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

Example 1 with EntityFeature

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

the class PathwayReader method addObjectEntityFeature.

private EntityFeature addObjectEntityFeature(Element element) {
    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, entityFeature);
            }
        }
    }
    pathwayModel.add(entityFeature);
    return entityFeature;
}

Example 2 with EntityFeature

use of org.vcell.pathway.EntityFeature 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;
}

Example 3 with EntityFeature

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

the class PathwayProducerBiopax3 method addContentEntityFeature.

// featureLocation 		SequenceLocation 			multiple
// featureLocationType 	SequenceRegionVocabulary 	multiple
// memberFeature 			EntityFeature 				multiple
// evidence 				Evidence 					multiple
private Element addContentEntityFeature(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    EntityFeature ob = (EntityFeature) bpObject;
    Element tmpElement = null;
    if (ob.getFeatureLocation() != null && ob.getFeatureLocation().size() > 0) {
        List<SequenceLocation> list = ob.getFeatureLocation();
        for (SequenceLocation item : list) {
            tmpElement = new Element("featureLocation", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getFeatureLocationType() != null && ob.getFeatureLocationType().size() > 0) {
        List<SequenceRegionVocabulary> list = ob.getFeatureLocationType();
        for (SequenceRegionVocabulary item : list) {
            tmpElement = new Element("featureLocationType", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getMemberFeature() != null && ob.getMemberFeature().size() > 0) {
        List<EntityFeature> list = ob.getMemberFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("memberFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 4 with EntityFeature

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

the class PathwayProducerBiopax3 method addContentEntityReference.

// memberEntityReference	EntityReference					multiple
// entityReferenceType		EntityReferenceTypeVocabulary	single
// entityFeature			EntityFeature					multiple
// name					String							multiple
// xref					Xref							multiple
// evidence				Evidence						multiple
private Element addContentEntityReference(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    EntityReference ob = (EntityReference) bpObject;
    Element tmpElement = null;
    if (ob.getMemberEntityReference() != null && ob.getMemberEntityReference().size() > 0) {
        List<EntityReference> list = ob.getMemberEntityReference();
        for (EntityReference item : list) {
            tmpElement = new Element("memberEntityReference", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEntityReferenceType() != null) {
        tmpElement = new Element("entityReferenceType", bp);
        addIDToProperty(tmpElement, ob.getEntityReferenceType());
        mustPrintObject(ob.getEntityReferenceType());
        element.addContent(tmpElement);
    }
    if (ob.getEntityFeature() != null && ob.getEntityFeature().size() > 0) {
        List<EntityFeature> list = ob.getEntityFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("entityFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            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);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 5 with EntityFeature

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

the class PathwayProducerBiopax3 method addContentPhysicalEntity.

// feature					EntityFeature				multiple
// notFeature				EntityFeature				multiple
// memberPhysicalEntity	PhysicalEntity				multiple
// cellularLocation		CellularLocationVocabulary	single
private Element addContentPhysicalEntity(BioPaxObject bpObject, Element element) {
    element = addContentEntity(bpObject, element);
    PhysicalEntity ob = (PhysicalEntity) bpObject;
    Element tmpElement = null;
    if (ob.getFeature() != null && ob.getFeature().size() > 0) {
        List<EntityFeature> list = ob.getFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("feature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getNotFeature() != null && ob.getNotFeature().size() > 0) {
        List<EntityFeature> list = ob.getNotFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("notFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getMemberPhysicalEntity() != null && ob.getMemberPhysicalEntity().size() > 0) {
        List<PhysicalEntity> list = ob.getMemberPhysicalEntity();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("memberPhysicalEntity", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getCellularLocation() != null) {
        tmpElement = new Element("cellularLocation", bp);
        addIDToProperty(tmpElement, ob.getCellularLocation());
        mustPrintObject(ob.getCellularLocation());
        element.addContent(tmpElement);
    }
    return element;
}