public Collection<GeneralMessage> check( BioSource bs ) throws SanityRuleException { Collection<GeneralMessage> messages = new ArrayList<GeneralMessage>(); int validIdentityXref = 0; for ( BioSourceXref bioSourceXref : bs.getXrefs() ) { String qualifierMi = bioSourceXref.getCvXrefQualifier().getMiIdentifier(); if ( CvXrefQualifier.IDENTITY_MI_REF.equals( qualifierMi ) ) { String dbMi = bioSourceXref.getCvDatabase().getMiIdentifier(); if ( CvDatabase.NEWT_MI_REF.equals( dbMi ) ) { validIdentityXref++; } } } if ( validIdentityXref == 0 ) { messages.add( new GeneralMessage( MessageDefinition.BIOSOURCE_WITHOUT_NEWT_XREF, bs ) ); } return messages; } }
for ( Iterator iterator = bioSource.getXrefs().iterator(); iterator.hasNext() && foundNewtIdentityXref == false; )