Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 47dceec..e0ffe33 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -78,7 +78,7 @@ import jalview.workers.StrucConsensusThread;
 public abstract class AlignmentViewport implements AlignViewportI,
         CommandListener, VamsasSource
 {
-  protected ViewportRanges ranges;
+  final protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -95,6 +95,17 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
 
   /**
+   * alignment displayed in the viewport. Please use get/setter
+   */
+  protected AlignmentI alignment;
+
+  public AlignmentViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    ranges = new ViewportRanges(al);
+  }
+
+  /**
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
    */
@@ -554,10 +565,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-  /**
-   * alignment displayed in the viewport. Please use get/setter
-   */
-  protected AlignmentI alignment;
+
 
   @Override
   public AlignmentI getAlignment()