Method findBackbonePath

src/rnabloom/util/GraphUtils.java:4776–4794

(Kmer seed, BloomFilterDeBruijnGraph graph, int lookahead, int windowSize, int maxIteration)

    }
    
    public static ArrayList<Kmer> findBackbonePath(Kmer seed, BloomFilterDeBruijnGraph graph, int lookahead, int windowSize, int maxIteration) {
        Kmer best = seed;
        ArrayList<Kmer> path = greedyExtend(best, graph, lookahead);
        boolean randomSeed = false;
        
        for (int i=1; i<maxIteration; ++i) {
            if (randomSeed) {
                best = path.get((int) (Math.random() * (path.size()-1)));
                randomSeed = false;
            }
            else {
                best = findMaxCoverageWindowKmer(path, graph, windowSize);
                randomSeed = true;
            }
            path = greedyExtend(best, graph, lookahead);
        }
        
        return path;
    }
    
    public static String getBestSegment(ArrayList<String> segments, BloomFilterDeBruijnGraph graph) {
        int numSeqs = segments.size();