-
- // /**
- // * Since we are traversing the sorted feature array in a forward direction,
- // * all elements prior to the one we are working on have been fully linked.
- // All
- // * we are doing is following those links until we find the first array
- // feature
- // * with a containedBy element that has an end >= our begin point. It is
- // * generally a very short list -- maybe one or two depths. But it might be
- // * more than that.
- // *
- // * @param sf
- // * @param sf0
- // * @return
- // */
- // private SequenceFeature getContainedBy(SequenceFeature sf,
- // SequenceFeature sf0)
- // {
- // int begin = sf0.begin;
- // while (sf != null)
- // {
- // if (begin <= sf.end)
- // {
- // // System.out.println("\nFSJS found " + sf0 + "\nFS in " + sf);
- // return sf;
- // }
- // sf = sf.containedBy;
- // }
- // return null;
- // }
-
- // /**
- // * Fast find of known features already on the list; slower removal of
- // * equivalent feature, not necessarily identical.
- // *
- // * @param feature
- // * @return 0-based index for this feature in featureList
- // */
- // @Override
- // protected int getEquivalentFeatureIndex(List<SequenceFeature> list,
- // SequenceFeature feature)
- // {
- // int pos = feature.index - 1;
- // if (!isTainted && pos >= 0)
- // {
- // return pos;
- // }
- // return super.getEquivalentFeatureIndex(list, feature);
- // }
- //
- // /**
- // * Find all overlaps; special case when there is only one feature. The
- // * required array of start-sorted SequenceFeature is created lazily.
- // *
- // * @param start
- // * @param end
- // * @param result
- // */
- // private void getOverlaps(long start, long end,
- // List<SequenceFeature> result)
- // {
- // int n = featureList.size();
- // switch (n)
- // {
- // case 0:
- // return;
- // case 1:
- // justCheckOne(featureList.get(0), start, end, result);
- // return;
- // default:
- // if (isTainted)
- // {
- // orderedFeatureStarts = featureList
- // .toArray(new SequenceFeature[featureList.size()]);
- // linkFeatures(orderedFeatureStarts);
- // isTainted = false;
- // }
- // break;
- // }
- //
- // // (1) Find the closest feature to this position.
- //
- // int index = getClosestFeature(orderedFeatureStarts, start);
- // SequenceFeature sf = (index < 0 ? null : orderedFeatureStarts[index]);
- //
- // // (2) Traverse the containedBy field, checking for overlap.
- //
- // while (sf != null)
- // {
- // if (sf.end >= start)
- // {
- // result.add(sf);
- // }
- // sf = sf.containedBy;
- // }
- //
- // // (3) For an interval, find the last feature that starts in this interval,
- // // and add all features up through that feature.
- //
- // if (end > start)
- // {
- // // fill in with all features that start within this interval, fully
- // // inclusive
- // int index2 = getClosestFeature(orderedFeatureStarts, end);
- // while (++index <= index2)
- // {
- // result.add(orderedFeatureStarts[index]);
- // }
- //
- // }
- // }
- //
- // /**
- // * Quick check when we only have one feature.
- // *
- // * @param sf
- // * @param start
- // * @param end
- // * @param result
- // */
- // private void justCheckOne(SequenceFeature sf, long start, long end,
- // List<SequenceFeature> result)
- // {
- // if (sf.begin <= end && sf.end >= start)
- // {
- // result.add(sf);
- // }
- // return;
- // }
- //
- // /**
- // * Run through the sorted sequence array once, building the containedBy
- // linked
- // * list references. Does a check first to make sure there is actually
- // * something out there that is overlapping. A null for sf.containedBy means
- // * there are no overlaps for this feature.
- // *
- // * @param features
- // */
- // private void linkFeatures(SequenceFeature[] features)
- // {
- // int n = features.length;
- // switch (n)
- // {
- // case 0:
- // return;
- // case 1:
- // features[0].index = 1;
- // return;
- // }
- // int maxEnd = features[0].end;
- // for (int i = 1; i < n;)
- // {
- // SequenceFeature sf = features[i];
- // if (sf.begin <= maxEnd)
- // {
- // sf.containedBy = getContainedBy(features[i - 1], sf);
- // }
- // if (sf.end > maxEnd)
- // {
- // maxEnd = sf.end;
- // }
- // sf.index = ++i;
- // }
- // }