JAL-4034 fix #3 change uniprot ref fetch dialog to a ‘warning’ shown when many ids...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index aed1125..dda5624 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -518,7 +518,7 @@ label.search_3dbeacons = Search 3D-Beacons
 label.find_models_from_3dbeacons = Search 3D-Beacons for 3D structures and models
 label.3dbeacons = 3D-Beacons
 label.fetch_references_for = Fetch database references for {0} sequences ?
-label.fetch_references_for_3dbeacons = 3D Beacons needs Uniprot References. Fetch database references for {0} sequences ?
+label.fetch_references_for_3dbeacons = 3D Beacons needs to fetch Uniprot References for {0} sequences.  Do you want to continue ?
 label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
 label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
 label.threshold_feature_display_by_score = Threshold the feature display by score.

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5ea68fb..b32e435 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;
@@ -81,6 +80,11 @@ 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 +201,7 @@ public class StructureChooser extends GStructureChooser
 
     Executors.defaultThreadFactory().newThread(new Runnable()
     {
+      @Override
       public void run()
       {
         populateSeqsWithoutSourceDBRef();
@@ -339,6 +344,7 @@ public class StructureChooser extends GStructureChooser
     };
     final Runnable revertview = new Runnable()
     {
+      @Override
       public void run()
       {
         if (lastSelected != null)
@@ -347,7 +353,8 @@ public class StructureChooser extends GStructureChooser
         }
       };
     };
-    if (ignoreGui)
+    if (ignoreGui || seqsWithoutSourceDBRef
+            .size() < THRESHOLD_WARN_UNIPROT_FETCH_NEEDED)
     {
       Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
               .start();
@@ -866,6 +873,7 @@ public class StructureChooser extends GStructureChooser
       popup.add(viewUrl);
       SwingUtilities.invokeLater(new Runnable()
       {
+        @Override
         public void run()
         {
           popup.show(getResultTable(), x, y);