Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --combined src/jalview/gui/StructureViewer.java
index ddcb214,ad7b675..22f12ea
--- 1/src/jalview/gui/StructureViewer.java
--- 2/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@@ -20,15 -20,14 +20,14 @@@
   */
  package jalview.gui;
  
- import java.awt.Rectangle;
- 
  import jalview.api.structures.JalviewStructureDisplayI;
  import jalview.bin.Cache;
  import jalview.datamodel.PDBEntry;
  import jalview.datamodel.SequenceI;
- import jalview.gui.StructureViewer.Viewer;
  import jalview.structure.StructureSelectionManager;
  
+ import java.awt.Rectangle;
+ 
  /**
   * proxy for handling structure viewers.
   * 
@@@ -49,13 -48,14 +48,14 @@@ public class StructureViewe
  
    public Viewer getViewerType()
    {
-     String viewType = Cache.getDefault("STRUCTURE_DISPLAY", "JMOL");
+     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
+             Viewer.JMOL.name());
      return Viewer.valueOf(viewType);
    }
  
    public void setViewerType(Viewer type)
    {
-     Cache.setProperty("STRUCTURE_DISPLAY", type.toString());
+     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
    }
  
    public StructureViewer(StructureSelectionManager structureSelectionManager)
@@@ -115,24 -115,25 +115,24 @@@
      return viewStructures(getViewerType(), ap, pdb, sequenceIs);
    }
  
 -  public JalviewStructureDisplayI createView(Viewer jmol, String[] pdbf,
 +  public JalviewStructureDisplayI createView(Viewer viewer, String[] pdbf,
            String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
            boolean useinJmolsuperpos, boolean usetoColourbyseq,
            boolean jmolColouring, String fileloc, Rectangle rect, String vid)
    {
      JalviewStructureDisplayI sview = null;
 -    switch (getViewerType())
 +    switch (viewer)
      {
      case JMOL:
 -
        sview = new AppJmol(pdbf, id, sq, alignPanel, useinJmolsuperpos,
                usetoColourbyseq, jmolColouring, fileloc, rect, vid);
 -
        break;
      case CHIMERA:
 +      Cache.log.error("Unsupported structure viewer type "
 +              + viewer.toString());
        break;
      default:
 -      Cache.log.error("Unknown structure viewer type "
 -              + getViewerType().toString());
 +      Cache.log.error("Unknown structure viewer type " + viewer.toString());
      }
      return sview;
    }