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 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>(); }
private List<UnificationXref> getUnificationXrefsSorted(XReferrable referrable) { List<UnificationXref> urefs = new ArrayList<UnificationXref>( new ClassFilterSet<Xref,UnificationXref>( referrable.getXref(), UnificationXref.class) ); for(UnificationXref ux : new ArrayList<UnificationXref>(urefs)) { if(ux.getDb() == null || ux.getId() == null) { // report error, try next xref log.warn("Won't consider the UnificationXref " + "having NULL 'db' or 'id' property: " + ux + ", " + ux.getRDFId() + ". " + extraInfo()); urefs.remove(ux); } } Comparator<UnificationXref> comparator = new Comparator<UnificationXref>() { @Override public int compare(UnificationXref o1, UnificationXref o2) { String s1 = o1.getDb() + o1.getId(); String s2 = o2.getDb() + o2.getId(); return s1.compareTo(s2); } }; Collections.sort(urefs, comparator); return urefs; }
for (UnificationXref x : new ClassFilterSet<Xref, UnificationXref>(((XReferrable) ele).getXref(), UnificationXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set); for (RelationshipXref x : new ClassFilterSet<Xref, RelationshipXref>(((XReferrable) ele).getXref(), RelationshipXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set);
/** * 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>(); }
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>(); }
/** * 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>(); }
/** * Gets an ArrayList of all Unification XRefs. * * @param bpe BioPAX element * @return ArrayList of ExternalLink Objects. */ public static List<ExternalLink> getUnificationXRefs(BioPAXElement bpe) { if(bpe instanceof physicalEntityParticipant) { return getUnificationXRefs(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof org.biopax.paxtools.model.level2.XReferrable) { return extractXrefs(new ClassFilterSet<unificationXref>( ((org.biopax.paxtools.model.level2.XReferrable)bpe).getXREF(), unificationXref.class) ); } else if(bpe instanceof org.biopax.paxtools.model.level3.XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(new ClassFilterSet<UnificationXref>( ((org.biopax.paxtools.model.level3.XReferrable)bpe).getXref(), UnificationXref.class) )); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(new ClassFilterSet<UnificationXref>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), UnificationXref.class) )); } return erefs; } return new ArrayList<ExternalLink>(); }
/** * Gets an ArrayList of all Relationship XRefs. * * @param bpe BioPAX element * @return ArrayList of ExternalLink Objects. */ public static List<ExternalLink> getRelationshipXRefs(BioPAXElement bpe) { if(bpe instanceof physicalEntityParticipant) { return getRelationshipXRefs(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof org.biopax.paxtools.model.level2.XReferrable) { return extractXrefs(new ClassFilterSet<relationshipXref>( ((org.biopax.paxtools.model.level2.XReferrable)bpe).getXREF(), relationshipXref.class) ); } else if(bpe instanceof org.biopax.paxtools.model.level3.XReferrable) { List<ExternalLink> erefs = new ArrayList<ExternalLink>(); erefs.addAll(extractXrefs(new ClassFilterSet<RelationshipXref>( ((org.biopax.paxtools.model.level3.XReferrable)bpe).getXref(), RelationshipXref.class) )); if(bpe instanceof SimplePhysicalEntity && ((SimplePhysicalEntity)bpe).getEntityReference() != null) { erefs.addAll(extractXrefs(new ClassFilterSet<RelationshipXref>( ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), RelationshipXref.class) )); } return erefs; } return new ArrayList<ExternalLink>(); }