From 61f891719b37bdc88c1c48d85ebf8b656c2bdcd0 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 21 Mar 2017 11:26:31 +0000
Subject: [PATCH] JAL-2388 Made ViewportRanges final

---
 src/jalview/appletgui/AlignViewport.java     |    6 ++----
 src/jalview/gui/AlignViewport.java           |   12 ++++++------
 src/jalview/viewmodel/AlignmentViewport.java |   18 +++++++++++++-----
 3 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 065c503..b289be7 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -39,7 +39,6 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 
@@ -71,11 +70,10 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
-    super();
+    super(al);
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
-    alignment = al;
-    ranges = new ViewportRanges(this.alignment);
+
     // we always pad gaps
     this.setPadGaps(true);
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 602e3a1..ef3593c 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -51,7 +51,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -105,7 +104,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al)
   {
-    setAlignment(al);
+    super(al);
     init();
   }
 
@@ -123,6 +122,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -135,8 +135,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
     init();
+
   }
 
   /**
@@ -149,7 +149,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
   {
-    setAlignment(al);
+    super(al);
     if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
@@ -184,6 +184,7 @@ public class AlignViewport extends AlignmentViewport implements
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
           String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -196,7 +197,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
+
     if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
@@ -238,7 +239,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5f84a5d..d1b593e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -78,7 +78,7 @@ import java.util.Map;
 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()
-- 
1.7.10.2