X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=dbd270f97839eff32805cf6ebe0e5eb1ad9fd61f;hb=77c09ec649cf7f3e9152d93431ff30121885af57;hp=5ea68fb5e2f825d838b7dc0233fc008eb08ca0ba;hpb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5ea68fb..dbd270f 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -30,12 +30,12 @@ import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
+import java.util.concurrent.Callable;
 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 +44,7 @@ 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 +82,11 @@ 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 +203,7 @@ public class StructureChooser extends GStructureChooser
 
     Executors.defaultThreadFactory().newThread(new Runnable()
     {
+      @Override
       public void run()
       {
         populateSeqsWithoutSourceDBRef();
@@ -310,52 +317,50 @@ public class StructureChooser extends GStructureChooser
     };
 
     // fetch db refs if OK pressed
-    final Runnable discoverCanonicalDBrefs = new Runnable()
-    {
-      @Override
-      public void run()
+    final Callable discoverCanonicalDBrefs = () -> {
+      btn_queryTDB.setEnabled(false);
+      populateSeqsWithoutSourceDBRef();
+
+      final int y = seqsWithoutSourceDBRef.size();
+      if (y > 0)
       {
-        populateSeqsWithoutSourceDBRef();
+        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
 
-        final int y = seqsWithoutSourceDBRef.size();
-        if (y > 0)
-        {
-          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();
-        }
+        dbRefFetcher.fetchDBRefs(true);
       }
-
+      else
+      {
+        // call finished action directly
+        afterDbRefFetch.finished();
+      }
+      return null;
     };
-    final Runnable revertview = new Runnable()
-    {
-      public void run()
+    final Callable revertview = () -> {
+      if (lastSelected != null)
       {
-        if (lastSelected != null)
-        {
-          cmb_filterOption.setSelectedItem(lastSelected);
-        }
-      };
+        cmb_filterOption.setSelectedItem(lastSelected);
+      }
+      return null;
     };
-    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();
+      Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
       return;
     }
     // 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 +374,7 @@ 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 +871,7 @@ public class StructureChooser extends GStructureChooser
       popup.add(viewUrl);
       SwingUtilities.invokeLater(new Runnable()
       {
+        @Override
         public void run()
         {
           popup.show(getResultTable(), x, y);
@@ -1376,6 +1382,7 @@ public class StructureChooser extends GStructureChooser
   {
     if (selectedSequences != null)
     {
+      lbl_loading.setVisible(true);
       Thread refreshThread = new Thread(new Runnable()
       {
         @Override
@@ -1387,6 +1394,7 @@ public class StructureChooser extends GStructureChooser
           filterResultSet(
                   ((FilterOption) cmb_filterOption.getSelectedItem())
                           .getValue());
+          lbl_loading.setVisible(false);
         }
       });
       refreshThread.start();