protected List<List<Match>> filterOutlierTranspositions(
VariantGraph into, List<List<Match>> transpositions) {
into.rank();
LOG.debug("{}: Registering transpositions", into);
List<List<Match>> filteredTranspositions = Lists.newArrayList(transpositions);
for (List<Match> transposedPhrase : transpositions) {
Match firstMatch = transposedPhrase.get(0);
VariantGraphVertex from = firstMatch.vertex;
Token token = firstMatch.token;
VariantGraphVertex to = witnessTokenVertices.get(token);
LOG.info("matchPhrase={}", transposedPhrase);
int fromRank = from.getRank();
// LOG.info("from={}, rank={}", from, fromRank);
int toRank = to.getRank();
// LOG.info("to={}, rank={}", to, toRank);
int diff = Math.abs(toRank - fromRank);
int size = transposedPhrase.size();
int relDiff = diff / size;
boolean acceptTransposition = relDiff < 5;
LOG.info(
"accept={}, relDiff={}, size={}, diff={}, from={}, to={}\n",
new Object[] {acceptTransposition, relDiff, size, diff, from, to});
if (acceptTransposition) {
for (Match match : transposedPhrase) {
into.transpose(match.vertex, witnessTokenVertices.get(match.token));
}
} else {
filteredTranspositions.remove(transposedPhrase);
}
}
return filteredTranspositions;
}
protected void merge(
VariantGraph into,
Iterable<Token> witnessTokens,
Map<Token, VariantGraphVertex> alignments) {
Preconditions.checkArgument(!Iterables.isEmpty(witnessTokens), "Empty witness");
final Witness witness = Iterables.getFirst(witnessTokens, null).getWitness();
LOG.debug("{} + {}: Merge comparand into graph", into, witness);
witnessTokenVertices = Maps.newHashMap();
VariantGraphVertex last = into.getStart();
final Set<Witness> witnessSet = Collections.singleton(witness);
for (Token token : witnessTokens) {
VariantGraphVertex matchingVertex = alignments.get(token);
if (matchingVertex == null) {
matchingVertex = into.add(token);
} else {
if (LOG.isTraceEnabled()) {
LOG.trace("Adding matched {} to {}", token, matchingVertex);
}
matchingVertex.add(Collections.singleton(token));
}
witnessTokenVertices.put(token, matchingVertex);
into.connect(last, matchingVertex, witnessSet);
last = matchingVertex;
}
into.connect(last, into.getEnd(), witnessSet);
}