bugfix for Jmol and new classloader reading capability

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index aa81764..e272f97 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -690,7 +690,6 @@ public class AppletJmol extends EmbmenuFrame
           "select backbone;restrict;cartoon;wireframe off;spacefill off");
 
       ssm = StructureSelectionManager.getStructureSelectionManager();
-
       MCview.PDBfile pdb;
       if (loadedInline)
       {
@@ -701,9 +700,12 @@ public class AppletJmol extends EmbmenuFrame
       }
       else
       {
-         pdb = ssm.setMapping(sequence,chains,
+        // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs to be tested. See mantis bug https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+        
+        pdb = ssm.setMapping(sequence,chains,
                               pdbentry.getFile(),
-                              protocol);
+                              AppletFormatAdapter.URL); 
+         
       }
 
       pdbentry.setId(pdb.id);

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 8f2b3d4..7a4b6bc 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -829,10 +829,11 @@ public class JalviewLite extends Applet
             }
             param = setProtocolState(param);
 
-            if (!jmolAvailable
-                    && protocol == AppletFormatAdapter.CLASSLOADER)
+            if (//!jmolAvailable
+                    // &&
+                    protocol == AppletFormatAdapter.CLASSLOADER)
             {
-              // TODO: pass PDB file in classloader on to Jmol
+              // TODO: verify this Re: https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
               // This exception preserves the current behaviour where, even if
               // the local pdb file was identified in the class loader
               protocol = AppletFormatAdapter.URL; // this is probably NOT