From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Nov 2016 21:37:48 +0000 (+0000)
Subject: JAL-966 JAL-345 JAL-1738 quick rewrite of scrollToPosition in applet - further refact... 
X-Git-Tag: Release_2_10_1~10^2~6^2~1^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ea8826bea12e5d811e47463d22413c33dae3738a;p=jalview.git

JAL-966 JAL-345 JAL-1738 quick rewrite of scrollToPosition in applet - further refactoring needed to merge applet/desktop scroll logic
---

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 4198960..f77d6a1 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -323,7 +323,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   public boolean scrollToPosition(SearchResultsI results,
           boolean redrawOverview)
   {
-    return scrollToPosition(results, redrawOverview, false);
+    return scrollToPosition(results, 0, redrawOverview, false);
   }
 
   /**
@@ -336,6 +336,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResultsI results,
+          int verticalOffset,
           boolean redrawOverview, boolean centre)
   {
     // do we need to scroll the panel?
@@ -347,6 +348,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         return false;
       }
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+
       SequenceI seq = alignment.getSequenceAt(seqIndex);
       int[] r = results.getResults(seq, 0, alignment.getWidth());
       if (r == null)
@@ -391,6 +396,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         return false;
       }
+
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+      seqIndex = Math.max(0, seqIndex - verticalOffset);
       return scrollTo(start, end, seqIndex, false, redrawOverview);
     }
     return true;
@@ -419,6 +429,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       start = ostart;
     }
+
     if (!av.getWrapAlignment())
     {
       /*
@@ -931,16 +942,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       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. Also set a state flag
      * to prevent adjustmentValueChanged performing this recursively.
      */
     setFollowingComplementScroll(true);
-    scrollToPosition(sr, true, true);
+    // this should be scrollToPosition(sr,verticalOffset,
+    scrollToPosition(sr, seqOffset, true, true);
   }
 
   private void sendViewPosition()