public void check(EntityReference er, boolean fix) { if(er.getMemberEntityReference().isEmpty()) { // for non-generic ERs only if (er.getXref().isEmpty()) { error(er, "no.xrefs", false); } else { boolean present = false; for (Xref x : er.getXref()) { Class<? extends BioPAXElement> face = x.getModelInterface(); if (UnificationXref.class.equals(face)) { present = true; } } if (!present) { error(er, "no.unification.xref", false); } } } }
public void check(EntityReference er, boolean fix) { if(!er.getMemberEntityReference().isEmpty()) { if (er.getXref().isEmpty()) { error(er, "no.xrefs", false); } else { boolean present = false; for (Xref x : er.getXref()) { Class<? extends BioPAXElement> face = x.getModelInterface(); if (UnificationXref.class.equals(face)) { present = true; } } if (!present) { error(er, "no.unification.xref", false); } } } }
public void check(final Validation validation, EntityReference er) { if(!er.getMemberEntityReference().isEmpty()) { if (er.getXref().isEmpty()) { error(validation, er, "no.xrefs", false); } else { boolean present = false; for (Xref x : er.getXref()) { Class<? extends BioPAXElement> face = x.getModelInterface(); if (UnificationXref.class.equals(face)) { present = true; } } if (!present) { error(validation, er, "no.unification.xref", false); } } } }
public void check(final Validation validation, EntityReference er) { if(er.getMemberEntityReference().isEmpty()) { // for non-generic ERs only if (er.getXref().isEmpty()) { error(validation, er, "no.xrefs", false); } else { boolean present = false; for (Xref x : er.getXref()) { Class<? extends BioPAXElement> face = x.getModelInterface(); if (UnificationXref.class.equals(face)) { present = true; } } if (!present) { error(validation, er, "no.unification.xref", false); } } } }
private static <T extends Xref> List<T> getXRefs(BioPAXElement bpe, Class<T> xrefClass, boolean withMembersIfGeneric) { if(bpe instanceof XReferrable) { List<T> erefs = new ArrayList<T>(); erefs.addAll(new ClassFilterSet<Xref,T>( ((XReferrable)bpe).getXref(), xrefClass) ); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { EntityReference entityReference = ((SimplePhysicalEntity)bpe).getEntityReference(); erefs.addAll(new ClassFilterSet<Xref,T>(entityReference.getXref(), xrefClass) ); //add xrefs from all member ERs (though, not going into members' members...) if(withMembersIfGeneric) for(EntityReference memberEntityReference : entityReference.getMemberEntityReference()) erefs.addAll(new ClassFilterSet<Xref,T>(memberEntityReference.getXref(), xrefClass) ); } else if(bpe instanceof EntityReference) { erefs.addAll(new ClassFilterSet<Xref,T>(((EntityReference)bpe).getXref(), xrefClass) ); //add xrefs from all member ERs (though, not going into members' members...) if(withMembersIfGeneric) for(EntityReference memberEntityReference : ((EntityReference)bpe).getMemberEntityReference()) erefs.addAll(new ClassFilterSet<Xref,T>(memberEntityReference.getXref(), xrefClass) ); } return erefs; } return new ArrayList<T>(); }
private Group inferGroupFromER(EntityReference element, Model model) { Group group = new Group(false, element); for (EntityReference member : element.getMemberEntityReference()) { if(group.genericClass==null) { group.genericClass = member.getModelInterface(); } group.addMember(member); } Set<Group> owners = delegated.get(element); if (owners != null) { for (Group owner : owners) { owner.addSubgroup(group); } } ModelUtils.copySimplePointers(model, element, group); return group.isEmpty() ? null : group; } }