public boolean canCheck(Object thing) { return (thing instanceof SimplePhysicalEntity) && (((SimplePhysicalEntity) thing).getEntityReference() != null); } }
@Override public boolean canCheck(Object thing) { return thing instanceof SimplePhysicalEntity && ((SimplePhysicalEntity) thing).getEntityReference() != null; } }
boolean sameKindEntityExists(SimplePhysicalEntity spe, Set<SimplePhysicalEntity> side) { assert !(spe instanceof SmallMolecule); boolean ret = false; for (SimplePhysicalEntity value : side) { if (!(value instanceof SmallMolecule)) { if(value.getEntityReference() != null && value.getEntityReference().isEquivalent(spe.getEntityReference())) return true; } } return ret; }
private static boolean checkEntity(GroupMap map, PhysicalEntity pe, BioPAXElement element) { return pe instanceof SimplePhysicalEntity && (element.equals(((SimplePhysicalEntity) pe).getEntityReference())) || element.equals(map.getEntityReferenceOrGroup(pe)); }
@Override public boolean match(SimplePhysicalEntity a, SimplePhysicalEntity b) { return !a.equals(b) && a.getEntityReference() != null && !a.getName().isEmpty() && !b.getName().isEmpty() && !a.getEntityReference().isEquivalent(b.getEntityReference()) && !BiopaxValidatorUtils.namesInCommon(a, b).isEmpty(); } };
private void appendXrefs(Controller controller, StringBuilder builder) { HashSet<SimplePhysicalEntity> simple = new HashSet<SimplePhysicalEntity>(); if(controller instanceof PhysicalEntity) { Simplify.getSimpleMembers((PhysicalEntity) controller, simple); for (SimplePhysicalEntity spe : simple) { builder.append("(").append(spe.getEntityReference().getXref()).append(")"); } } } }
/** * @param spe a physical entity but complex * @return all preceding states of a SimplePhysicalEntity. Preceding states are other spes of the * same EntityReference that are converted into this spe in one conversion. */ public Set<SimplePhysicalEntity> getPrecedingStates(SimplePhysicalEntity spe) { Set<SimplePhysicalEntity> result = new HashSet<SimplePhysicalEntity>(); EntityReference er = spe.getEntityReference(); Set<PEStateChange> peStateChanges = stateChangeMap.get(er); for (PEStateChange peStateChange : peStateChanges) { SimplePhysicalEntity next = peStateChange.changedInto(spe); if (next != null) { result.add(peStateChange.left); } } return result; }
/** * @param spe a physical entity but complex * @return all succeeding states of a SimplePhysicalEntity. Preceding states are other spes of the * same EntityReference that this spe is converted into in one conversion. */ public Set<SimplePhysicalEntity> getSucceedingStates(SimplePhysicalEntity spe) { Set<SimplePhysicalEntity> result = new HashSet<SimplePhysicalEntity>(); EntityReference er = spe.getEntityReference(); Set<PEStateChange> peStateChanges = stateChangeMap.get(er); for (PEStateChange peStateChange : peStateChanges) { SimplePhysicalEntity next = peStateChange.changedFrom(spe); if (next != null) { result.add(peStateChange.left); } } return result; }
protected BioPAXElement getEntityReferenceOrGroup(BioPAXElement bpe) { BioPAXElement entity = map.get(bpe); if (entity == null) { if (bpe instanceof EntityReference) { entity = bpe; } else if (bpe instanceof SimplePhysicalEntity) { EntityReference er = ((SimplePhysicalEntity) bpe).getEntityReference(); if (er != null) { entity = map.get(er); if (entity == null) entity = er; } else { if (log.isWarnEnabled()) log.warn("SimplePhysicalEntity with ID " + bpe.getRDFId() + " has NULL EntityReference"); } } } return entity; }
@Override public boolean match(SimplePhysicalEntity a, SimplePhysicalEntity b) { return !a.equals(b) && a.getEntityReference() != null && !a.getName().isEmpty() && !b.getName().isEmpty() && !a.getEntityReference().isEquivalent(b.getEntityReference()) && CollectionUtils.containsAny(a.getName(), b.getName()); } };
private static <T extends Xref> List<T> getXRefs(BioPAXElement bpe, Class<T> xrefClass) { 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) { erefs.addAll(new ClassFilterSet<Xref,T>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), xrefClass) ); } return erefs; } return new ArrayList<T>(); }
public Set<EntityReference> getRelatedERs(PhysicalEntity pe) { Set<EntityReference> ers = new HashSet<EntityReference>(); if (pe instanceof Complex) { ers.addAll(((Complex) pe).getMemberReferences()); } else if (pe instanceof SimplePhysicalEntity) { EntityReference er = ((SimplePhysicalEntity) pe).getEntityReference(); if (er != null) ers.add(er); for (Object o : TO_SUB_ERS.getValueFromBean(pe)) { if (o instanceof EntityReference) ers.add((EntityReference) o); } } return ers; } }
boolean sameKindEntityExists(SimplePhysicalEntity spe, Set<PhysicalEntity> side) { assert !(spe instanceof SmallMolecule); boolean ret = false; for (PhysicalEntity value : side) { if (value instanceof SimplePhysicalEntity) { SimplePhysicalEntity that = (SimplePhysicalEntity) value; if( !(value instanceof SmallMolecule) && that.getEntityReference() != null && that.getEntityReference().isEquivalent(spe.getEntityReference())) return true; } else { // Complex if(sameKindEntityExists(spe, ((Complex)value).getComponent())) return true; } //still false - check member PEs as well ;) if(sameKindEntityExists(spe, value.getMemberPhysicalEntity())) return true; } return ret; }
public static <T extends Xref> List<ExternalLink> xrefToExternalLinks(BioPAXElement bpe, Class<T> xrefClass) { if(bpe instanceof XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>( ((XReferrable)bpe).getXref(), xrefClass) )); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), xrefClass) )); } return erefs; } return new ArrayList<ExternalLink>(); }
private static <T extends Xref> List<ExternalLink> xrefToExternalLinks(BioPAXElement bpe, Class<T> xrefClass) { if(bpe instanceof XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>( ((XReferrable)bpe).getXref(), xrefClass) )); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), xrefClass) )); } return erefs; } return new ArrayList<ExternalLink>(); }
/** * Gets an ArrayList of all XRefs. * * @return ArrayList of ExternalLink Objects. */ public static List<ExternalLink> getAllXRefs(BioPAXElement bpe) { if(bpe instanceof physicalEntityParticipant) { return getAllXRefs(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof org.biopax.paxtools.model.level2.XReferrable) { return extractXrefs(((org.biopax.paxtools.model.level2.XReferrable)bpe).getXREF()); } else if(bpe instanceof org.biopax.paxtools.model.level3.XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(((org.biopax.paxtools.model.level3.XReferrable)bpe).getXref())); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(((SimplePhysicalEntity)bpe).getEntityReference().getXref())); } return erefs; } return new ArrayList<ExternalLink>(); }
@Override public void check(SimplePhysicalEntity thing, boolean fix) { EntityReference er = thing.getEntityReference(); Set<EntityFeature> erefs = er.getEntityFeature(), peefs = new HashSet<EntityFeature>(); peefs.addAll(thing.getFeature()); peefs.addAll(thing.getNotFeature()); for(EntityFeature ef: peefs) { if(!erefs.contains(ef)) { if(fix) er.addEntityFeature(ef); error(thing, "improper.feature.use", fix, ef.getRDFId(), er.getRDFId()); } } }
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 Map<String, String> calculateIdMapings(Model model) { Map<String, String> idMappings = new HashMap<String, String>(); final Set<SimplePhysicalEntity> proteins = model.getObjects(SimplePhysicalEntity.class); for (SimplePhysicalEntity protein : proteins) { final String protRefId = protein.getEntityReference().getRDFId(); for (Xref xref : protein.getXref()) { if ("uniprotkb".equals(xref.getDb())) { String newId = IDENTIFIERS_ORG + "uniprot/" + xref.getId(); idMappings.put(protRefId, newId); break; } else if ("chebi".equals(xref.getDb())) { String newId = IDENTIFIERS_ORG + xref.getDb() + "/" + xref.getId(); idMappings.put(protRefId, newId); break; } } } return idMappings; }
/** * Gets an ArrayList of all Publication XRefs. * * @param bpe BioPAX element * @return ArrayList of ExternalLink Objects. */ public static List<ExternalLink> getPublicationXRefs(BioPAXElement bpe) { if(bpe instanceof physicalEntityParticipant) { return getPublicationXRefs(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof org.biopax.paxtools.model.level2.XReferrable) { return extractXrefs(new ClassFilterSet<publicationXref>( ((org.biopax.paxtools.model.level2.XReferrable)bpe).getXREF(), publicationXref.class) ); } else if(bpe instanceof org.biopax.paxtools.model.level3.XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(new ClassFilterSet<PublicationXref>( ((org.biopax.paxtools.model.level3.XReferrable)bpe).getXref(), PublicationXref.class) )); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(new ClassFilterSet<PublicationXref>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), PublicationXref.class) )); } return erefs; } return new ArrayList<ExternalLink>(); }