X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d24f6c4b90e3ad6831776a52312a96f32b92852b;hb=50bc9bfda9c71e968f53e6a77ba3ea9cdfd6d3ee;hp=d331e825a80d72079c85f6a3830d01a391a25589;hpb=25883b542d1908492cb82041d7dcb16f533e8862;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d331e82..d24f6c4 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -42,9 +42,8 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
@@ -140,9 +139,9 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean gatherViewsHere = false;
 
-  Stack historyList = new Stack();
+  Stack<CommandI> historyList = new Stack<CommandI>();
 
-  Stack redoList = new Stack();
+  Stack<CommandI> redoList = new Stack<CommandI>();
 
   int thresholdTextColour = 0;
 
@@ -337,10 +336,6 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
     }
     initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -366,9 +361,10 @@ public class AlignViewport extends AlignmentViewport implements
     sortByTree = Cache.getDefault("SORT_BY_TREE", false);
     followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
     sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
-            "SORT_ANNOTATIONS", SequenceAnnotationOrder.NONE.name()));
-    showAutocalculatedAbove = Cache
-            .getDefault("SHOW_AUTOCALC_ABOVE", false);
+            Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name()));
+    showAutocalculatedAbove = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
   }
 
   /**