/**
* Calculate the comparison of all x all individuals. Since all individuals are being compared,
* and will be necessary for evaluating statistics we will store in an array.
*
* @throws IncoherentStateException
* @throws UnknownFilterException
*/
public void computeIxI() throws UnknownFilterException, IncoherentStateException {
Set<String> individualIds = kb.getIndividualIdsInSignature();
for (String iid : individualIds) {
int ibit = kb.getIndividualIndex(iid);
EWAHCompressedBitmap ibm = kb.getDirectTypesBM(iid);
Set<String> iids = kb.getClassIds(ibm);
ProfileQuery q = ProfileQueryFactory.createQuery(iids);
// compare against all other individuals
q.setLimit(-1);
MatchSet ms = profileMatcher.findMatchProfile(q);
matchScores[ibit] = ms.getScores();
}
}