From 0089e3442ccafc1073eff6055ef458745aabce18 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 27 Apr 2015 11:03:48 +0100
Subject: [PATCH] JAL-1691 more stable linked scrolling across split frame
 (+javadoc)

---
 src/jalview/gui/AlignmentPanel.java          |    6 ++++--
 src/jalview/gui/SeqPanel.java                |   16 ++++++++++++++--
 src/jalview/viewmodel/AlignmentViewport.java |    5 +++++
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c7ef3ce..80f568d 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -397,14 +397,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll left to make start of search results visible
            */
-          setScrollValues(start - 1, seqIndex);
+          // setScrollValues(start - 1, seqIndex); // plus one residue
+          setScrollValues(start, seqIndex);
         }
         else if ((endv = av.getEndRes()) <= end)
         {
           /*
            * Scroll right to make end of search results visible
            */
-          setScrollValues(startv + 1 + end - endv, seqIndex);
+          // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
+          setScrollValues(startv + end - endv, seqIndex);
         }
         else if ((starts = av.getStartSeq()) > seqIndex)
         {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 791a371..e34a864 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -167,6 +167,13 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   int wrappedBlock = -1;
 
+  /**
+   * Returns the aligned sequence position (base 0) at the mouse position, or
+   * the closest visible one
+   * 
+   * @param evt
+   * @return
+   */
   int findRes(MouseEvent evt)
   {
     int res = 0;
@@ -203,13 +210,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
+      if (x > seqCanvas.getX() + seqCanvas.getWidth())
       {
         // make sure we calculate relative to visible alignment, rather than
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
       res = (x / av.getCharWidth()) + av.getStartRes();
+      if (res > av.getEndRes())
+      {
+        // moused off right
+        res = av.getEndRes();
+      }
     }
 
     if (av.hasHiddenColumns())
@@ -650,7 +662,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.isFollowHighlight())
     {
       /*
-       * if scrollToPosition requires scroll adjustment, this flag prevents
+       * if scrollToPosition requires a scroll adjustment, this flag prevents
        * another scroll event being propagated back to the originator
        * 
        * @see AlignmentPanel#adjustmentValueChanged
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d6aa400..d8ade26 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2549,6 +2549,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int seqOffset = 0;
     SequenceI sequence = null;
+
+    /*
+     * locate 'middle' column (true middle if an odd number visible, left of
+     * middle if an even number visible)
+     */
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-- 
1.7.10.2