X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ef903e36a6af34ad2a4e67d6bb0f9a1b6d43e440;hb=6684899d56d5bfb61faf814560010d7cb7b8bd95;hp=ed70dd4ea4d923b9d8f754822b10e7f0df56b6a6;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ed70dd4..ef903e3 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -32,7 +32,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
 import jalview.util.ColorUtils;
 
 import java.awt.Color;
@@ -110,23 +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;
     }
   }
 
@@ -152,7 +152,7 @@ public class AnnotationFile
       }
       if (list == null)
       {
-        list = view.visibleGroups;
+        // list = view.visibleGroups;
       }
       if (cs == null)
       {
@@ -537,7 +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)
@@ -583,7 +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)
         {
@@ -1677,9 +1678,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("idColour"))
         {
-          // consider warning if colour doesn't resolve to a real colour
-          def = new UserColourScheme(value);
-          sg.setIdColour(def.findColour());
+          Color idColour = ColorUtils.parseColourString(value);
+          sg.setIdColour(idColour == null ? Color.black : idColour);
         }
         else if (key.equalsIgnoreCase("hide"))
         {