SearchResultMatchI addResult(SequenceI seq, int start, int end);
/**
+ * Adds one ore more [start, end] ranges to the results (unless already added
+ * to avoid duplicates). This method only increments the match count by 1.
+ * This is for the case where a match spans ignored hidden residues - it is
+ * formally two or more contiguous matches, but only counted as one match.
+ *
+ * @param seq
+ * @param positions
+ */
+ void addResult(SequenceI seq, int[] positions);
+
+ /**
* adds all match results in the argument to this set
*
* @param toAdd
int[] getResults(SequenceI sequence, int start, int end);
/**
- * Returns the number of matches found
+ * Returns the number of matches found. Note that if a match straddles ignored
+ * hidden residues, it is counted as one match, although formally recorded as
+ * two (or more) contiguous matched sequence regions
*
* @return
*/
- int getSize();
+ int getCount();
/**
* Returns true if no search result matches are held.