patch for bizarre ConcurrentModificationException that I've never seen before !

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b4bc3c7..e88b190 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -38,7 +38,6 @@ import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
-import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -1670,6 +1669,8 @@ public class Jalview2XML
 
     try
     {
+      // create list to store references for any new Jmol viewers created
+      newStructureViewers=new Vector<AppJmol>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -1677,11 +1678,27 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = LoadJalviewAlign(jprovider);
+      
     } catch (MalformedURLException e)
     {
       errorMessage = "Invalid URL format for '" + file + "'";
       reportErrors();
     }
+    finally {
+      try
+      {
+        SwingUtilities.invokeAndWait(new Runnable()
+        {
+          public void run()
+          {
+            setLoadingFinishedForNewStructureViewers();
+          };
+        });
+      } catch (Exception x)
+      {
+
+      }
+    }
     return af;
   }
 
@@ -2969,6 +2986,7 @@ public class Jalview2XML
                       sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
                               useinJmolsuperpos, usetoColourbyseq,
                               jmolColouring, fileloc, rect, vid);
+                      addNewStructureViewer(sview);
                     } catch (OutOfMemoryError ex)
                     {
                       new OOMWarning("restoring structure view for PDB id "
@@ -3038,6 +3056,27 @@ public class Jalview2XML
     // and finally return.
     return af;
   }
+  Vector<AppJmol> newStructureViewers=null;
+  protected void addNewStructureViewer(AppJmol sview)
+  {
+    if (newStructureViewers!=null)
+    {
+      sview.jmb.setFinishedLoadingFromArchive(false);
+      newStructureViewers.add(sview);
+    }
+  }
+  protected void setLoadingFinishedForNewStructureViewers()
+  {
+    if (newStructureViewers!=null)
+    {
+      for (AppJmol sview:newStructureViewers)
+      {
+        sview.jmb.setFinishedLoadingFromArchive(true);
+      }
+      newStructureViewers.clear();
+      newStructureViewers=null;
+    }
+  }
 
   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
           Alignment al, JalviewModelSequence jms, Viewport view,