Method greedyExtend

src/rnabloom/util/GraphUtils.java:4695–4744

(Kmer seed, BloomFilterDeBruijnGraph graph, int lookahead)

    }
        
    public static ArrayList<Kmer> greedyExtend(Kmer seed, BloomFilterDeBruijnGraph graph, int lookahead) {
        /**@TODO store smallest strand kmers for non-strand specific sequences */
                
        HashSet<String> pathKmerStr = new HashSet<>(1000);
        pathKmerStr.add(seed.toString());
        
        ArrayList<Kmer> rightPath = new ArrayList<>(1000);
        
        /* extend on right side */
        Kmer best = seed;
        while (true) {
            best = greedyExtendRightOnce(graph, best, lookahead);
            if (best != null) {
                String seq = best.toString();
                if (pathKmerStr.contains(seq)) {
                    break;
                }
                pathKmerStr.add(seq);
                rightPath.add(best);
            }
            else {
                break;
            }
        }
        
        ArrayList<Kmer> leftPath = new ArrayList<>(100);
        
        /* extend on left side */
        best = seed;
        while (true) {
            best = greedyExtendLeftOnce(graph, best, lookahead);
            if (best != null) {
                String seq = best.toString();
                if (pathKmerStr.contains(seq)) {
                    break;
                }
                pathKmerStr.add(seq);
                leftPath.add(best);
            }
            else {
                break;
            }
        }
        
        Collections.reverse(leftPath);
        leftPath.add(seed);
        leftPath.addAll(rightPath);
        
        return leftPath;
    }
    
    public static Kmer findMaxCoverageWindowKmer(ArrayList<Kmer> path, BloomFilterDeBruijnGraph graph, int windowSize) {
        int pathLen = path.size();