Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/featu...

[jalview.git] / src / jalview / ext / archaeopteryx / ArchaeopteryxTreeBuilder.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 82f215a..7096eff 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -4,9 +4,6 @@ import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
 import jalview.math.MatrixI;
 
-import org.forester.evoinference.distance.NeighborJoiningF;
-import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
-import org.forester.msa.Msa;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
@@ -24,17 +21,15 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
 
   protected MatrixI distances;
 
-  protected Msa msa;
-
-  protected SymmetricalDistanceMatrixParser distanceParser = SymmetricalDistanceMatrixParser
-          .createInstance();
+  {
+    this.aptxTree = new Phylogeny();
+  }
 
 
   public ArchaeopteryxTreeBuilder()
   {
 
     this.rootNode = new PhylogenyNode();
-    this.aptxTree = new Phylogeny();
 
   }
 
@@ -42,28 +37,28 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
   {
 
     this.rootNode = treeRoot;
-    this.aptxTree = new Phylogeny();
 
   }
 
   public Phylogeny buildAptxTree(TreeBuilder tree)
   {
     this.sequences = tree.getSequences();
+    this.distances = tree.getDistances();
+
     aptxTree.setName(
             "PLEASE FIX ME reheaheth35yheqhb3q5hyq3bt3q5u4jwqjwuh6");
 
-    final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
-    distances = tree.getDistances();
-
-
+    // final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
 
-    final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
-            .convertJalviewToForester(distances));
+    //
+    // final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
+    // .convertJalviewToForester(distances));
 
     return buildAptxTree(sequences);
 
   }
 
+  // testing method to be removed
   public Phylogeny buildAptxTree(SequenceI[] sequences)
   {