JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation...

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5ea68fb..6eb8d10 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -35,7 +35,6 @@ 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;
@@ -44,6 +43,7 @@ import javax.swing.table.AbstractTableModel;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -81,6 +81,11 @@ public class StructureChooser extends GStructureChooser
 {
   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
 
+  /**
+   * warn user if need to fetch more than this many uniprot records at once
+   */
+  private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
+
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -197,6 +202,7 @@ public class StructureChooser extends GStructureChooser
 
     Executors.defaultThreadFactory().newThread(new Runnable()
     {
+      @Override
       public void run()
       {
         populateSeqsWithoutSourceDBRef();
@@ -315,6 +321,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
+        btn_queryTDB.setEnabled(false);
         populateSeqsWithoutSourceDBRef();
 
         final int y = seqsWithoutSourceDBRef.size();
@@ -327,6 +334,7 @@ public class StructureChooser extends GStructureChooser
                   { new jalview.ws.dbsources.Uniprot() }, null, false);
           dbRefFetcher.addListener(afterDbRefFetch);
           // ideally this would also gracefully run with callbacks
+
           dbRefFetcher.fetchDBRefs(true);
         }
         else
@@ -339,6 +347,7 @@ public class StructureChooser extends GStructureChooser
     };
     final Runnable revertview = new Runnable()
     {
+      @Override
       public void run()
       {
         if (lastSelected != null)
@@ -347,7 +356,10 @@ public class StructureChooser extends GStructureChooser
         }
       };
     };
-    if (ignoreGui)
+    int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
+            THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
+    Console.debug("Using Uniprot fetch threshold of " + threshold);
+    if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
     {
       Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
               .start();
@@ -355,7 +367,9 @@ public class StructureChooser extends GStructureChooser
     }
     // need cancel and no to result in the discoverPDB action - mocked is
     // 'cancel' TODO: mock should be OK
-    JvOptionPane.newOptionDialog(this)
+
+    StructureChooser thisSC = this;
+    JvOptionPane.newOptionDialog(thisSC.getFrame())
             .setResponseHandler(JvOptionPane.OK_OPTION,
                     discoverCanonicalDBrefs)
             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
@@ -369,7 +383,7 @@ public class StructureChooser extends GStructureChooser
                     null, new Object[]
                     { MessageManager.getString("action.ok"),
                         MessageManager.getString("action.cancel") },
-                    MessageManager.getString("action.ok"));
+                    MessageManager.getString("action.ok"), false);
   }
 
   /**
@@ -866,6 +880,7 @@ public class StructureChooser extends GStructureChooser
       popup.add(viewUrl);
       SwingUtilities.invokeLater(new Runnable()
       {
+        @Override
         public void run()
         {
           popup.show(getResultTable(), x, y);