X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=34fa75188f9dd7a90d66d0aaf7a7a11cc82cb717;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=09eb7af4de104da68acdf247b8298874ed3dea9f;hpb=a20a6bc5758a4c6cb221d42174ace2f48e0002b3;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 09eb7af..34fa751 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -168,7 +168,8 @@ public class StructureChooser extends GStructureChooser
       canQueryTDB = true;
       if (needCanonical)
       {
-        notQueriedTDBYet = false;
+        // triggers display of the 'Query TDB' button
+        notQueriedTDBYet = true;
       }
     }
   };
@@ -190,7 +191,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        promptForTDBFetch();
+        promptForTDBFetch(false);
       }
     });
 
@@ -241,7 +242,11 @@ public class StructureChooser extends GStructureChooser
     updateCurrentView();
   }
 
-  private void promptForTDBFetch()
+  /**
+   * raises dialog for Uniprot fetch followed by 3D beacons search
+   * @param ignoreGui - when true, don't ask, just fetch 
+   */
+  public void promptForTDBFetch(boolean ignoreGui)
   {
     final long progressId = System.currentTimeMillis();
 
@@ -259,6 +264,9 @@ public class StructureChooser extends GStructureChooser
         // redo initial discovery - this time with 3d beacons
         // Executors.
         previousWantedFields=null;
+        lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+        cmb_filterOption.setSelectedItem(null);
+        cachedPDBExists=false; // reset to initial
         initialStructureDiscovery();
         if (!isStructuresDiscovered())
         {
@@ -266,6 +274,7 @@ public class StructureChooser extends GStructureChooser
           btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
           btn_queryTDB.setEnabled(false);
         } else {
+          cmb_filterOption.setSelectedIndex(0); // select 'best'
           btn_queryTDB.setVisible(false);
           progressBar.setProgressBar(null, progressId);
         }
@@ -321,8 +330,13 @@ public class StructureChooser extends GStructureChooser
         }
       };
     };
+    if (ignoreGui)
+    {
+      Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+      return;
+    }
     // need cancel and no to result in the discoverPDB action - mocked is
-    // 'cancel'
+    // 'cancel' TODO: mock should be OK
     JvOptionPane.newOptionDialog(this)
             .setResponseHandler(JvOptionPane.OK_OPTION,
                     discoverCanonicalDBrefs)
@@ -610,7 +624,7 @@ public class StructureChooser extends GStructureChooser
     // StructureChooser
     // works
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.formatMessage("label.select_pdb_file_for",
@@ -623,7 +637,7 @@ public class StructureChooser extends GStructureChooser
     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
     {
       selectedPdbFileName = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
       validateSelections();
     }
   }
@@ -1503,4 +1517,16 @@ public class StructureChooser extends GStructureChooser
             && mainFrame.isVisible()
             && cmb_filterOption.getSelectedItem() != null;
   }
+  /**
+   * 
+   * @return true if the 3D-Beacons query button will/has been displayed
+   */
+  public boolean isCanQueryTDB() {
+	  return canQueryTDB;
+  }
+
+  public boolean isNotQueriedTDBYet()
+  {
+    return notQueriedTDBYet;
+  }
 }