/**
* @param xref
* @return the hashcode consistent with the equals method for this comparator
*/
public static int hashCode(Xref xref) {
if (unambiguousXrefComparator == null) {
unambiguousXrefComparator = new UnambiguousXrefComparator();
}
if (xref == null) {
return 0;
}
int hashcode = 31;
CvTerm database1 = xref.getDatabase();
String mi1 = database1.getMIIdentifier();
if (mi1 != null) {
hashcode = 31 * hashcode + mi1.hashCode();
} else {
hashcode = 31 * hashcode + database1.getShortName().toLowerCase().trim().hashCode();
}
hashcode = 31 * hashcode + xref.getId().hashCode();
CvTerm qualifier = xref.getQualifier();
if (qualifier != null) {
String qualifierMi = qualifier.getMIIdentifier();
if (qualifierMi != null) {
hashcode = 31 * hashcode + qualifierMi.hashCode();
} else {
hashcode = 31 * hashcode + qualifier.getShortName().toLowerCase().trim().hashCode();
}
}
return hashcode;
}
/**
* It compares first the databases and then the ids (case sensitive) but ignores the version. To
* compare the databases, it looks first at the identifiers id (the database with identifier will
* always come first), otherwise it looks at the database shortlabel only. If one database
* identifier is null, it will always comes after an ExternalIdentifier having a non null database
* id. Then it will compare the qualifier. To compare the qualifiers, it looks first at the
* identifiers id if they both exist, otherwise it looks at the qualifier shortnames only. If one
* qualifier identifier is null, it will always comes after a Xref having a non null qualifiers
* id.
*
* <p>- Two xrefs which are null are equals - The xref which is not null is before null. - Use
* UnambiguousExternalIdentifierComparator to compare first the database and id. - If both xref
* databases and ids are the same, compare the qualifiers.
*
* @param xref1
* @param xref2
*/
public int compare(Xref xref1, Xref xref2) {
int EQUAL = 0;
int BEFORE = -1;
int AFTER = 1;
if (xref1 == xref2) {
return EQUAL;
} else if (xref1 == null) {
return AFTER;
} else if (xref2 == null) {
return BEFORE;
} else {
// compares databases first (cannot use CvTermComparator because have to break the loop)
CvTerm database1 = xref1.getDatabase();
CvTerm database2 = xref2.getDatabase();
String mi1 = database1.getMIIdentifier();
String mi2 = database2.getMIIdentifier();
// if external id of database is set, look at database id only otherwise look at shortname
int comp;
if (mi1 != null && mi2 != null) {
comp = mi1.compareTo(mi2);
} else if (mi1 == null && mi2 != null) {
return AFTER;
} else if (mi2 == null && mi1 != null) {
return BEFORE;
} else {
comp =
database1
.getShortName()
.toLowerCase()
.trim()
.compareTo(database2.getShortName().toLowerCase().trim());
}
if (comp != 0) {
return comp;
}
// check identifiers which cannot be null
String id1 = xref1.getId();
String id2 = xref2.getId();
comp = id1.compareTo(id2);
if (comp != 0) {
return comp;
}
CvTerm qualifier1 = xref1.getQualifier();
CvTerm qualifier2 = xref2.getQualifier();
if (qualifier1 == null && qualifier2 == null) {
return EQUAL;
} else if (qualifier1 == null) {
return AFTER;
} else if (qualifier2 == null) {
return BEFORE;
} else {
String qualifierMi1 = qualifier1.getMIIdentifier();
String qualifierMi2 = qualifier2.getMIIdentifier();
// if external id of qualifier is set, look at qualifier id only otherwise look at shortname
if (qualifierMi1 != null && qualifierMi2 != null) {
return qualifierMi1.compareTo(qualifierMi2);
} else if (qualifierMi1 == null && qualifierMi2 != null) {
return AFTER;
} else if (qualifierMi1 != null && qualifierMi2 == null) {
return BEFORE;
} else {
return qualifier1
.getShortName()
.toLowerCase()
.trim()
.compareTo(qualifier2.getShortName().toLowerCase().trim());
}
}
}
}
