inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / Archaeopteryx.java

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 546a8c0..a15ef51 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -36,12 +36,6 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.util.ForesterUtil;
 
-//
-// java -javaagent:shiftone-jrat.jar -cp
-// $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/java/forester.jar:.
-// org.forester.archaeopteryx.Archaeopteryx
-// -c $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/_aptx_configuration_file
-//
 public final class Archaeopteryx {
 
     public static MainFrame createApplication( final Phylogeny phylogeny ) {
@@ -108,7 +102,7 @@ public final class Archaeopteryx {
                     phylogenies = PhylogenyMethods.readPhylogenies( p, f );
                     if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
                         for( final Phylogeny phy : phylogenies ) {
-                            PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+                            PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
                         }
                     }
                 }