From a73cc918a63c07cfa5291b9b52f28cc201571ef5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 Feb 2017 15:22:40 +0000
Subject: [PATCH] JAL-2403 code tidy

---
 src/jalview/analysis/NJTree.java |   44 --------------------------------------
 1 file changed, 44 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index db2efba..2c6b61d 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -289,15 +289,11 @@ public class NJTree
       distance = result;
     }
 
-    // System.err.println("Made distances");// dbg
     makeLeaves();
-    // System.err.println("Made leaves");// dbg
 
     noClus = cluster.size();
 
     cluster();
-    // System.err.println("Made clusters");// dbg
-
   }
 
   /**
@@ -764,46 +760,6 @@ public class NJTree
   }
 
   /**
-   * Calculate a distance matrix given the sequence input data and score model
-   * 
-   * @return
-   */
-  public MatrixI findDistances(ScoreModelI scoreModel)
-  {
-    MatrixI result = null;
-
-    if (scoreModel == null)
-    {
-      // Resolve substitution model
-      scoreModel = ScoreModels.getInstance().forName(pwtype);
-      if (scoreModel == null)
-      {
-        scoreModel = ScoreModels.getInstance().forName("BLOSUM62");
-      }
-    }
-    if (scoreModel instanceof DistanceScoreModelI)
-    {
-      result = ((DistanceScoreModelI) scoreModel).findDistances(seqData);
-    }
-    else if (scoreModel instanceof SimilarityScoreModelI)
-    {
-      /*
-       * compute similarity and invert it to give a distance measure
-       */
-      result = ((SimilarityScoreModelI) scoreModel)
-              .findSimilarities(seqData);
-      result.reverseRange(true);
-    }
-    else
-    {
-      System.err
-              .println("Unexpected type of score model, can't compute distances");
-    }
-
-    return result;
-  }
-
-  /**
    * DOCUMENT ME!
    */
   public void makeLeaves()
-- 
1.7.10.2