JAL-4034 Fix #2 show an icon and a button to press to initiate search

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index e400b51..5ea68fb 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -191,7 +191,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        promptForTDBFetch();
+        promptForTDBFetch(false);
       }
     });
 
@@ -242,7 +242,13 @@ 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();
 
@@ -254,20 +260,34 @@ public class StructureChooser extends GStructureChooser
       {
         mainFrame.setEnabled(false);
         cmb_filterOption.setEnabled(false);
-        progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
+        progressBar.setProgressBar(
+                MessageManager.getString("status.searching_3d_beacons"),
+                progressId);
+        btn_queryTDB.setEnabled(false);
         // TODO: warn if no accessions discovered
         populateSeqsWithoutSourceDBRef();
         // redo initial discovery - this time with 3d beacons
         // Executors.
-        previousWantedFields=null;
+        previousWantedFields = null;
+        lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
+        cmb_filterOption.setSelectedItem(null);
+        cachedPDBExists = false; // reset to initial
         initialStructureDiscovery();
         if (!isStructuresDiscovered())
         {
-          progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId);
-          btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
+          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 {
+          pnl_queryTDB.setVisible(false);
+        }
+        else
+        {
+          cmb_filterOption.setSelectedIndex(0); // select 'best'
           btn_queryTDB.setVisible(false);
+          pnl_queryTDB.setVisible(false);
           progressBar.setProgressBar(null, progressId);
         }
         mainFrame.setEnabled(true);
@@ -277,7 +297,7 @@ public class StructureChooser extends GStructureChooser
 
     final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
     {
-      
+
       @Override
       public void finished()
       {
@@ -285,12 +305,12 @@ public class StructureChooser extends GStructureChooser
         notQueriedTDBYet = false;
         // new thread to discover structures - via 3d beacons
         Executors.defaultThreadFactory().newThread(strucDiscovery).start();
-        
+
       }
     };
-    
+
     // fetch db refs if OK pressed
-    final Runnable discoverCanonicalDBrefs = new Runnable() 
+    final Runnable discoverCanonicalDBrefs = new Runnable()
     {
       @Override
       public void run()
@@ -308,22 +328,33 @@ public class StructureChooser extends GStructureChooser
           dbRefFetcher.addListener(afterDbRefFetch);
           // ideally this would also gracefully run with callbacks
           dbRefFetcher.fetchDBRefs(true);
-        } else {
+        }
+        else
+        {
           // call finished action directly
           afterDbRefFetch.finished();
         }
       }
 
     };
-    final Runnable revertview = new Runnable() {
-      public void run() {
-        if (lastSelected!=null) {
+    final Runnable revertview = new Runnable()
+    {
+      public void run()
+      {
+        if (lastSelected != null)
+        {
           cmb_filterOption.setSelectedItem(lastSelected);
         }
       };
     };
+    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)
@@ -333,8 +364,7 @@ public class StructureChooser extends GStructureChooser
                     MessageManager.formatMessage(
                             "label.fetch_references_for_3dbeacons",
                             seqsWithoutSourceDBRef.size()),
-                    MessageManager
-                            .getString("label.3dbeacons"),
+                    MessageManager.getString("label.3dbeacons"),
                     JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
                     null, new Object[]
                     { MessageManager.getString("action.ok"),
@@ -611,7 +641,7 @@ 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",
@@ -624,7 +654,7 @@ 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();
     }
   }
@@ -680,6 +710,7 @@ public class StructureChooser extends GStructureChooser
     if (canQueryTDB && notQueriedTDBYet)
     {
       btn_queryTDB.setVisible(true);
+      pnl_queryTDB.setVisible(true);
     }
 
     if (cachedPDBExist)
@@ -707,7 +738,7 @@ public class StructureChooser extends GStructureChooser
   {
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
-    
+
     if (lastSelected == selectedFilterOpt)
     {
       // don't need to do anything, probably
@@ -722,7 +753,7 @@ public class StructureChooser extends GStructureChooser
     String filterTitle = mainFrame.getTitle();
     mainFrame.setTitle(frameTitle);
     chk_invertFilter.setVisible(false);
-    
+
     if (selectedFilterOpt.getView() == VIEWS_FILTER)
     {
       mainFrame.setTitle(filterTitle);
@@ -813,32 +844,39 @@ public class StructureChooser extends GStructureChooser
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
     String currentView = selectedFilterOpt.getView();
-     
-    if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource)
+
+    if (currentView == VIEWS_FILTER
+            && data instanceof ThreeDBStructureChooserQuerySource)
     {
-      
-      TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet);
-      String pageUrl = row.getModelViewUrl(); 
+
+      TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
+              .getFTSDataFor(getResultTable(), selectedRow,
+                      discoveredStructuresSet);
+      String pageUrl = row.getModelViewUrl();
       JPopupMenu popup = new JPopupMenu("3D Beacons");
       JMenuItem viewUrl = new JMenuItem("View model web page");
-      viewUrl.addActionListener(
-              new ActionListener() {
-                @Override
-                public void actionPerformed(ActionEvent e)
-                {
-                  Desktop.showUrl(pageUrl);
-                }
-              }
-              );
+      viewUrl.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          Desktop.showUrl(pageUrl);
+        }
+      });
       popup.add(viewUrl);
-      SwingUtilities.invokeLater(new Runnable()  {
-        public void run() { popup.show(getResultTable(), x, y); }
+      SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
+        {
+          popup.show(getResultTable(), x, y);
+        }
       });
       return true;
     }
     // event not handled by us
     return false;
   }
+
   /**
    * Validates inputs from the Manual PDB entry panel
    */
@@ -910,7 +948,9 @@ public class StructureChooser extends GStructureChooser
   {
     validateSelections();
   }
-  private FilterOption lastSelected=null;
+
+  private FilterOption lastSelected = null;
+
   /**
    * Handles the state change event for the 'filter' combo-box and 'invert'
    * check-box
@@ -1067,7 +1107,8 @@ public class StructureChooser extends GStructureChooser
             if (pdbIdStr.split(":").length > 1)
             {
               pdbEntry.setId(pdbIdStr.split(":")[0]);
-              pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
+              pdbEntry.setChainCode(
+                      pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
             }
             else
             {
@@ -1504,12 +1545,14 @@ 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 isCanQueryTDB()
+  {
+    return canQueryTDB;
   }
 
   public boolean isNotQueriedTDBYet()