From 3b1a35f953ef3bcfd8c0dd8a00919212b69ba25d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 30 Jun 2015 12:14:45 +0100
Subject: [PATCH 1/1] JAL-1691 trackpad scrolling goes to full width even with
 short sequences

---
 src/jalview/gui/AlignViewport.java           |    4 ++--
 src/jalview/gui/AlignmentPanel.java          |   25 +++++++++++++++----------
 src/jalview/viewmodel/AlignmentViewport.java |    8 ++++----
 3 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fc889ad..cf82bfe 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1027,13 +1027,13 @@ public class AlignViewport extends AlignmentViewport implements
      * is found, the result will be empty.
      */
     SearchResults sr = new SearchResults();
-    int seqOffset = findComplementScrollTarget(sr);
+    int verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
       complementPanel.setFollowingComplementScroll(true);
-      complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.scrollToCentre(sr, verticalOffset);
     }
   }
 
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);
   }
 
   /**
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5617bcf..899e8a7 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2501,14 +2501,14 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   protected int findComplementScrollTarget(SearchResults sr)
   {
-    final AlignViewportI codingComplement = getCodingComplement();
-    if (codingComplement == null || !codingComplement.isFollowHighlight())
+    final AlignViewportI complement = getCodingComplement();
+    if (complement == null || !complement.isFollowHighlight())
     {
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
     AlignmentI proteinAlignment = iAmProtein ? getAlignment()
-            : codingComplement.getAlignment();
+            : complement.getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
@@ -2546,7 +2546,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .findMappingsForSequence(sequence, mappings);
       if (!seqMappings.isEmpty())
       {
-        break;
+          break;
       }
     }
   
-- 
1.7.10.2