Method extendPE

src/rnabloom/util/GraphUtils.java:6567–6678

(ArrayList<Kmer> kmers, 
                                            BloomFilterDeBruijnGraph graph,
                                            int maxTipLength,
                                            float minKmerCov)

    }
    
    public static int[] extendPE(ArrayList<Kmer> kmers, 
                                            BloomFilterDeBruijnGraph graph,
                                            int maxTipLength,
                                            float minKmerCov) {
        final int d = graph.getFragPairedKmerDistance();
        final float multiplier = 0.1f;
        
        int origLen = kmers.size();
        
        HashSet<Kmer> usedKmers = new HashSet<>(kmers);

        Collections.reverse(kmers);
        
        while (true) {
            float covThreshold = getMinimumKmerCoverage(kmers, Math.max(0, kmers.size()-d), kmers.size());
            
            ArrayDeque<Kmer> e =  null;
                
            while (true) {
                covThreshold = Math.max(minKmerCov, covThreshold * multiplier);
                
                e =  extendLeftPE(kmers, graph, maxTipLength, covThreshold);
                
                if ((e != null && !e.isEmpty()) || covThreshold == minKmerCov) {
                    break;
                }
            }

            if (e == null || e.isEmpty()) {
                break;
            }
            
            Iterator<Kmer> itr = e.iterator();
            boolean used = true;
            
            while (itr.hasNext() && used) {
                Kmer kmer = itr.next();
                
                if (!usedKmers.contains(kmer)) {
                    used = false;
                }
            }
            
            int endIndex = Math.max(0, kmers.size()-d+e.size());
            for (int i=kmers.size()-1; i>=endIndex && used; --i) {
                Kmer kmer = kmers.get(i);
                
                if (!usedKmers.contains(kmer)) {
                    used = false;
                }
            }
            
            if (used && (kmers.size() < d || hasDuplicatedKmerPair(kmers, e.getLast(), d, kmers.size()-1-d+e.size()))) {
                break;
            }
            
            kmers.addAll(e);
            usedKmers.addAll(e);