house keeping

[jalview.git] / src / jalview / gui / StructureViewer.java

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index e307aa9..ad7b675 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -20,15 +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 @@ public class StructureViewer
 
   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)
@@ -68,16 +68,40 @@ public class StructureViewer
   {
     return viewStructures(getViewerType(), ap, pr, collateForPDB);
   }
-  public JalviewStructureDisplayI viewStructures(Viewer viewerType,AlignmentPanel ap,
-          PDBEntry[] pr, SequenceI[][] collateForPDB)
+
+  public JalviewStructureDisplayI viewStructures(Viewer viewerType,
+          AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
   {
     JalviewStructureDisplayI sview = null;
-    if (viewerType.equals(Viewer.JMOL)){
+    if (viewerType.equals(Viewer.JMOL))
+    {
       sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
-    } else
-    if (viewerType.equals(Viewer.CHIMERA)) {
+    }
+    else if (viewerType.equals(Viewer.CHIMERA))
+    {
       sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
-    }else 
+    }
+    else
+    {
+      Cache.log.error("Unknown structure viewer type "
+              + getViewerType().toString());
+    }
+    return sview;
+  }
+
+  public JalviewStructureDisplayI viewStructures(Viewer viewerType,
+          AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+  {
+    JalviewStructureDisplayI sview = null;
+    if (viewerType.equals(Viewer.JMOL))
+    {
+      sview = new AppJmol(pr, collateForPDB, null, ap);
+    }
+    else if (viewerType.equals(Viewer.CHIMERA))
+    {
+      sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+    }
+    else
     {
       Cache.log.error("Unknown structure viewer type "
               + getViewerType().toString());
@@ -88,9 +112,7 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
   {
-    return viewStructures(ap, new PDBEntry[]
-    { pdb }, new SequenceI[][]
-    { sequenceIs });
+    return viewStructures(getViewerType(), ap, pdb, sequenceIs);
   }
 
   public JalviewStructureDisplayI createView(Viewer jmol, String[] pdbf,