+ /**
+ * Removes from the list of features any that start after, or end before, the
+ * given column position. This allows us to retain only those features
+ * adjacent to a gapped position that straddle the position.
+ *
+ * @param features
+ * @param column
+ * alignment column (1..)
+ * @param sequence
+ */
+ protected void removeAdjacentFeatures(List<SequenceFeature> features,
+ int column, SequenceI sequence)
+ {
+ // TODO should this be an AlignViewController method (shared by gui)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
+ {
+ it.remove();
+ }
+ }
+ }
+