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(")"); } } } }
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); } } } }
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(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); } } } }
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 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>(); }
writer.write(er.getName().toString()); writer.write("\t"); writer.write(er.getXref().toString()); writer.write("\t"); writer.write(printControls(getDeltaControl(sChange)));
/** * 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>(); }
for (Xref xref : er.getXref())
/** * 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>(); }
/** * 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>(); }
private org.opencb.bionetdb.core.models.Rna createRna(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Rna rna = new org.opencb.bionetdb.core.models.Rna(); Rna rnaBP = (Rna) bioPAXElement; // Common properties setPhysicalEntityCommonProperties(rnaBP, rna); // Rna properties if (rnaBP.getEntityReference() != null) { EntityReference entityReference = rnaBP.getEntityReference(); // altIds for (String name : entityReference.getName()) { org.opencb.bionetdb.core.models.Xref xref = new org.opencb.bionetdb.core.models.Xref(); xref.setSource(REACTOME_FEAT + "biopax"); xref.setId(name); rna.setXref(xref); } // description rna.setDescription(new ArrayList<>(entityReference.getComment())); // xref Set<Xref> xrefs = entityReference.getXref(); for (Xref xref : xrefs) { org.opencb.bionetdb.core.models.Xref x = new org.opencb.bionetdb.core.models.Xref(); x.setSource(xref.getDb()); x.setSourceVersion(xref.getDbVersion()); x.setId(xref.getId()); x.setIdVersion(xref.getIdVersion()); rna.setXref(x); } } return rna; }
private org.opencb.bionetdb.core.models.Protein createProtein(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Protein protein = new org.opencb.bionetdb.core.models.Protein(); Protein proteinBP = (Protein) bioPAXElement; // Common properties setPhysicalEntityCommonProperties(proteinBP, protein); // Protein properties if (proteinBP.getEntityReference() != null) { EntityReference entityReference = proteinBP.getEntityReference(); // altIds for (String name : entityReference.getName()) { org.opencb.bionetdb.core.models.Xref xref = new org.opencb.bionetdb.core.models.Xref(); xref.setSource(REACTOME_FEAT + "biopax"); xref.setId(name); protein.setXref(xref); } // description protein.setDescription(new ArrayList<>(entityReference.getComment())); // xref Set<Xref> xrefs = entityReference.getXref(); for (Xref xref : xrefs) { org.opencb.bionetdb.core.models.Xref x = new org.opencb.bionetdb.core.models.Xref(); x.setSource(xref.getDb()); x.setSourceVersion(xref.getDbVersion()); x.setId(xref.getId()); x.setIdVersion(xref.getIdVersion()); protein.setXref(x); } } return protein; }
Set<Xref> xrefs = entityReference.getXref(); for (Xref xref : xrefs) { org.opencb.bionetdb.core.models.Xref x = new org.opencb.bionetdb.core.models.Xref();
private org.opencb.bionetdb.core.models.Dna createDna(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Dna dna = new org.opencb.bionetdb.core.models.Dna(); Dna dnaBP = (Dna) bioPAXElement; // Common properties setPhysicalEntityCommonProperties(dnaBP, dna); // Dna properties if (dnaBP.getEntityReference() != null) { EntityReference entityReference = dnaBP.getEntityReference(); // altIds for (String name : entityReference.getName()) { org.opencb.bionetdb.core.models.Xref xref = new org.opencb.bionetdb.core.models.Xref(); xref.setSource(REACTOME_FEAT + "biopax"); xref.setId(name); dna.setXref(xref); } // description dna.setDescription(new ArrayList<>(entityReference.getComment())); // xref Set<Xref> xrefs = entityReference.getXref(); for (Xref xref : xrefs) { org.opencb.bionetdb.core.models.Xref x = new org.opencb.bionetdb.core.models.Xref(); x.setSource(xref.getDb()); x.setSourceVersion(xref.getDbVersion()); x.setId(xref.getId()); x.setIdVersion(xref.getIdVersion()); dna.setXref(x); } } return dna; }