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);
}
