refactor to use model API

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..e58099d 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -15,11 +15,13 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-package jalview.gui;
+package jalview.schemes;
 
 import java.util.*;
 import java.awt.event.*;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
@@ -33,9 +35,9 @@ import jalview.schemes.*;
 public class RNAHelicesColourChooser
 {
 
-  AlignViewport av;
+  AlignViewportI av;
 
-  AlignmentPanel ap;
+  AlignmentViewPanel ap;
 
   ColourSchemeI oldcs;
 
@@ -45,13 +47,13 @@ public class RNAHelicesColourChooser
 
   boolean adjusting = false;
 
-  public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+  public RNAHelicesColourChooser(AlignViewportI av, final AlignmentViewPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.getAlignment().getGroups();
+      Vector allGroups = ap.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {
@@ -102,12 +104,12 @@ public class RNAHelicesColourChooser
     RNAHelicesColour rhc = null;
 
     rhc = new RNAHelicesColour(currentAnnotation);
-
+   
     av.setGlobalColourScheme(rhc);
 
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
+      Vector allGroups = ap.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {
@@ -131,7 +133,7 @@ public class RNAHelicesColourChooser
     av.setGlobalColourScheme(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
+      Vector allGroups = ap.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {