Merge develop to Release_2_8_3_Branch

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1d9655b..3322689 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,15 +21,19 @@
 package jalview.io;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
 
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import jalview.util.MessageManager;
 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
@@ -148,6 +152,7 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
   {
     this.source = source;
+
     file = source.getInFile();
     protocol = source.type;
     this.format = format;
@@ -272,7 +277,7 @@ public class FileLoader implements Runnable
                   .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
       }
       else
       {
@@ -310,15 +315,24 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0))
         {
-          if (viewport != null)
+          for (SequenceI sq : al.getSequences())
           {
-            // TODO: create undo object for this JAL-1101
-            for (int i = 0; i < al.getHeight(); i++)
+            while (sq.getDatasetSequence() != null)
             {
-              viewport.getAlignment().addSequence(al.getSequenceAt(i));
+              sq = sq.getDatasetSequence();
+            }
+            if (sq.getPDBId() != null)
+            {
+              for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+              {
+                StructureSelectionManager.getStructureSelectionManager(
+                        Desktop.instance).registerPDBEntry(pdbe);
+              }
             }
-            viewport.firePropertyChange("alignment", null, viewport
-                    .getAlignment().getSequences());
+          }
+          if (viewport != null)
+          {
+            viewport.addAlignment(al, title);
           }
           else
           {
@@ -333,6 +347,11 @@ public class FileLoader implements Runnable
             {
               alignFrame.setFileName(file, format);
             }
+            if (source instanceof HtmlFile)
+            {
+              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
+
+            }
             if (raiseGUI)
             {
               // add the window to the GUI