/** * Use DefaultAliasComparator to know if two aliases are equals. * @param alias1 * @param alias2 * @return true if the two aliases are equal */ public static boolean areEquals(Alias alias1, Alias alias2){ if (alias1 == alias2){ return true; } else if (alias1 == null || alias2 == null){ return false; } else { CvTerm type1 = alias1.getType(); CvTerm type2 = alias2.getType(); if (!DefaultCvTermComparator.areEquals(type1, type2)){ return false; } // check identifiers which cannot be null String name1 = alias1.getName(); String name2 = alias2.getName(); return name1.equals(name2); } } }
public void writeAlias(Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(alias)); // write xref separator writer.write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ writer.write("("); escapeAndWriteString(alias.getType().getShortName()); writer.write(")"); } } }
/** * * @param alias * @return the hashcode consistent with the equals method for this comparator */ public static int hashCode(Alias alias){ if (unambiguousAliasComparator == null){ unambiguousAliasComparator = new UnambiguousAliasComparator(); } if (alias == null){ return 0; } int hashcode = 31; CvTerm type = alias.getType(); hashcode = 31*hashcode + UnambiguousCvTermComparator.hashCode(type); String name = alias.getName(); hashcode = 31*hashcode + name.hashCode(); return hashcode; } }
/** * To know if an alias have a specific type. * @param alias : the alias * @param typeId : alias type MI identifier * @param typeName : alias type name * @return true if the alias has the type with given name/identifier */ public static boolean doesAliasHaveType(Alias alias, String typeId, String typeName){ if (alias == null || (typeName == null && typeId == null)){ return false; } CvTerm type = alias.getType(); if (type == null){ return false; } // we can compare identifiers if (typeId != null && type.getMIIdentifier() != null){ // we have the same type id return type.getMIIdentifier().equals(typeId); } // we need to compare type names else if (typeName != null) { return typeName.equalsIgnoreCase(type.getShortName()); } return false; }
public void writeAlias(ParticipantEvidence participant, Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(participant, alias)); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } }
public void writeAlias(ModelledParticipant participant, Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(participant, alias)); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } }
CvTerm type = alias.getType(); if (type == null){ return false;
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else{ super.writeAlias(alias); } }
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else{ super.writeAlias(alias); } }
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else { super.writeAlias(alias); } }
if (alias.getType() != null && alias.getType().getMIIdentifier() != null){ final OntologyAccess access = ontologyManager.getOntologyAccess("MI"); final OntologyTermI dbTerm = access.getTermForAccession(alias.getType().getMIIdentifier()); messages = new ArrayList<ValidatorMessage>(); messages.add( new ValidatorMessage( "The alias type MI identifier "+alias.getType().getMIIdentifier()+" does not exist in the PSI-MI ontology. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0300&termName=alias%20type", MessageLevel.ERROR, context, messages = new ArrayList<ValidatorMessage>(); messages.add( new ValidatorMessage( "The MI identifier "+alias.getType().getMIIdentifier()+" is not a valid MI identifier for alias types. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0300&termName=alias%20type", MessageLevel.ERROR, context,