LineageSequence seq = (LineageSequence) trainParser.next();
lineageMap.put(seq.getSeqName(), seq.getAncestors());
}
trainParser.close();
NuclSeqMatch sabCal = new NuclSeqMatch(trainSeqFile);
LineageSequenceParser parser = new LineageSequenceParser(new File(testSeqFile));
int count = 0;
while (parser.hasNext()) {
LineageSequence seq = (LineageSequence) parser.next();
HashMap<String,HierarchyTree> queryAncestorNodes = getAncestorNodes(factory.getRoot(), seq.getSeqName(), seq.getAncestors());
TreeSet<KmerMatchCore.BestMatch> matchResults = sabCal.findAllMatches(seq);
short withinLowestRankSab = -1;
short diffLowestRankSab = -1;
String bestDiffLowestRankMatch = null;
for (KmerMatchCore.BestMatch match: matchResults){