X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=31736e506ac3e715f1f42105b357b0227b1ca599;hb=c0a37536d35fb247404187b367228e71f85ce373;hp=8ed47dcda0e432a13bc654645036518532011bf0;hpb=c55e1fa5d2782cc46e515c11a91cf502f37386ab;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 8ed47dc..31736e5 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -91,27 +91,18 @@ public class SearchResults implements SearchResultsI
       }
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getSequence()
-     */
     @Override
     public SequenceI getSequence()
     {
       return sequence;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getStart()
-     */
     @Override
     public int getStart()
     {
       return start;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getEnd()
-     */
     @Override
     public int getEnd()
     {
@@ -159,25 +150,28 @@ public class SearchResults implements SearchResultsI
         return false;
       }
       SearchResultMatchI m = (SearchResultMatchI) obj;
-      return (sequence == m.getSequence() && start == m.getStart() && end == m
-              .getEnd());
+      return (sequence == m.getSequence() && start == m.getStart()
+              && end == m.getEnd());
+    }
+
+    @Override
+    public boolean contains(SequenceI seq, int from, int to)
+    {
+      return (sequence == seq && start <= from && end >= to);
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
-   */
   @Override
   public SearchResultMatchI addResult(SequenceI seq, int start, int end)
   {
     Match m = new Match(seq, start, end);
-    matches.add(m);
+    if (!matches.contains(m))
+    {
+      matches.add(m);
+    }
     return m;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
-   */
   @Override
   public boolean involvesSequence(SequenceI sequence)
   {
@@ -193,9 +187,6 @@ public class SearchResults implements SearchResultsI
     return false;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
-   */
   @Override
   public int[] getResults(SequenceI sequence, int start, int end)
   {
@@ -254,7 +245,7 @@ public class SearchResults implements SearchResultsI
         else
         {
           // debug
-          // System.err.println("Outwith bounds!" + matchStart+">"+end +"  or "
+          // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
           // + matchEnd+"<"+start);
         }
       }
@@ -267,9 +258,12 @@ public class SearchResults implements SearchResultsI
   {
     int count = 0;
     BitSet mask = new BitSet();
+    int startRes = sqcol.getStartRes();
+    int endRes = sqcol.getEndRes();
+
     for (SequenceI s : sqcol.getSequences())
     {
-      int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+      int[] cols = getResults(s, startRes, endRes);
       if (cols != null)
       {
         for (int pair = 0; pair < cols.length; pair += 2)
@@ -287,27 +281,18 @@ public class SearchResults implements SearchResultsI
     return count;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getSize()
-   */
   @Override
   public int getSize()
   {
     return matches.size();
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#isEmpty()
-   */
   @Override
   public boolean isEmpty()
   {
     return matches.isEmpty();
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResults()
-   */
   @Override
   public List<SearchResultMatchI> getResults()
   {