X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=e68562762987f5e438b06f7d1618e0857fcd7597;hb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c;hp=31aeffae0a1af0928ab7ede1381686a3425dbc74;hpb=df98ae3e601ff44c9a1d7beb5c9014aebf0e960e;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 31aeffa..e685627 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -110,23 +110,22 @@ public class AnnotationFile
    */
   public class ViewDef
   {
-    public String viewname;
+    // TODO this class is not used - remove?
+    public final String viewname;
 
-    public HiddenSequences hidseqs;
+    public final HiddenSequences hidseqs;
 
-    public HiddenColumns hiddencols;
+    public final HiddenColumns hiddencols;
 
-    public Vector visibleGroups;
+    public final Hashtable hiddenRepSeqs;
 
-    public Hashtable hiddenRepSeqs;
-
-    public ViewDef(String viewname, HiddenSequences hidseqs,
-            HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
+    public ViewDef(String vname, HiddenSequences hseqs,
+            HiddenColumns hcols, Hashtable hRepSeqs)
     {
-      this.viewname = viewname;
-      this.hidseqs = hidseqs;
-      this.hiddencols = hiddencols;
-      this.hiddenRepSeqs = hiddenRepSeqs;
+      this.viewname = vname;
+      this.hidseqs = hseqs;
+      this.hiddencols = hcols;
+      this.hiddenRepSeqs = hRepSeqs;
     }
   }
 
@@ -153,7 +152,7 @@ public class AnnotationFile
       }
       if (list == null)
       {
-        list = view.visibleGroups;
+        // list = view.visibleGroups;
       }
       if (cs == null)
       {
@@ -538,7 +537,7 @@ public class AnnotationFile
     return false;
   }
 
-  public void printGroups(List<SequenceGroup> list)
+  protected void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
     for (SequenceGroup sg : list)
@@ -584,7 +583,8 @@ public class AnnotationFile
       if (sg.cs != null)
       {
         text.append("colour=");
-        text.append(sg.cs.toString());
+        text.append(ColourSchemeProperty.getColourName(sg.cs
+                .getColourScheme()));
         text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {