Merge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073

Conflicts:
	src/jalview/datamodel/Alignment.java
	src/jalview/gui/ScalePanel.java
	src/jalview/gui/SeqPanel.java

diff --cc src/jalview/datamodel/Alignment.java
Simple merge

diff --cc src/jalview/gui/AnnotationPanel.java
Simple merge

diff --cc src/jalview/gui/IdPanel.java
index 1fd9e49,3f43008..113fd9f
--- 1/src/jalview/gui/IdPanel.java
--- 2/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@@ -484,9 -409,8 +485,9 @@@ public class IdPanel extends JPane
    {
      if (scrollThread != null)
      {
-       scrollThread.running = false;
+       scrollThread.stopScrolling();
      }
 +    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
  
      mouseDragging = false;
      PaintRefresher.Refresh(this, av.getSequenceSetId());

diff --cc src/jalview/gui/ScalePanel.java
index 9788ec6,6a44d06..0f2b765
--- 1/src/jalview/gui/ScalePanel.java
--- 2/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@@ -274,12 -276,11 +275,11 @@@ public class ScalePanel extends JPane
    public void mouseReleased(MouseEvent evt)
    {
      mouseDragging = false;
+     ap.getSeqPanel().stopScrolling();
  
 -    // todo res calculation should be a method on AlignViewport
 -    int res = (evt.getX() / av.getCharWidth())
 +    int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
- 
 +    int res = (xCords / av.getCharWidth())
              + av.getRanges().getStartRes();
- 
      if (av.hasHiddenColumns())
      {
        res = av.getAlignment().getHiddenColumns()

diff --cc src/jalview/gui/SeqPanel.java
index 7abbd7d,401bd0a..4a1a9ee
--- 1/src/jalview/gui/SeqPanel.java
--- 2/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@@ -2337,66 -1997,48 +2331,74 @@@ public class SeqPanel extends JPane
  
      mouseDragging = true;
  
-     if ((scrollThread != null) && (scrollThread.isRunning()))
+     if (scrollThread != null)
      {
-       scrollThread.setEvent(evt);
+       scrollThread.setMousePosition(evt.getPoint());
      }
 +
 +    /*
 +     * construct a status message showing the range of the selection
 +     */
 +    StringBuilder status = new StringBuilder(64);
 +    List<SequenceI> seqs = stretchGroup.getSequences();
 +    String name = seqs.get(0).getName();
 +    if (name.length() > 20)
 +    {
 +      name = name.substring(0, 20);
 +    }
 +    status.append(name).append(" - ");
 +    name = seqs.get(seqs.size() - 1).getName();
 +    if (name.length() > 20)
 +    {
 +      name = name.substring(0, 20);
 +    }
 +    status.append(name).append(" ");
 +    int startRes = stretchGroup.getStartRes();
 +    status.append(" cols ").append(String.valueOf(startRes + 1))
 +            .append("-");
 +    int endRes = stretchGroup.getEndRes();
 +    status.append(String.valueOf(endRes + 1));
 +    status.append(" (").append(String.valueOf(seqs.size())).append(" x ")
 +            .append(String.valueOf(endRes - startRes + 1)).append(")");
 +    ap.alignFrame.setStatus(status.toString());
    }
  
-   void scrollCanvas(MouseEvent evt)
+   /**
+    * Stops the scroll thread if it is running
+    */
+   void stopScrolling()
    {
-     if (evt == null)
+     if (scrollThread != null)
      {
-       if ((scrollThread != null) && (scrollThread.isRunning()))
-       {
-         scrollThread.stopScrolling();
-         scrollThread = null;
-       }
-       mouseDragging = false;
+       scrollThread.stopScrolling();
+       scrollThread = null;
      }
-     else
-     {
-       if (scrollThread == null)
-       {
-         scrollThread = new ScrollThread();
-       }
+     mouseDragging = false;
+   }
  
-       mouseDragging = true;
-       scrollThread.setEvent(evt);
+   /**
+    * Starts a thread to scroll the alignment, towards a given mouse position
+    * outside the panel bounds
+    * 
+    * @param mousePos
+    */
+   void startScrolling(Point mousePos)
+   {
+     if (scrollThread == null)
+     {
+       scrollThread = new ScrollThread();
      }
  
+     mouseDragging = true;
+     scrollThread.setMousePosition(mousePos);
    }
  
-   // this class allows scrolling off the bottom of the visible alignment
+   /**
+    * Performs scrolling of the visible alignment left, right, up or down
+    */
    class ScrollThread extends Thread
    {
-     MouseEvent evt;
+     private Point mousePos;
  
      private volatile boolean threadRunning = true;