JAL-3490 match count independent of contiguous matches count

[jalview.git] / src / jalview / datamodel / SearchResultsI.java

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 3c3ad4e..c89f363 100644 (file)
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -41,6 +41,17 @@ public interface SearchResultsI
   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
@@ -74,11 +85,13 @@ public interface SearchResultsI
   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.