JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index d81a6b0..84d31f0 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -33,6 +33,7 @@ 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.viewmodel.AlignmentViewport;
 
@@ -388,7 +389,6 @@ public class VamsasAppDatastore
         {
           dssmods.addElement(sequence);
         }
-        ;
       }
       if (dssmods.size() > 0)
       {
@@ -584,7 +584,6 @@ public class VamsasAppDatastore
                           (AlignmentSequence) alsref, aa[i]);
                   break;
                 }
-                ;
               }
             }
           }
@@ -719,9 +718,9 @@ 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++)
@@ -1311,7 +1310,8 @@ 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
@@ -1360,7 +1360,7 @@ 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);
@@ -1476,8 +1476,7 @@ public class VamsasAppDatastore
           // active
           if (mappings != null)
           {
-            jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+            Desktop.getStructureSelectionManager()
                     .registerMappings(mappings);
           }
         }
@@ -1531,7 +1530,7 @@ 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);
@@ -2018,17 +2017,17 @@ public class VamsasAppDatastore
   }
 
   // bitfields - should be a template in j1.5
-  private static int HASSECSTR = 0;
+  private static final int HASSECSTR = 0;
 
-  private static int HASVALS = 1;
+  private static final int HASVALS = 1;
 
-  private static int HASHPHOB = 2;
+  private static final int HASHPHOB = 2;
 
-  private static int HASDC = 3;
+  private static final int HASDC = 3;
 
-  private static int HASDESCSTR = 4;
+  private static final int HASDESCSTR = 4;
 
-  private static int HASTWOSTATE = 5; // not used yet.
+  private static final int HASTWOSTATE = 5; // not used yet.
 
   /**
    * parses the AnnotationElements - if they exist - into