(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

[jalview.git] / src / jalview / gui / RNAHelicesColourChooser.java

diff --git a/src/jalview/gui/RNAHelicesColourChooser.java b/src/jalview/gui/RNAHelicesColourChooser.java
index cdb000a..e575b91 100644 (file)
--- a/src/jalview/gui/RNAHelicesColourChooser.java
+++ b/src/jalview/gui/RNAHelicesColourChooser.java
@@ -48,10 +48,10 @@ public class RNAHelicesColourChooser
   public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
+      Vector allGroups = ap.av.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {
@@ -74,9 +74,9 @@ public class RNAHelicesColourChooser
     adjusting = true;
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       if (!list.contains(label))
         list.addElement(label);
       else
@@ -97,7 +97,7 @@ public class RNAHelicesColourChooser
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
 
     RNAHelicesColour rhc = null;
 
@@ -105,9 +105,9 @@ public class RNAHelicesColourChooser
 
     av.setGlobalColourScheme(rhc);
 
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
+      Vector allGroups = ap.av.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {
@@ -129,9 +129,9 @@ public class RNAHelicesColourChooser
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
+      Vector allGroups = ap.av.getAlignment().getGroups();
       SequenceGroup sg;
       for (int g = 0; g < allGroups.size(); g++)
       {