Merge branch 'features/JAL-653_gffalignments' into trial/JAL-1780_JAL-653

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 015cd8e..2e3b37a 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -22,19 +22,6 @@
 
 package jalview.gui;
 
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -49,6 +36,19 @@ import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -100,9 +100,13 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        String msg = MessageManager.getString("status.fetching_db_refs");
-        updateProgressIndicator(msg, startTime);
+        updateProgressIndicator(MessageManager
+                .getString("status.loading_cached_pdb_entries"), startTime);
         loadLocalCachedPDBEntries();
+        updateProgressIndicator(null, startTime);
+        updateProgressIndicator(MessageManager
+                .getString("status.searching_for_pdb_structures"),
+                startTime);
         fetchStructuresMetaData();
         populateFilterComboBox();
         updateProgressIndicator(null, startTime);
@@ -418,8 +422,7 @@ public class StructureChooser extends GStructureChooser
                   + totalTime + ")");
           if (errors.size() > 0)
           {
-            StringBuilder errorMsg = new StringBuilder(
-                    "Operation unsucessful due to the following: \n");
+            StringBuilder errorMsg = new StringBuilder();
             for (String error : errors)
             {
               errorMsg.append(error).append("\n");
@@ -743,17 +746,17 @@ public class StructureChooser extends GStructureChooser
 
   private void launchStructureViewer(StructureSelectionManager ssm,
           PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
-          SequenceI[] selectedSequences)
+          SequenceI[] sequences)
   {
     StructureViewer sViewer = new StructureViewer(ssm);
     if (pdbEntriesToView.length > 1)
     {
-      sViewer.viewStructures(alignPanel, pdbEntriesToView,
-              alignPanel.av.collateForPDB(pdbEntriesToView));
+      sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
+              alignPanel);
     }
     else
     {
-      sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+      sViewer.viewStructures(pdbEntriesToView[0], sequences,
               alignPanel);
     }
   }
@@ -825,13 +828,10 @@ public class StructureChooser extends GStructureChooser
         resultList = pdbRestCleint.executeRequest(pdbRequest);
       } catch (Exception e)
       {
-        // JOptionPane.showMessageDialog(this, e.getMessage(),
-        // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
         errorWarning.append(e.getMessage());
         return;
       } finally
       {
-        // System.out.println(">>>>> executing finally block");
         validateSelections();
       }
       if (resultList.getSearchSummary() != null