X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7228e1b20b0c5005afeea6d274c1515024633a7a;hb=3b1a35f953ef3bcfd8c0dd8a00919212b69ba25d;hp=588411e9935fc5880bd6a697727f6e88fce3c4a6;hpb=4a7adcc9f6c0d05e12f8ea5460b0c9372020b98a;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 588411e..7228e1b 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -305,7 +305,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public boolean scrollToPosition(SearchResults results)
   {
-    return scrollToPosition(results, true, false);
+    return scrollToPosition(results, 0, true, false);
   }
 
   /**
@@ -318,7 +318,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
   {
-    return scrollToPosition(searchResults, redrawOverview, false);
+    return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
 
   /**
@@ -326,6 +326,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * (if any)
    * 
    * @param results
+   * @param verticalOffset
+   *          if greater than zero, allows scrolling to a position below the
+   *          first displayed sequence
    * @param redrawOverview
    *          - when set, the overview will be recalculated (takes longer)
    * @param centre
@@ -333,6 +336,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResults results,
+          int verticalOffset,
           boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
@@ -391,6 +395,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
           }
         }
       }
+
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+      seqIndex = Math.max(0, seqIndex - verticalOffset);
+
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -1727,10 +1737,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param sr
    *          holds mapped region(s) of this alignment that we are scrolling
    *          'to'; may be modified for sequence offset by this method
-   * @param seqOffset
+   * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int seqOffset)
+  public void scrollToCentre(SearchResults sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
@@ -1744,7 +1754,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * This is like AlignmentI.findIndex(seq) but here we are matching the
      * dataset sequence not the aligned sequence
      */
-    int sequenceIndex = 0;
     boolean matched = false;
     for (SequenceI seq : seqs)
     {
@@ -1753,20 +1762,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
         matched = true;
         break;
       }
-      sequenceIndex++;
     }
     if (!matched)
     {
       return; // failsafe, shouldn't happen
     }
-    sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
-    sr.getResults().get(0)
-            .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
 
     /*
      * Scroll to position but centring the target residue.
      */
-    scrollToPosition(sr, true, true);
+    scrollToPosition(sr, verticalOffset, true, true);
   }
 
   /**