element) {
element = addContentEntityFeature(bpObject, element);
BindingFeature ob = (BindingFeature) bpObject;
Element tmpElement = null;
if (ob.getIntraMolecular() != null) {
tmpElement = new Element("intraMolecular", bp);
tmpElement.setAttribute("datatype", schemaBoolean, rdf);
tmpElement.setText(ob.getIntraMolecular().toString());
element.addContent(tmpElement);
}
if (ob.getBindsTo() != null) {
tmpElement = new Element("bindsTo", bp);
addIDToProperty(tmpElement, ob.getBindsTo());
mustPrintObject(ob.getBindsTo());
element.addContent(tmpElement);
}
return element;
}
use of org.vcell.pathway.BindingFeature in project vcell by virtualcell.
the class PathwayReader method addObjectBindingFeature.
private BindingFeature addObjectBindingFeature(Element element) {
BindingFeature bindingFeature = new BindingFeatureImpl();
addAttributes(bindingFeature, element);
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentBindingFeature(bindingFeature, element, childElement)) {
showUnexpected(childElement, bindingFeature);
}
}
}
pathwayModel.add(bindingFeature);
return bindingFeature;
}
use of org.vcell.pathway.BindingFeature in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addObjectEntityFeature.
private EntityFeature addObjectEntityFeature(Element element) {
if (element.getChildren().size() == 0) {
EntityFeatureProxy proxy = new EntityFeatureProxy();
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("BindingFeature")) {
BindingFeature thingie = addObjectBindingFeature(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("FragmentFeature")) {
FragmentFeature thingie = addObjectFragmentFeature(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("ModificationFeature")) {
ModificationFeature thingie = addObjectModificationFeature(childElement);
pathwayModel.add(thingie);
return thingie;
}
}
}
EntityFeature entityFeature = new EntityFeatureImpl();
addAttributes(entityFeature, element);
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentEntityFeature(entityFeature, element, childElement)) {
showUnexpected(childElement);
}
}
}
pathwayModel.add(entityFeature);
return entityFeature;
}
use of org.vcell.pathway.BindingFeature in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addObjectBindingFeature.
private BindingFeature addObjectBindingFeature(Element element) {
BindingFeature bindingFeature = new BindingFeatureImpl();
addAttributes(bindingFeature, element);
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentBindingFeature(bindingFeature, element, childElement)) {
showUnexpected(childElement);
}
}
}
pathwayModel.add(bindingFeature);
return bindingFeature;
}
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