refactored external structure viewer binding API calls so they do not reference Jmol...

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 338b319..90092b6 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -281,9 +281,9 @@ public class JalviewLite extends Applet
   // //////////////////////////////////////////////
   // //////////////////////////////////////////////
 
-  static int lastFrameX = 200;
+  public static int lastFrameX = 200;
 
-  static int lastFrameY = 200;
+  public static int lastFrameY = 200;
 
   boolean fileFound = true;
 
@@ -982,16 +982,8 @@ public class JalviewLite extends Applet
                 }
               }
 
-              if (jmolAvailable)
-              {
-                new jalview.appletgui.AppletJmol(pdb, seqs, chains,
-                        newAlignFrame.alignPanel, protocol);
-                lastFrameX += 40;
-                lastFrameY += 40;
-              }
-              else
-                new MCview.AppletPDBViewer(pdb, seqs, chains,
-                        newAlignFrame.alignPanel, protocol);
+              newAlignFrame.newStructureView(applet, pdb, seqs, chains, protocol);
+              
             }
           }
 
@@ -1303,40 +1295,25 @@ public class JalviewLite extends Applet
    */
   public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile)
   {
-    System.err.println("addPdbFile not yet implemented.");
-      return true;
-  }
-  /**
-   * bind the viewer instance to the pdbFile associated with sequences in the given alFrame.
-   * @param alFrame
-   * @param pdbFile - pdbFile URI as given via applet's parameters or by addPdb 
-   * @param viewer
-   * @return binding for viewer 
-   * TODO: consider making an exception structure for indicating when binding fails
-   */
-  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer) 
-  {
-    System.err.println("addJmolInstance not yet implemented.");
-    /**
-     */
-    return null;
+    return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
   }
   /**
-   * bind structures in a viewer to any matching sequences in an alignFrame (use seuqenceIds to limit scope of search to specific sequences)
+   * bind structures in a viewer to any matching sequences in an alignFrame (use sequenceIds to limit scope of search to specific sequences)
    * @param alFrame
    * @param viewer
    * @param sequenceIds
    * @return
+   * TODO: consider making an exception structure for indicating when binding fails
    */
-  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, org.jmol.api.JmolViewer viewer, String sequenceIds) 
+  public SequenceStructureBinding addStructureViewInstance(AlignFrame alFrame, Object viewer, String sequenceIds) 
   {
     if (viewer!=null)
     {
       if (sequenceIds!=null && sequenceIds.length()>0)
       {
-        return alFrame.addJmolInstance(viewer, separatorListToArray(sequenceIds));
+        return alFrame.addStructureViewInstance(viewer, separatorListToArray(sequenceIds));
       } else {
-        return alFrame.addJmolInstance(viewer, null);
+        return alFrame.addStructureViewInstance(viewer, null);
       }
     }
     return null;