X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=74410a186d56b127812138108093f65b46073e8e;hb=refs%2Fheads%2Ffeatures%2FJAL-1641_JSON;hp=dfbdf86f14dc01f4460b06cb3ce7d6cfcc38b04b;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dfbdf86..74410a1 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -259,17 +259,20 @@ public class FormatAdapter extends AppletFormatAdapter
           throws java.io.IOException
   {
     Alignment al;
-    if (format.equals("HTML"))
+    if (format.equals(JSONFile.FILE_DESC))
     {
-      afile = new HtmlFile(inFile, type);
+      afile = new JSONFile(inFile, type);
       al = new Alignment(afile.getSeqsAsArray());
       afile.addAnnotations(al);
+      for (SequenceGroup sg : afile.getSeqGroups())
+      {
+        al.addGroup(sg);
+      }
     }
     else
     {
       al = super.readFile(inFile, type, format);
     }
-
     return al;
   }
 
@@ -277,11 +280,12 @@ public class FormatAdapter extends AppletFormatAdapter
           throws java.io.IOException
   {
     Alignment al;
-    if (format.equals("HTML"))
+    if (format.equals(JSONFile.FILE_DESC))
     {
-      afile = new HtmlFile(source);
+      afile = new JSONFile(source);
       al = new Alignment(afile.getSeqsAsArray());
       afile.addAnnotations(al);
+      afile.addSeqGroups(al);
     }
     else
     {
@@ -323,4 +327,5 @@ public class FormatAdapter extends AppletFormatAdapter
     return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
   }
 
+
 }