X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=666ff7409b7b68a38cc66845a37ce35900493548;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=cbf381a6f453f556ee67ab0bc17f22349f7f4742;hpb=4f2ae706a69e1b75fb371488ca85038dd0987097;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index cbf381a..666ff74 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -140,6 +140,12 @@ public class StructureChooser extends GStructureChooser
 
   private boolean showChooserGUI = true;
 
+  /**
+   * when true, queries to external services are supressed (no SIFTs, no PDBe,
+   * no 3D-Beacons, etc)
+   */
+  private boolean dontQueryServices = false;
+
   private static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
@@ -151,6 +157,13 @@ public class StructureChooser extends GStructureChooser
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap, boolean showGUI)
   {
+    this(selectedSeqs, selectedSeq, ap, showGUI, false);
+  }
+
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap, boolean showGUI, boolean dontQueryServices)
+  {
+
     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
@@ -160,6 +173,7 @@ public class StructureChooser extends GStructureChooser
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     this.showChooserGUI = showGUI;
+    this.dontQueryServices = dontQueryServices;
     init();
 
   }
@@ -231,17 +245,24 @@ public class StructureChooser extends GStructureChooser
       }
     });
 
-    Executors.defaultThreadFactory().newThread(new Runnable()
+    if (!dontQueryServices)
     {
-      @Override
-      public void run()
+      Executors.defaultThreadFactory().newThread(new Runnable()
       {
-        populateSeqsWithoutSourceDBRef();
-        initialStructureDiscovery();
-      }
-
-    }).start();
+        @Override
+        public void run()
+        {
+          populateSeqsWithoutSourceDBRef();
+          initialStructureDiscovery();
+        }
 
+      }).start();
+    }
+    else
+    {
+      Console.debug(
+              "Structure chooser not querying services to discover metadata.");
+    }
   }
 
   // called by init
@@ -506,7 +527,7 @@ public class StructureChooser extends GStructureChooser
         }
       } catch (Exception e)
       {
-        Console.debugPrintStackTrace(e);
+        Console.printStackTrace(e);
         errors.add(e.getMessage());
         continue;
       }
@@ -992,8 +1013,14 @@ public class StructureChooser extends GStructureChooser
               .getFTSDataFor(getResultTable(), selectedRow,
                       discoveredStructuresSet);
       String pageUrl = row.getModelViewUrl();
+
       JPopupMenu popup = new JPopupMenu("3D Beacons");
       JMenuItem viewUrl = new JMenuItem("View model web page");
+      if (pageUrl == null || "".equals(pageUrl.trim()))
+      {
+        viewUrl.setEnabled(false);
+        viewUrl.setText("No model page available.");
+      }
       viewUrl.addActionListener(new ActionListener()
       {
         @Override
@@ -1792,7 +1819,9 @@ public class StructureChooser extends GStructureChooser
     {
       // headless = true;
       prompt = false;
-      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
+      // suppress structure viewer's external service queries
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,
+              true);
     }
     if (ssm == null)
     {