JAL-1360 refactored utility method to ColorUtils class

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index ce22d84..ccb3c18 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -66,17 +66,43 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
           PDBEntry[] pr, SequenceI[][] collateForPDB)
   {
+    return viewStructures(getViewerType(), ap, pr, collateForPDB);
+  }
+
+  public JalviewStructureDisplayI viewStructures(Viewer viewerType,
+          AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+  {
     JalviewStructureDisplayI sview = null;
-    switch (getViewerType())
+    if (viewerType.equals(Viewer.JMOL))
     {
-    case JMOL:
-
       sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+    }
+    else if (viewerType.equals(Viewer.CHIMERA))
+    {
+      sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+    }
+    else
+    {
+      Cache.log.error("Unknown structure viewer type "
+              + getViewerType().toString());
+    }
+    return sview;
+  }
 
-      break;
-    case CHIMERA:
-      break;
-    default:
+  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());
     }
@@ -86,9 +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,