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 cd9258c..a27777f 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -296,7 +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)
           {
@@ -348,11 +348,11 @@ public class FileLoader implements Runnable
             }
             if (source instanceof HtmlFile)
             {
-              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
+              ((HtmlFile) source).applySettingsToAlignmentView(alignFrame);
             }
             else if (source instanceof JSONFile)
             {
-              ((JSONFile) source).LoadAlignmentFeatures(alignFrame);
+              ((JSONFile) source).applySettingsToAlignmentView(alignFrame);
             }
 
             if (raiseGUI)