Method naiveExtendLeft

src/rnabloom/util/GraphUtils.java:6959–7012

(Kmer kmer, BloomFilterDeBruijnGraph graph, int maxTipLength, HashSet<Kmer> terminators, float minKmerCov)

    }
    
    public static ArrayDeque<Kmer> naiveExtendLeft(Kmer kmer, BloomFilterDeBruijnGraph graph, int maxTipLength, HashSet<Kmer> terminators, float minKmerCov) {        
        int k = graph.getK();
        int numHash = graph.getMaxNumHash();
        
        HashSet<Kmer> usedKmers = new HashSet<>();
        
        ArrayDeque<Kmer> result = new ArrayDeque<>();
        
        ArrayDeque<Kmer> neighbors = new ArrayDeque<>(4);
        kmer.getPredecessors(k, numHash, graph, neighbors, minKmerCov);
        Kmer best = kmer;
        while (!neighbors.isEmpty()) {
            /** look for back branches*/
            for (Kmer s : best.getRightVariants(k, numHash, graph)) {
                if (s.hasDepthRight(k, numHash, graph, maxTipLength)) {
                    return result;
                }
            }
            
            if (neighbors.size() == 1) {
                best = neighbors.pop();
            }
            else {
                best = null;
                while (!neighbors.isEmpty()) {
                    Kmer n = neighbors.pop();
                    if (n.hasDepthLeft(k, numHash, graph, maxTipLength)) {
                        if (best == null) {
                            best = n;
                        }
                        else {
                            // too many good branches
                            return result;
                        }
                    }
                }
            }
            
            if (best == null) {
                break;
            }
            
            if (terminators.contains(best) || usedKmers.contains(best)) {
                break;
            }
            
            result.addLast(best);
            usedKmers.add(best);
            
            best.getPredecessors(k, numHash, graph, neighbors, minKmerCov);
        }
        
        return result;
    }
    
    public static ArrayDeque<Kmer> naiveExtendLeft(Kmer kmer, BloomFilterDeBruijnGraph graph, int maxTipLength, int bound, float minKmerCov) {        
        int k = graph.getK();