Examples with AnnotationMapping org.vcell.relationship.AnnotationMapping used on opensource projects

Example 1 with AnnotationMapping

use of org.vcell.relationship.AnnotationMapping in project vcell by virtualcell.

the class VCMetaData method createBioPaxObjects.

public void createBioPaxObjects(BioModel bioModel) {
    AnnotationMapping annoMapping = new AnnotationMapping();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    Set<Identifiable> identifiables = vcMetaData.getIdentifiableProvider().getAllIdentifiables();
    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
    for (Identifiable identifiable : identifiables) {
        Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
        if (refGroupMap != null) {
            String info = annoMapping.annotation2BioPaxObject(bioModel, identifiable);
            boolean printInfo = false;
            if (printInfo) {
                System.out.println(info);
            }
        }
    }
}