X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ef903e36a6af34ad2a4e67d6bb0f9a1b6d43e440;hb=95702b58b4a81f53147aa5e4add078f965966437;hp=ae34f6b8c1b42e7d9b3b4a5fbe12bbd5ae262ec4;hpb=dfd021096780038aa9389ed96f6ce938244f95c4;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ae34f6b..ef903e3 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -109,23 +109,24 @@ 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 ColumnSelection hiddencols;
+    public final ColumnSelection hiddencols;
 
-    public Vector visibleGroups;
+    // public final Vector visibleGroups;
 
-    public Hashtable hiddenRepSeqs;
+    public final Hashtable hiddenRepSeqs;
 
-    public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+    public ViewDef(String vname, HiddenSequences hseqs,
+            ColumnSelection 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;
     }
   }
 
@@ -151,7 +152,7 @@ public class AnnotationFile
       }
       if (list == null)
       {
-        list = view.visibleGroups;
+        // list = view.visibleGroups;
       }
       if (cs == null)
       {
@@ -536,7 +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)
@@ -582,7 +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)
         {
@@ -1609,8 +1611,7 @@ public class AnnotationFile
     if (sg != null)
     {
       String keyValue, key, value;
-      ColourSchemeI def = sg.cs;
-      sg.cs = null;
+      ColourSchemeI def = sg.getColourScheme();
       while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
@@ -1623,7 +1624,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColourScheme(al, value);
+          sg.cs.setColourScheme(ColourSchemeProperty
+                  .getColourScheme(al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
@@ -1691,9 +1693,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }