X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=9a61f5fc350998c2a81a637ae530c427b9e5f20b;hb=9317de4ce997ec39dee25ec507c12807c5067d7d;hp=fc7c46efe45fd7bcee134a31dbf41bced285c318;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index fc7c46e..9a61f5f 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -335,7 +335,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
     }
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -417,7 +417,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of column in sequence or -1 if at gap
    */
   void setStatusMessage(SequenceI sequence, int column, int seq)
   {
@@ -983,7 +982,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       lastMousePress = evt.getPoint();
 
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
       ap.annotationPanel.image = null;
       return;
     }
@@ -1402,7 +1401,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.threadRunning = false;
       scrollThread = null;
     }
 
@@ -1450,7 +1449,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (links == null)
           {
-            links = new Vector<String>();
+            links = new Vector<>();
           }
           links.addAll(sf.links);
         }
@@ -1524,7 +1523,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
+    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
     needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
@@ -1649,7 +1648,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       mouseExited(evt);
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
       scrollThread.setEvent(evt);
     }
@@ -1665,9 +1664,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = 0;
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
       scrollThread = null;
     }
   }
@@ -1690,9 +1689,9 @@ 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;
@@ -1715,7 +1714,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     MouseEvent evt;
 
-    boolean running = false;
+    private volatile boolean threadRunning = true;
 
     public ScrollThread()
     {
@@ -1729,14 +1728,18 @@ 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)
@@ -1745,23 +1748,23 @@ 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);
           }
         }