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); }
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 mergeTranspositions(VariantGraph into, List<List<Match>> transpositions) { final Map<Token, VariantGraphVertex> transposedTokens = Maps.newHashMap(); for (List<Match> transposedPhrase : transpositions) { for (Match match : transposedPhrase) { transposedTokens.put(match.token, match.vertex); } } for (Token token : transposedTokens.keySet()) { into.transpose(transposedTokens.get(token), witnessTokenVertices.get(token)); } }