X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=cd9258c36416bc9c21e2f1eb4065928cdf5eb0d9;hb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;hp=38033ff1a19542d495789270535d32b217483027;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 38033ff..cd9258c 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -30,7 +30,6 @@ import jalview.gui.Jalview2XML;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -323,7 +322,7 @@ public class FileLoader implements Runnable
             }
             if (sq.getPDBId() != null)
             {
-              for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+              for (PDBEntry pdbe : sq.getPDBId())
               {
                 StructureSelectionManager.getStructureSelectionManager(
                         Desktop.instance).registerPDBEntry(pdbe);
@@ -332,13 +331,7 @@ public class FileLoader implements Runnable
           }
           if (viewport != null)
           {
-            // TODO: create undo object for this JAL-1101
-            for (int i = 0; i < al.getHeight(); i++)
-            {
-              viewport.getAlignment().addSequence(al.getSequenceAt(i));
-            }
-            viewport.firePropertyChange("alignment", null, viewport
-                    .getAlignment().getSequences());
+            viewport.addAlignment(al, title);
           }
           else
           {
@@ -356,8 +349,12 @@ public class FileLoader implements Runnable
             if (source instanceof HtmlFile)
             {
               ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
-
             }
+            else if (source instanceof JSONFile)
+            {
+              ((JSONFile) source).LoadAlignmentFeatures(alignFrame);
+            }
+
             if (raiseGUI)
             {
               // add the window to the GUI