Method updateNormalizedCounts

src/rnabloom/util/PafUtils.java:276–350

(ArrayList<Overlap> targets, HashMap<String, Float> counts)

    }
    
    private static void updateNormalizedCounts(ArrayList<Overlap> targets, HashMap<String, Float> counts) {
        if (!targets.isEmpty()) {
            if (targets.size() == 1) {
                Overlap t = targets.get(0);
                Float c = counts.get(t.tName);
                if (c == null) {
                    c = (t.tEnd - t.tStart)/(float) t.tLen;
                }
                else {
                    c += (t.tEnd - t.tStart)/(float) t.tLen;
                }
                counts.put(t.tName, c);
            }
            else {
                Collections.sort(targets);

                ArrayList<Overlap> targetsKept = new ArrayList<>();
                HashMap<Overlap, ArrayList<Overlap>> multiTargets = new HashMap<>();
                for (Overlap m : targets) {
                    Overlap c = getOverlapContainer(m, targetsKept, 0.95f);
                    if (c == null) {
                        // region not contained
                        targetsKept.add(m);
                    }
                    else if (m.qEnd - m.qStart >= (c.qEnd - c.qStart) * 0.95f) {
                        // region multimaps
                        ArrayList<Overlap> multimaps = multiTargets.get(c);
                        if (multimaps == null) {
                            multimaps = new ArrayList<>();
                            multiTargets.put(c, multimaps);
                        }
                        multimaps.add(m);
                    }
                }

                for (Overlap t : targetsKept) {
                    ArrayList<Overlap> multimaps = multiTargets.get(t);
                    if (multimaps != null) {
                        // fractional assignment of multimapped region
                        float fraction = 1f/(multimaps.size() + 1);

                        Float c = counts.get(t.tName);
                        if (c == null) {
                            c = (t.tEnd - t.tStart)/(float) t.tLen * fraction;
                        }
                        else {
                            c += (t.tEnd - t.tStart)/(float) t.tLen * fraction;
                        }
                        counts.put(t.tName, c);

                        for (Overlap mm : multimaps) {
                            c = counts.get(mm.tName);
                            if (c == null) {
                                c = (mm.tEnd - mm.tStart)/(float) mm.tLen * fraction;
                            }
                            else {
                                c += (mm.tEnd - mm.tStart)/(float) mm.tLen * fraction;
                            }