X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a3b7527186f3341b5a9d77635ac346615cc8412a;hb=d131f05c68757d57e5e4a1f440196ae1b70f3b8a;hp=899e8a7872378e10e5c66264e71ebda022f3da04;hpb=3b1a35f953ef3bcfd8c0dd8a00919212b69ba25d;p=jalview.git

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))