+ * Answers true if the list contains the feature, else false. This method is
+ * optimised for the condition that the list is sorted on feature start
+ * position ascending, and will give unreliable results if this does not hold.
+ *
+ * @param features
+ * @param feature
+ * @return
+ */
+ protected static boolean contains(List<SequenceFeature> features,
+ SequenceFeature feature)
+ {
+ if (features == null || feature == null)
+ {
+ return false;
+ }
+
+ /*
+ * locate the first entry in the list which does not precede the feature
+ */
+ int pos = binarySearch(features,
+ SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
+ int len = features.size();
+ while (pos < len)
+ {
+ SequenceFeature sf = features.get(pos);
+ if (sf.getBegin() > feature.getBegin())
+ {
+ return false; // no match found
+ }
+ if (sf.equals(feature))
+ {
+ return true;
+ }
+ pos++;
+ }
+ return false;
+ }
+
+ /**