forester as submodule with InternalFrame + start of distance conversion

[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 fb1ebe3..82cabcd 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -4,6 +4,7 @@ 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;
@@ -48,7 +49,17 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
   public Phylogeny buildAptxTree(TreeBuilder tree)
   {
     this.sequences = tree.getSequences();
-    aptxTree.setName("word");
+    aptxTree.setName(
+            "PLEASE FIX ME reheaheth35yheqhb3q5hyq3bt3q5u4jwqjwuh6");
+
+    final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
+    distances = tree.getDistances();
+
+
+
+    // final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
+    // .convertJalviewToForester(distances));
+
     return buildAptxTree(sequences);
 
   }
@@ -58,8 +69,7 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
 
     for (SequenceI sequence : sequences)
     {
-      PhylogenyNode treeNode = new PhylogenyNode();
-      treeNode.setName(sequence.getName());
+      PhylogenyNode treeNode = new PhylogenyNode(sequence.getName());
       rootNode.addAsChild(treeNode);
 
     }
@@ -69,6 +79,7 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
 
   }
 
+
   /**
    * Formats a localised title for the tree panel, like
    * <p>