/** * Method to know if a Xref is a potential identifier. * It can be an identity xref or a secondary xref. * @param ref : the Xref * @return true if the Xref has a qualifier identity or secondary-ac */ public static boolean isXrefAnIdentifier(Xref ref){ if (ref == null || ref.getQualifier() == null){ return false; } String qualifierMI = ref.getQualifier().getMIIdentifier(); if (qualifierMI != null){ return (Xref.IDENTITY_MI.equals(qualifierMI) || Xref.SECONDARY_MI.equals(qualifierMI)); } else { String qualifier = ref.getQualifier().getShortName(); return (Xref.IDENTITY.equalsIgnoreCase(qualifier) || Xref.SECONDARY.equalsIgnoreCase(qualifier)); } }
public void writeXref(Xref xref) throws IOException { if (xref != null){ // write identifier first writeIdentifier(xref); // write qualifier if (xref.getQualifier() != null){ getWriter().write("("); escapeAndWriteString(xref.getQualifier().getShortName()); getWriter().write(")"); } } }
if ( ref.getQualifier() == null ) { continue; else if (ref.getQualifier().getMIIdentifier() != null && !typeMiRefs.isEmpty()){ if ( !typeMiRefs.contains( ref.getQualifier().getMIIdentifier() )){ continue; else if (!typeRefs.contains( ref.getQualifier().getShortName() )){ continue;
/** * Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname) * @param ref : the Xref * @param qualifierId : the qualifier MI identifier * @param qualifierName : the qualifier shortname * @return true if the Xref has a qualifier MI which is qualifierId or qualifier shortname which is qualifierName */ public static boolean doesXrefHaveQualifier(Xref ref, String qualifierId, String qualifierName){ if (ref == null || (qualifierName == null && qualifierId == null)){ return false; } CvTerm qualifier = ref.getQualifier(); if (qualifier == null){ return false; } // we can compare identifiers if (qualifierId != null && qualifier.getMIIdentifier() != null){ // we have the same database id return qualifier.getMIIdentifier().equals(qualifierId); } // we need to compare dbNames else if (qualifierName != null) { return qualifierName.equalsIgnoreCase(qualifier.getShortName()); } return false; }
CvTerm qualifier = xref.getQualifier(); if (qualifier != null){ String qualifierMi = qualifier.getMIIdentifier();
CvTerm qualifier = ref.getQualifier(); if (qualifier == null){ return false;
hashcode = 31 * hashcode + (xref.getVersion() != null ? xref.getVersion().hashCode():0); CvTerm qualifier = xref.getQualifier(); if (qualifier != null){ String qualifierMi = qualifier.getMIIdentifier();
/** * For each cross reference of this XrefContainer, collects all respective cross reference type(s) and * check if the dependencies are correct. * * @param container to check on. * @return a collection of validator messages. * if we fail to retreive the MI Ontology. */ public Collection<ValidatorMessage> check( Experiment container) throws ValidatorException { Collection<ValidatorMessage> messages = Collections.EMPTY_LIST; // Collect the db references Collection<Xref> databaseReferences = container.getXrefs(); if (!databaseReferences.isEmpty()){ messages = new ArrayList<ValidatorMessage>(); for ( Xref reference : databaseReferences) { MiContext context = RuleUtils.buildContext(reference, "database cross reference"); context.addAssociatedContext(RuleUtils.buildContext(container, "experiment")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } } return messages; }
CvTerm qualifier1 = xref1.getQualifier(); CvTerm qualifier2 = xref2.getQualifier(); if (qualifier1 == null && qualifier2 == null){ return EQUAL;
CvTerm qualifier1 = xref1.getQualifier(); CvTerm qualifier2 = xref2.getQualifier();
messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) );
/** * For each cross reference of this XrefContainer, collects all respective cross reference type(s) and * check if the dependencies are correct. * * @param container to check on. * @return a collection of validator messages. * if we fail to retreive the MI Ontology. */ public Collection<ValidatorMessage> check( Interaction container) throws ValidatorException { Collection<ValidatorMessage> messages = new ArrayList<ValidatorMessage>(); // Collect the db references Collection<Xref> databaseReferences = container.getXrefs(); for ( Xref reference : databaseReferences) { MiContext context = RuleUtils.buildContext(reference, "database xref"); context.addAssociatedContext(RuleUtils.buildContext(container, "interaction")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } // Collect the identifiers Collection<Xref> identifiers = container.getIdentifiers(); for ( Xref reference : identifiers) { MiContext context = RuleUtils.buildContext(reference, "database xref"); context.addAssociatedContext(RuleUtils.buildContext(container, "interaction")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } return messages; }
/** * For each cross reference of this XrefContainer, collects all respective cross reference type(s) and * check if the dependencies are correct. * * @param container to check on. * @return a collection of validator messages. * if we fail to retreive the MI Ontology. */ public Collection<ValidatorMessage> check( Feature container) throws ValidatorException { Collection<ValidatorMessage> messages = new ArrayList<ValidatorMessage>(); // Collect the identifiers Collection<Xref> identifiers = container.getIdentifiers(); for ( Xref reference : identifiers) { MiContext context = RuleUtils.buildContext(reference, "database xref"); context.addAssociatedContext(RuleUtils.buildContext(container, "feature")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } // Collect the db references Collection<Xref> databaseReferences = container.getXrefs(); for ( Xref reference : databaseReferences) { MiContext context = RuleUtils.buildContext(reference, "database xref"); context.addAssociatedContext(RuleUtils.buildContext(container, "feature")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } return messages; }
CvTerm qualifier = xref.getQualifier();