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

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 2b9787f..7fb868f 100755 (executable)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -51,10 +51,10 @@ public class AnnotationColourChooser extends JPanel
   public AnnotationColourChooser(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++)
       {
@@ -91,7 +91,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    if (av.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
@@ -113,9 +113,9 @@ public class AnnotationColourChooser extends JPanel
     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
@@ -378,7 +378,7 @@ public class AnnotationColourChooser extends JPanel
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
             .getSelectedIndex()];
 
     int aboveThreshold = -1;
@@ -450,9 +450,9 @@ public class AnnotationColourChooser extends JPanel
 
     av.setGlobalColourScheme(acg);
 
-    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++)
       {
@@ -508,9 +508,9 @@ public class AnnotationColourChooser extends JPanel
   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++)
       {