X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=c89f3633648ad14efd14cb9ae5aeeeaf79f78463;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=93183f222325cc92f544239717a2af24b4a3e5b4;hpb=1145ab823ba8ffd317754588efeb259d70c1f4a1;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 93183f2..c89f363 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.util.BitSet;
@@ -11,19 +31,34 @@ public interface SearchResultsI
 {
 
   /**
-   * 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 all match results in the argument to this set
+   * 
+   * @param toAdd
+   */
+  void addSearchResults(SearchResultsI toAdd);
+
+  /**
    * Answers true if the search results include the given sequence (or its
    * dataset sequence), else false
    * 
@@ -50,11 +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.