X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=f774c0759d728af9e15dc8bdf3121279ebfe36e8;hb=30df9d507ac08bdb0c09d929252985c66f2f84ef;hp=ae7971c83f711cc4f92d61a10b2cecbdfb79e8ae;hpb=aa96618cbd41b40e2377f3f1f105aea90a5a86e0;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index ae7971c..f774c07 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,6 +21,8 @@
 
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -58,6 +60,7 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -239,18 +242,38 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
+        progressBar.setProgressBar("status.searching_3d_beacons", progressId);
         // TODO: warn if no accessions discovered
         populateSeqsWithoutSourceDBRef();
         // redo initial discovery - this time with 3d beacons
         // Executors.
         previousWantedFields=null;
-        
         initialStructureDiscovery();
+        if (!isStructuresDiscovered())
+        {
+          progressBar.setProgressBar("status.no_structures_discovered_from_3d_beacons", progressId);
+        } else {
+          progressBar.setProgressBar(null, progressId);
+        }
       }
     };
 
+    final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
+    {
+      
+      @Override
+      public void finished()
+      {
+        // filter has been selected, so we set flag to remove ourselves
+        notQueriedTDBYet = false;
+        // new thread to discover structures - via 3d beacons
+        Executors.defaultThreadFactory().newThread(strucDiscovery).start();
+        
+      }
+    };
+    
     // fetch db refs if OK pressed
-    final Runnable discoverCanonicalDBrefs = new Runnable()
+    final Runnable discoverCanonicalDBrefs = new Runnable() 
     {
       @Override
       public void run()
@@ -260,42 +283,20 @@ public class StructureChooser extends GStructureChooser
         final int y = seqsWithoutSourceDBRef.size();
         if (y > 0)
         {
-          SwingUtilities.invokeLater(new Runnable() {
-            @Override
-            public void run()
-            {
-              updateProgressIndicator(MessageManager.formatMessage(
-                      "status.fetching_dbrefs_for_sequences_without_valid_refs",
-                      y), progressId);
-              
-            }
-          });
-          
           final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
                   .toArray(new SequenceI[y]);
           DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
                   progressBar, new DbSourceProxy[]
                   { new jalview.ws.dbsources.Uniprot() }, null, false);
-
+          dbRefFetcher.addListener(afterDbRefFetch);
           // ideally this would also gracefully run with callbacks
           dbRefFetcher.fetchDBRefs(true);
+        } else {
+          // call finished action directly
+          afterDbRefFetch.finished();
         }
-        SwingUtilities.invokeLater(new Runnable() {
-          @Override
-          public void run()
-          {
-            if (y>0) {
-              updateProgressIndicator("Fetch complete.", progressId); // todo i18n
-            }
-            // filter has been selected, so we set flag to remove ourselves
-            notQueriedTDBYet = false;
-
-            Executors.defaultThreadFactory().newThread(strucDiscovery).start();
-
-          }
-        });
-        
       }
+
     };
     final Runnable revertview = new Runnable() {
       public void run() {
@@ -1026,7 +1027,7 @@ public class StructureChooser extends GStructureChooser
             if (pdbIdStr.split(":").length > 1)
             {
               pdbEntry.setId(pdbIdStr.split(":")[0]);
-              pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+              pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
             }
             else
             {
@@ -1253,7 +1254,7 @@ public class StructureChooser extends GStructureChooser
             // TODO move this pdb id search into the PDB specific
             // FTSSearchEngine
             // for moment, it will work fine as is because it is self-contained
-            String searchTerm = text.toLowerCase();
+            String searchTerm = text.toLowerCase(Locale.ROOT);
             searchTerm = searchTerm.split(":")[0];
             // System.out.println(">>>>> search term : " + searchTerm);
             List<FTSDataColumnI> wantedFields = new ArrayList<>();