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

Example 21 with PhysicalEntity

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

the class PathwayProducerBiopax3 method addContentControl.

// controller 		Pathway 		multiple
// controller 		PhysicalEntity 	multiple
// controlType 	String 			single
// controlled 		Interaction 	single
// controlled 		Pathway 		single
private Element addContentControl(BioPaxObject bpObject, Element element) {
    element = addContentInteraction(bpObject, element);
    Control ob = (Control) bpObject;
    Element tmpElement = null;
    if (ob.getPathwayControllers() != null && ob.getPathwayControllers().size() > 0) {
        List<Pathway> list = ob.getPathwayControllers();
        for (Pathway item : list) {
            tmpElement = new Element("controller", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getPhysicalControllers() != null && ob.getPhysicalControllers().size() > 0) {
        List<PhysicalEntity> list = ob.getPhysicalControllers();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("controller", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getControlType() != null && ob.getControlType().length() > 0) {
        tmpElement = new Element("controlType", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getControlType());
        element.addContent(tmpElement);
    }
    if (ob.getControlledInteraction() != null) {
        tmpElement = new Element("controlled", bp);
        addIDToProperty(tmpElement, ob.getControlledInteraction());
        mustPrintObject(ob.getControlledInteraction());
        element.addContent(tmpElement);
    }
    if (ob.getControlledPathway() != null) {
        tmpElement = new Element("controlled", bp);
        addIDToProperty(tmpElement, ob.getControlledPathway());
        mustPrintObject(ob.getControlledPathway());
        element.addContent(tmpElement);
    }
    return element;
}

Example 22 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity 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;
}

Example 23 with PhysicalEntity

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

the class PathwayProducerBiopax3 method addContentComplex.

// componentStoichiometry 	Stoichiometry 		multiple
// component 				PhysicalEntity 		multiple
private Element addContentComplex(BioPaxObject bpObject, Element element) {
    element = addContentPhysicalEntity(bpObject, element);
    Complex ob = (Complex) bpObject;
    Element tmpElement = null;
    if (ob.getComponentStoichiometry() != null && ob.getComponentStoichiometry().size() > 0) {
        List<Stoichiometry> list = ob.getComponentStoichiometry();
        for (Stoichiometry item : list) {
            tmpElement = new Element("componentStoichiometry", bp);
            // if(item instanceof RdfObjectProxy) {
            // tmpElement.setAttribute("resource", ((RdfObjectProxy)item).getResource(), rdf);
            // } else {
            // tmpElement.setAttribute("resource", item.resourceFromID(), rdf);
            // }
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getComponents() != null && ob.getComponents().size() > 0) {
        List<PhysicalEntity> list = ob.getComponents();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("component", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 24 with PhysicalEntity

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

the class PathwayReader method addObjectPhysicalEntity.

private PhysicalEntity addObjectPhysicalEntity(Element element) {
    PhysicalEntity physicalEntity = new PhysicalEntity();
    Namespace rdf = Namespace.getNamespace("rdf", DefaultNameSpaces.RDF.uri);
    if (element.getAttributes().size() > 0) {
        physicalEntity = new PhysicalEntity();
        addAttributes(physicalEntity, element);
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentPhysicalEntity(physicalEntity, element, childElement)) {
                showUnexpected(childElement, physicalEntity);
            }
        }
    }
    pathwayModel.add(physicalEntity);
    return physicalEntity;
}

Example 25 with PhysicalEntity

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

the class AnnotationMapping method createPhysicalEntity.

private PhysicalEntity createPhysicalEntity(ArrayList<Xref> xRef, ArrayList<String> refName, String name) {
    PhysicalEntity physicalEntity = null;
    if (isSmallMolecule(xRef)) {
        physicalEntity = new SmallMolecule();
    } else {
        physicalEntity = new PhysicalEntity();
    }
    physicalEntity.setName(refName);
    physicalEntity.setID("BIOMODEL_" + name);
    // physicalEntity.setxRef(xRef);
    for (Xref ref : xRef) {
        physicalEntity.getxRef().add(ref);
    }
    return physicalEntity;
}