Merge branch 'patch/JAL-4317_enablefeaturewhenadjustingstyle' into develop

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 487e85e..9a39ac0 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -22,7 +22,7 @@ package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceNode;
+import jalview.datamodel.BinaryNode;
 import jalview.viewmodel.AlignmentViewport;
 
 /**
@@ -81,7 +81,7 @@ public class NJTree extends TreeBuilder
    * {@inheritDoc}
    */
   @Override
-  protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+  protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
           double dist)
   {
     nodei.dist = ((dist + ri) - rj) / 2;
@@ -108,25 +108,25 @@ public class NJTree extends TreeBuilder
    * @param j
    */
   @Override
-  protected
-  void findClusterDistance(int i, int j)
+  protected void findClusterDistance(int i, int j)
   {
     // New distances from cluster i to others
     double[] newdist = new double[noseqs];
-  
+
     double ijDistance = distances.getValue(i, j);
     for (int l = 0; l < noseqs; l++)
     {
       if ((l != i) && (l != j))
       {
-        newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - ijDistance) / 2;
+        newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l)
+                - ijDistance) / 2;
       }
       else
       {
         newdist[l] = 0;
       }
     }
-  
+
     for (int ii = 0; ii < noseqs; ii++)
     {
       distances.setValue(i, ii, newdist[ii]);