X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=ec6f5ee68f343d80a51ce4b19dd7e71e95cfe2a4;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=3c3ad4e9bef81b6a2ebab87c7dace1e4a7441ee3;hpb=745806901cdcda04d9b5c496cb5249a03af19971;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 3c3ad4e..ec6f5ee 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -41,6 +41,29 @@ 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 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
@@ -74,11 +97,13 @@ 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.
@@ -105,4 +130,12 @@ public interface SearchResultsI
    * @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