From 2ca31c294c758a1f7e6c314ff671ddd03f937e60 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 4 Sep 2017 16:31:00 +0100
Subject: [PATCH] JAL-2673 turn off update to running flag from
 scrollUp/scrollRight

---
 src/jalview/appletgui/SeqPanel.java |   32 ++++++++++++++++++--------------
 src/jalview/gui/SeqPanel.java       |    2 +-
 2 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index be4f9e6..57bfa68 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1451,7 +1451,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.threadRunning = false;
       scrollThread = null;
     }
 
@@ -1701,7 +1701,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       mouseExited(evt);
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
       scrollThread.setEvent(evt);
     }
@@ -1717,9 +1717,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = 0;
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
       scrollThread = null;
     }
   }
@@ -1742,9 +1742,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (evt == null)
     {
-      if (scrollThread != null)
+      if ((scrollThread != null) && (scrollThread.isRunning()))
       {
-        scrollThread.running = false;
+        scrollThread.stopScrolling();
         scrollThread = null;
       }
       mouseDragging = false;
@@ -1767,7 +1767,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     MouseEvent evt;
 
-    boolean running = false;
+    private volatile boolean threadRunning = true;
 
     public ScrollThread()
     {
@@ -1781,14 +1781,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     public void stopScrolling()
     {
-      running = false;
+      threadRunning = false;
+    }
+
+    public boolean isRunning()
+    {
+      return threadRunning;
     }
 
     @Override
     public void run()
     {
-      running = true;
-      while (running)
+      while (threadRunning)
       {
 
         if (evt != null)
@@ -1797,23 +1801,23 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (mouseDragging && evt.getY() < 0
                   && av.getRanges().getStartSeq() > 0)
           {
-            running = av.getRanges().scrollUp(true);
+            av.getRanges().scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height && av
                   .getAlignment().getHeight() > av.getRanges().getEndSeq())
           {
-            running = av.getRanges().scrollUp(false);
+            av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = av.getRanges().scrollRight(false);
+            av.getRanges().scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = av.getRanges().scrollRight(true);
+            av.getRanges().scrollRight(true);
           }
         }
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index cb29c3f..c3aa15f 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1542,7 +1542,7 @@ public class SeqPanel extends JPanel
       return;
     }
 
-    if (mouseDragging)
+    if (mouseDragging && scrollThread == null)
     {
       scrollThread = new ScrollThread();
     }
-- 
1.7.10.2