JAL-1807 explicit imports (jalview.viewmodel)

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 015cd8e..afadbea 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -22,9 +22,13 @@
 
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 import jalview.jbgui.GStructureChooser;
 import jalview.jbgui.PDBDocFieldPreferences;
 import jalview.structure.StructureSelectionManager;
@@ -100,9 +104,13 @@ 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 +426,7 @@ 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");
@@ -443,9 +450,9 @@ public class StructureChooser extends GStructureChooser
    */
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.formatMessage(
             "label.select_pdb_file_for", new String[]
             { selectedSequence.getDisplayId(false) }));
@@ -454,10 +461,10 @@ public class StructureChooser extends GStructureChooser
             { selectedSequence.getDisplayId(false) }));
 
     int value = chooser.showOpenDialog(null);
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       selectedPdbFileName = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
       validateSelections();
     }
   }
@@ -730,7 +737,7 @@ public class StructureChooser extends GStructureChooser
       }
       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
               .associatePdbWithSeq(
-              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+              selectedPdbFileName, AppletFormatAdapter.FILE,
               selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
@@ -743,17 +750,17 @@ 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 +832,10 @@ 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