Examples with PhysicalEntityProxy org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy used on opensource projects

Example 6 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReader method addContentControl.

private boolean addContentControl(Control control, Element element, Element childElement) {
    if (addContentInteraction(control, element, childElement)) {
        return true;
    }
    /**
     * InteractionImpl controlledInteraction
     * Pathway controlledPathway
     * String controlType
     * ArrayList<Pathway> pathwayControllers
     * ArrayList<PhysicalEntity> physicalControllers
     */
    if (childElement.getName().equals("CONTROLLER")) {
        Element physicalEntityParticipantElement = childElement.getChild("physicalEntityParticipant", bp);
        if (physicalEntityParticipantElement != null) {
            Element physicalEntityPropertyElement = physicalEntityParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    control.addPhysicalController(physicalEntityProxy);
                    return true;
                }
            }
        }
        Element sequenceParticipantElement = childElement.getChild("sequenceParticipant", bp);
        if (sequenceParticipantElement != null) {
            Element physicalEntityPropertyElement = sequenceParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    control.addPhysicalController(physicalEntityProxy);
                    return true;
                }
            }
        }
        // }
        return false;
    // // is it a pathway controller?
    // control.getPathwayControllers().add(addPathway(childElement));
    } else if (childElement.getName().equals("CONTROLLED")) {
        Attribute resourceAttribute = childElement.getAttribute("resource", rdf);
        if (resourceAttribute != null) {
            InteractionOrPathwayProxy controlledEntityProxy = new InteractionOrPathwayProxy();
            control.setControlledInteraction(controlledEntityProxy);
            pathwayModel.add(controlledEntityProxy);
            String uri = context.unRelativizeURI(childElement, resourceAttribute.getValue());
            controlledEntityProxy.setID(uri);
            return true;
        }
        return false;
    } else if (childElement.getName().equals("CONTROL-TYPE")) {
        control.setControlType(childElement.getTextTrim());
        return true;
    } else {
        return false;
    }
}