JAL-1605 merge commit

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a738991..497dad4 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;
@@ -98,7 +97,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean showSequenceFeatures = false;
 
-  boolean showAnnotation = true;
+  private boolean showAnnotation = true;
 
   SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -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;
 
@@ -150,7 +149,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   Color textColour2 = Color.white;
 
-  boolean rightAlignIds = false;
+  private boolean rightAlignIds = false;
 
   /**
    * Creates a new AlignViewport object.
@@ -287,9 +286,9 @@ public class AlignViewport extends AlignmentViewport implements
     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
     showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -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)
@@ -366,10 +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(
-            Cache.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name()));
-    showAutocalculatedAbove = Cache
-.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
-            false);
+            Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name()));
+    showAutocalculatedAbove = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
   }
 
   /**
@@ -844,7 +839,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public boolean getShowAnnotation()
   {
-    return showAnnotation;
+    return isShowAnnotation();
   }
 
   /**
@@ -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;
@@ -1298,4 +1303,19 @@ public class AlignViewport extends AlignmentViewport implements
   {
     this.showAutocalculatedAbove = showAutocalculatedAbove;
   }
+
+  public boolean isShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
 }