JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3ecca9b..34fa751 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -81,11 +81,6 @@ public class StructureChooser extends GStructureChooser
 {
   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
 
-  /**
-   * transient combo box choice for initiating 3db fetch
-   */
-  private static final String VIEWS_QUERYING_TDB = "QUERY_3DB";
-
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -173,7 +168,8 @@ public class StructureChooser extends GStructureChooser
       canQueryTDB = true;
       if (needCanonical)
       {
-        notQueriedTDBYet = false;
+        // triggers display of the 'Query TDB' button
+        notQueriedTDBYet = true;
       }
     }
   };
@@ -189,6 +185,15 @@ public class StructureChooser extends GStructureChooser
     }
 
     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+    btn_queryTDB.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        promptForTDBFetch(false);
+      }
+    });
 
     Executors.defaultThreadFactory().newThread(new Runnable()
     {
@@ -237,7 +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();
 
@@ -247,19 +256,30 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
-        progressBar.setProgressBar("status.searching_3d_beacons", progressId);
+        mainFrame.setEnabled(false);
+        cmb_filterOption.setEnabled(false);
+        progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
         // TODO: warn if no accessions discovered
         populateSeqsWithoutSourceDBRef();
         // 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())
         {
-          progressBar.setProgressBar("status.no_structures_discovered_from_3d_beacons", progressId);
+          progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId);
+          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);
         }
+        mainFrame.setEnabled(true);
+        cmb_filterOption.setEnabled(true);
       }
     };
 
@@ -310,8 +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)
@@ -599,7 +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",
@@ -612,7 +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();
     }
   }
@@ -667,10 +692,7 @@ public class StructureChooser extends GStructureChooser
                     "-", VIEWS_FROM_FILE, false, null));
     if (canQueryTDB && notQueriedTDBYet)
     {
-      FilterOption queryTDBOption = new FilterOption(
-              MessageManager.getString("label.search_3dbeacons"), "-",
-              VIEWS_QUERYING_TDB, false, null);
-      cmb_filterOption.addItem(queryTDBOption);
+      btn_queryTDB.setVisible(true);
     }
 
     if (cachedPDBExist)
@@ -699,12 +721,6 @@ public class StructureChooser extends GStructureChooser
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
     
-    // first check if we need to rebuild dialog
-    if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB)
-    {
-      promptForTDBFetch();
-      return;
-    }
     if (lastSelected == selectedFilterOpt)
     {
       // don't need to do anything, probably
@@ -1501,4 +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;
+  }
 }