X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f81e471e67966cb9aed1bb31f35455791399d9e0;hb=7c12f8eb9879172c5c437143ca5eb811a8daf5c7;hp=fdd01d3d09a8514ddd5083ca334a5a16978a8ab1;hpb=3a455483336b530b45d449270069815a933151d2;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fdd01d3..f81e471 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -240,24 +240,24 @@ public class AlignmentPanel extends GAlignmentPanel
    *
    * @param results DOCUMENT ME!
    */
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
     // do we need to scroll the panel?
     if (results != null)
     {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
       if(!av.wrapAlignment)
       {
-        if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-            ( (av.getStartSeq() > results[0]) ||
-             (av.getEndSeq() < results[0])))
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
-          setScrollValues(start, results[0]);
+          setScrollValues(start, seqIndex);
         }
       }
       else
@@ -266,6 +266,7 @@ public class AlignmentPanel extends GAlignmentPanel
         if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
         {
           vscroll.setValue(start / cwidth);
+          av.startRes = vscroll.getValue() * cwidth;
         }
       }
     }