JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop...

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index ae7971c..4807489 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,17 +21,23 @@
 
 package jalview.gui;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.concurrent.Executors;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
 import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
@@ -48,6 +54,7 @@ import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
@@ -58,6 +65,7 @@ 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;
 
@@ -249,8 +257,22 @@ public class StructureChooser extends GStructureChooser
       }
     };
 
+    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 +282,20 @@ 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() {
@@ -798,6 +798,38 @@ public class StructureChooser extends GStructureChooser
             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
   }
 
+  @Override
+  protected boolean showPopupFor(int selectedRow, int x, int y)
+  {
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    String currentView = selectedFilterOpt.getView();
+     
+    if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource)
+    {
+      
+      TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet);
+      String pageUrl = row.getModelViewUrl(); 
+      JPopupMenu popup = new JPopupMenu("3D Beacons");
+      JMenuItem viewUrl = new JMenuItem("View model web page");
+      viewUrl.addActionListener(
+              new ActionListener() {
+                @Override
+                public void actionPerformed(ActionEvent e)
+                {
+                  Desktop.showUrl(pageUrl);
+                }
+              }
+              );
+      popup.add(viewUrl);
+      SwingUtilities.invokeLater(new Runnable()  {
+        public void run() { popup.show(getResultTable(), x, y); }
+      });
+      return true;
+    }
+    // event not handled by us
+    return false;
+  }
   /**
    * Validates inputs from the Manual PDB entry panel
    */
@@ -1026,7 +1058,7 @@ 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 +1285,7 @@ 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<>();