Merge branch 'JAL-972-dasobert-to-jdas' into JAL-972-jdas

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6faa8ac..35690a9 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -313,15 +313,15 @@ public class FeatureSettings extends JPanel
     Vector allGroups = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
-      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+      if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
               .getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
 
       int index = 0;
@@ -442,10 +442,10 @@ public class FeatureSettings extends JPanel
     // Find out which features should be visible depending on which groups
     // are selected / deselected
     // and recompute average width ordering
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
       if (tmpfeatures == null)
       {