Merge branch 'bug/JAL-2846' into develop

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 8ed47dc..d1e3fcc 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -159,8 +159,8 @@ 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());
     }
   }
 
@@ -254,7 +254,7 @@ 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 +267,12 @@ 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)