Merge branch 'Jalview-JS/develop' into merge_js_develop

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 387dbfa..15c481d 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -35,8 +35,10 @@ import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
 import jalview.project.Jalview2XML;
 import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -720,9 +722,9 @@ public class VamsasAppDatastore
       // /SAVE THE TREES
       // /////////////////////////////////
       // FIND ANY ASSOCIATED TREES
-      if (Desktop.desktop != null)
+      if (Desktop.getDesktopPane() != null)
       {
-        javax.swing.JInternalFrame[] frames = Desktop.instance
+        javax.swing.JInternalFrame[] frames = Desktop.getInstance()
                 .getAllFrames();
 
         for (int t = 0; t < frames.length; t++)
@@ -1320,7 +1322,7 @@ public class VamsasAppDatastore
             // and
             // mapValuesToString
             fromxml.setSkipList(skipList);
-            jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+            jarInputStreamProvider jprovider = new jarInputStreamProvider()
             {
 
               @Override
@@ -1338,6 +1340,12 @@ public class VamsasAppDatastore
                         "Returning client input stream for Jalview from Vamsas Document.");
                 return new JarInputStream(cappdata.getClientInputStream());
               }
+
+              @Override
+              public File getFile()
+              {
+                return null;
+              }
             };
             if (dojvsync)
             {
@@ -1368,7 +1376,7 @@ public class VamsasAppDatastore
           fromxml.setSkipList(skipList);
           fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
                   mapValuesToString(jv2vobj));
-          jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
+          jarInputStreamProvider jarstream = new jarInputStreamProvider()
           {
 
             @Override
@@ -1386,6 +1394,12 @@ public class VamsasAppDatastore
                       "Returning user input stream for Jalview from Vamsas Document.");
               return new JarInputStream(cappdata.getUserInputStream());
             }
+
+            @Override
+            public File getFile()
+            {
+              return null;
+            }
           };
           if (dojvsync)
           {
@@ -1479,7 +1493,7 @@ public class VamsasAppDatastore
           if (mappings != null)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+                    .getStructureSelectionManager(Desktop.getInstance())
                     .registerMappings(mappings);
           }
         }