Method getBestSegment

src/rnabloom/util/GraphUtils.java:4796–4834

(ArrayList<String> segments, BloomFilterDeBruijnGraph graph)

    }
    
    public static String getBestSegment(ArrayList<String> segments, BloomFilterDeBruijnGraph graph) {
        int numSeqs = segments.size();
        switch (numSeqs) {
            case 0:
                return "";
            case 1:
                return segments.get(0);
            default:
                int k = graph.getK();
                
                String best = "";
                float bestCov = 0;
                
                NTHashIterator itr = graph.getHashIterator();
                long[] hVals = itr.hVals;
                
                for (String seg : segments) {
                    if (seg.length() >= k) {
                        itr.start(seg);
                        
                        float min = Float.MAX_VALUE;
                        while (itr.hasNext()) {
                            itr.next();
                            float c = graph.getCount(hVals);
                            if (c < min) {
                                min = c;
                            }
                        }
                        
                        if (min > bestCov) {
                            best = seg;
                            bestCov = min;
                        }
                    }
                }
                
                return best;
        }        
    }
    
    public static String connect(ArrayList<String> segments, BloomFilterDeBruijnGraph graph, int lookahead) {
        int numSeqs = segments.size();