From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 8 Nov 2017 17:43:44 +0000 (+0000)
Subject: JAL-2794 Added getter for AlignmentViewport to TreeBuilder
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ac824ee5fdc757e084fff782870ba29da0a5dbae;p=jalview.git

JAL-2794 Added getter for AlignmentViewport to TreeBuilder
---

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 0cd340e..c4a94eb 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -77,6 +77,8 @@ public abstract class TreeBuilder
 
   protected SimilarityParamsI scoreParams;
 
+  private AlignmentViewport avport;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -90,6 +92,7 @@ public abstract class TreeBuilder
           SimilarityParamsI scoreParameters)
   {
     int start, end;
+    avport = av;
     boolean selview = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 1;
     seqStrings = av.getAlignmentView(selview);
@@ -492,11 +495,6 @@ public abstract class TreeBuilder
     return distances;
   }
 
-  public AlignmentView getSeqData()
-  {
-    return seqData;
-  }
-
   public ScoreModelI getScoreModel()
   {
     return scoreModel;
@@ -507,4 +505,9 @@ public abstract class TreeBuilder
     return scoreParams;
   }
 
+  public AlignmentViewport getAvport()
+  {
+    return avport;
+  }
+
 }