JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability...

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3322689..a27777f 100755 (executable)
--- 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;
 
@@ -297,7 +296,7 @@ public class FileLoader implements Runnable
               // open a new source and read from it
               FormatAdapter fa = new FormatAdapter();
               al = fa.readFile(file, protocol, format);
-              source = fa.afile; // keep reference for later if necessary.
+              source = fa.getAlignFile(); // keep reference for later if necessary.
             }
           } catch (java.io.IOException ex)
           {
@@ -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);
@@ -349,9 +348,13 @@ public class FileLoader implements Runnable
             }
             if (source instanceof HtmlFile)
             {
-              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
-
+              ((HtmlFile) source).applySettingsToAlignmentView(alignFrame);
+            }
+            else if (source instanceof JSONFile)
+            {
+              ((JSONFile) source).applySettingsToAlignmentView(alignFrame);
             }
+
             if (raiseGUI)
             {
               // add the window to the GUI