{
/**
- * Adds one region to the results
+ * Adds one region to the results (unless already added, to avoid duplicates)
*
* @param seq
- * Sequence
* @param start
- * int
* @param end
- * int
* @return
*/
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 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
*
* @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.
* @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();
}
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