X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=15c481df1931ba758441c1e8879dd772d4360871;hb=d3bf4ae12b72df02dee34c95da750ab38a3816b9;hp=d81a6b08a63d763b32fe7c85d29e163891421072;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index d81a6b0..15c481d 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -33,9 +33,12 @@ import jalview.io.vamsas.Datasetsequence;
 import jalview.io.vamsas.DatastoreItem;
 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;
@@ -719,9 +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++)
@@ -1311,14 +1314,15 @@ public class VamsasAppDatastore
           // client data is shared over all app clients
           try
           {
-            jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+            // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+            Jalview2XML fromxml = new Jalview2XML();
             fromxml.attemptversion1parse = false;
             fromxml.setUniqueSetSuffix("");
             fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
             // and
             // mapValuesToString
             fromxml.setSkipList(skipList);
-            jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+            jarInputStreamProvider jprovider = new jarInputStreamProvider()
             {
 
               @Override
@@ -1336,6 +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)
             {
@@ -1360,13 +1370,13 @@ public class VamsasAppDatastore
         // user data overrides data shared over all app clients ?
         try
         {
-          jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+          Jalview2XML fromxml = new Jalview2XML();
           fromxml.attemptversion1parse = false;
           fromxml.setUniqueSetSuffix("");
           fromxml.setSkipList(skipList);
           fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
                   mapValuesToString(jv2vobj));
-          jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
+          jarInputStreamProvider jarstream = new jarInputStreamProvider()
           {
 
             @Override
@@ -1384,6 +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)
           {
@@ -1477,7 +1493,7 @@ public class VamsasAppDatastore
           if (mappings != null)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+                    .getStructureSelectionManager(Desktop.getInstance())
                     .registerMappings(mappings);
           }
         }
@@ -1531,7 +1547,7 @@ public class VamsasAppDatastore
     {
       try
       {
-        jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
+        Jalview2XML jxml = new Jalview2XML();
         jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
                 mapValuesToString(jv2vobj));
         jxml.setSkipList(skipList);
@@ -2246,7 +2262,7 @@ public class VamsasAppDatastore
           Float val = null;
           try
           {
-            val = new Float(props[p].getContent());
+            val = Float.valueOf(props[p].getContent());
           } catch (Exception e)
           {
             Cache.log.warn("Failed to parse threshold property");
@@ -2535,7 +2551,7 @@ public class VamsasAppDatastore
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(new Integer(p));
+            posList.add(Integer.valueOf(p));
           }
         }
       }
@@ -2546,7 +2562,7 @@ public class VamsasAppDatastore
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }