From 0308f6175bbbb29678ca9bac33feaea67d2973e0 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 17 Aug 2015 11:38:52 +0100
Subject: [PATCH] JAL-1691 scan full width and depth of alignment for smoother
 scrolling

---
 src/jalview/gui/AlignmentPanel.java          |   12 ++++++++----
 src/jalview/viewmodel/AlignmentViewport.java |    7 ++++++-
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ad7e75c..d88e207 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -362,8 +362,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
       // DEBUG
+//       System.err.println(this.av.viewName + " Seq : " + seqIndex
+//       + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -373,7 +374,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
       }
       if (start < 0)
       {
@@ -402,6 +403,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
+      // System.out.println("start=" + start + ", end=" + end + ", startv="
+      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -668,14 +672,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
    * @param x
-   *          visible column to scroll to DOCUMENT ME!
+   *          visible column to scroll to
    * @param y
    *          visible row to scroll to
    * 
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll to "+x+","+y);
+    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 899e8a7..a3b7527 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2531,7 +2531,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-    for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
+    
+    /*
+     * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+     */
+    int lastSeq = alignment.getHeight() - 1;
+    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
-- 
1.7.10.2