Merge branch 'bug/JAL-2727closeAllFreeMemory' into develop

diff --cc src/jalview/api/AlignViewportI.java
index 3cb06c1,248bae2..931eba6
--- 1/src/jalview/api/AlignViewportI.java
--- 2/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@@ -483,6 -494,9 +484,10 @@@ public interface AlignViewportI extend
     * 
     * @return
     */
 +  @Override
    void setProteinFontAsCdna(boolean b);
+ 
+   public abstract TreeModel getCurrentTree();
+ 
+   public abstract void setCurrentTree(TreeModel tree);
  }

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

diff --cc src/jalview/gui/AlignmentPanel.java
index 07c65fe,c8a0e1a..3a1dbe8
--- 1/src/jalview/gui/AlignmentPanel.java
--- 2/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@@ -476,10 -482,10 +475,10 @@@ public class AlignmentPanel extends GAl
      }
      else
      {
-       scrollNeeded = vpRanges.scrollToWrappedVisible(start);
+       scrollNeeded = ranges.scrollToWrappedVisible(start);
      }
  
 -    paintAlignment(redrawOverview);
 +    paintAlignment(redrawOverview, false);
  
      return scrollNeeded;
    }
@@@ -632,12 -637,12 +632,12 @@@
        }
        else
        {
 -        int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
 +        int widthInRes = (canvasWidth / av.getCharWidth());
          int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
 -                / av.getCharHeight()) - 1;
 +                / av.getCharHeight());
  
-         vpRanges.setViewportWidth(widthInRes);
-         vpRanges.setViewportHeight(heightInSeq);
+         ranges.setViewportWidth(widthInRes);
+         ranges.setViewportHeight(heightInSeq);
        }
      }
  
@@@ -766,9 -773,12 +768,9 @@@
        {
          return;
        }
-       vpRanges.setViewportStartAndHeight(y, height);
+       ranges.setViewportStartAndHeight(y, height);
      }
 -    if (!fastPaint)
 -    {
 -      repaint();
 -    }
 +    repaint();
    }
  
    /**

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
Simple merge