Merge branch 'bug/JAL-998_wrap-sequence-tooltip' into develop

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5c383d8..632d2b2 100644 (file)
--- 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;
@@ -130,7 +129,7 @@ public class AlignViewport extends AlignmentViewport implements
    * Keys are the feature types which are currently visible. Note: Values are
    * not used!
    */
-  Hashtable featuresDisplayed = null;
+  private Hashtable featuresDisplayed = null;
 
   boolean antiAlias = false;
 
@@ -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)
@@ -1279,6 +1274,16 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+
+  public Hashtable getFeaturesDisplayed()
+  {
+    return featuresDisplayed;
+  }
+
+  public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+  {
+    this.featuresDisplayed = featuresDisplayed;
+  }
   protected SequenceAnnotationOrder getSortAnnotationsBy()
   {
     return sortAnnotationsBy;