JAL-1264 adding show/hide annotation options to applet

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 2cfc1e6..7054ed3 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,18 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
@@ -51,17 +63,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -1190,6 +1191,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
+  protected SequenceAnnotationOrder sortAnnotationsBy = null;
+
+  protected boolean showAutocalculatedAbove;
+
   /**
    * Property change listener for changes in alignment
    * 
@@ -2386,4 +2391,24 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return this;
   }
+
+  public SequenceAnnotationOrder getSortAnnotationsBy()
+  {
+    return sortAnnotationsBy;
+  }
+
+  public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  {
+    this.sortAnnotationsBy = sortAnnotationsBy;
+  }
+
+  public boolean isShowAutocalculatedAbove()
+  {
+    return showAutocalculatedAbove;
+  }
+
+  public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+  {
+    this.showAutocalculatedAbove = showAutocalculatedAbove;
+  }
 }