X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FTreeModel.java;h=62b05944c3c9d8bb67864d74ccf62d45303e7b8d;hb=2ff143c5a47bd7bde7409ce1457bf84e332660a8;hp=2f8d7883f40d2fe37f1b875eb7026b8da517af8a;hpb=bde7de1e5fe8d7bb1a119b6193297755feaef52a;p=jalview.git

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 2f8d788..62b0594 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -46,7 +46,7 @@ public class TreeModel
    * SequenceData is a string representation of what the user
    * sees. The display may contain hidden columns.
    */
-  public AlignmentView seqData;
+  private AlignmentView seqData;
 
   int noseqs;
 
@@ -68,7 +68,7 @@ public class TreeModel
 
   /**
    * Create a new TreeModel object with leaves associated with sequences in
-   * seqs, and original alignment data represented by Cigar strings
+   * seqs, and (optionally) original alignment data represented by Cigar strings
    * 
    * @param seqs
    *          SequenceI[]
@@ -79,22 +79,9 @@ public class TreeModel
    */
   public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
   {
-    this(seqs, treefile);
-    seqData = odata;
-  }
-
-  /**
-   * Creates a new TreeModel object from a tree from an external source
-   * 
-   * @param seqs
-   *          SequenceI which should be associated with leafs of treefile
-   * @param treefile
-   *          A parsed tree
-   */
-  public TreeModel(SequenceI[] seqs, NewickFile treefile)
-  {
     this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
             .HasBootstrap(), treefile.HasRootDistance());
+    seqData = odata;
 
     associateLeavesToSequences(seqs);
   }
@@ -468,15 +455,6 @@ public class TreeModel
   }
 
   /**
-   * 
-   * @return true if original sequence data can be recovered
-   */
-  public boolean hasOriginalSequenceData()
-  {
-    return seqData != null;
-  }
-
-  /**
    * Returns original alignment data used for calculation - or null where not
    * available.
    * 
@@ -710,4 +688,9 @@ public class TreeModel
       ;
     }
   }
+
+  public AlignmentView getOriginalData()
+  {
+    return seqData;
+  }
 }