X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhylogeneticInferrer.java;h=cc627519c3625f4c51ce32aa4940589874eb4ea5;hb=09a8c723e9ab220999f25c6be635282f18186be7;hp=1e8f3fc8c4fb36e889cbb240ef1b7c88b4c016ab;hpb=b84a8ba7a9f12b179ae2a0c83bf8dfd8d1e97540;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 1e8f3fc..cc62751 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -37,6 +37,7 @@ import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.msa.BasicMsa;
 import org.forester.msa.Mafft;
@@ -116,7 +117,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
     }
 
     private Phylogeny inferPhylogeny( final Msa msa ) {
-        BasicSymmetricalDistanceMatrix m = null;
+        DistanceMatrix m = null;
         switch ( _options.getPwdDistanceMethod() ) {
             case KIMURA_DISTANCE:
                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
@@ -274,7 +275,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
+    private void writeToFiles( final DistanceMatrix m ) {
         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
             try {
                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()