JAL-1264 adding show/hide annotation options to applet

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 405782d..e4593a3 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -38,6 +38,18 @@
  */
 package jalview.gui;
 
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
@@ -63,18 +75,6 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
 /**
  * DOCUMENT ME!
  * 
@@ -92,9 +92,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   int endSeq;
 
-
-  SequenceAnnotationOrder sortAnnotationsBy = null;
-
   Font font;
 
   NJTree currentTree = null;
@@ -841,8 +838,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
 
-  private boolean showAutocalculatedAbove;
-
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);
@@ -861,26 +856,6 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  protected SequenceAnnotationOrder getSortAnnotationsBy()
-  {
-    return sortAnnotationsBy;
-  }
-
-  protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
-  {
-    this.sortAnnotationsBy = sortAnnotationsBy;
-  }
-
-  protected boolean isShowAutocalculatedAbove()
-  {
-    return showAutocalculatedAbove;
-  }
-
-  protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
-  {
-    this.showAutocalculatedAbove = showAutocalculatedAbove;
-  }
-
   /**
    * Method called when another alignment's edit (or possibly other) command is
    * broadcast to here.