*/
void addResult(SequenceI seq, int[] positions);
+
+ /**
+ * Adds the given start/end region to this search result. If sequence already
+ * has a search result and the range is adjacent to already highlighted
+ * positions, they will be merged
+ *
+ * @param sequence
+ * @param start
+ * @param end
+ * @return true if an existing range was updated with this one
+ */
+ boolean appendResult(SequenceI sequence, int start, int end);
+
/**
* adds all match results in the argument to this set
*
* @return number of bits set
*/
int markColumns(SequenceCollectionI sqcol, BitSet bs);
+
+ /**
+ * Return sub-sequences corresponding to distinct contiguous ranges in the
+ * matching set
+ *
+ * @return list of sequence objects
+ */
+ List<SequenceI> getMatchingSubSequences();
}
\ No newline at end of file