JAL-1333 JAL-1527 refactors to create core structure viewer binding architecture...

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8cad9ca..f3bc42e 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -32,6 +32,7 @@ import javax.swing.*;
 
 import org.exolab.castor.xml.*;
 
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -1795,7 +1796,7 @@ public class Jalview2XML
     try
     {
       // create list to store references for any new Jmol viewers created
-      newStructureViewers = new Vector<AppJmol>();
+      newStructureViewers = new Vector<JalviewStructureDisplayI>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -3132,10 +3133,11 @@ public class Jalview2XML
                   @Override
                   public void run()
                   {
-                    AppJmol sview = null;
+                    JalviewStructureDisplayI sview = null;
                     try
                     {
-                      sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+                      // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+                      sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel,
                               useinJmolsuperpos, usetoColourbyseq,
                               jmolColouring, fileloc, rect, vid);
                       addNewStructureViewer(sview);
@@ -3265,13 +3267,13 @@ public class Jalview2XML
     return true;
   }
 
-  Vector<AppJmol> newStructureViewers = null;
+  Vector<JalviewStructureDisplayI> newStructureViewers = null;
 
-  protected void addNewStructureViewer(AppJmol sview)
+  protected void addNewStructureViewer(JalviewStructureDisplayI sview)
   {
     if (newStructureViewers != null)
     {
-      sview.jmb.setFinishedLoadingFromArchive(false);
+      sview.getBinding().setFinishedLoadingFromArchive(false);
       newStructureViewers.add(sview);
     }
   }
@@ -3280,9 +3282,9 @@ public class Jalview2XML
   {
     if (newStructureViewers != null)
     {
-      for (AppJmol sview : newStructureViewers)
+      for (JalviewStructureDisplayI sview : newStructureViewers)
       {
-        sview.jmb.setFinishedLoadingFromArchive(true);
+        sview.getBinding().setFinishedLoadingFromArchive(true);
       }
       newStructureViewers.clear();
       newStructureViewers = null;