JAL-2428 simplify TreeModel constructors, add getOriginalData

[jalview.git] / src / jalview / analysis / TreeModel.java

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 2f8d788..62b0594 100644 (file)
--- 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;
+  }
 }