X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryx.java;h=648fd6537f678a6d01b60cd15694fbfbf3b6a82b;hb=3d2b4742a8c0f3c5e5abfc73139351b8aa6ec2dc;hp=73afe58b3f3835c89c43a8c6197c9c7157a658e8;hpb=6fbecc5890472ea8419c338c278cb4e0b3dd7cc7;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 73afe58..648fd65 100644
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -36,7 +36,6 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.util.ForesterUtil;
 
-
 public final class Archaeopteryx {
 
     public static MainFrame createApplication( final Phylogeny phylogeny ) {
@@ -55,6 +54,12 @@ public final class Archaeopteryx {
         return MainFrameApplication.createInstance( phylogenies, config_file_name, title );
     }
 
+    public static MainFrame createApplication( final Phylogeny phylogeny, final Configuration config, final String title ) {
+        final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
+        phylogenies[ 0 ] = phylogeny;
+        return MainFrameApplication.createInstance( phylogenies, config, title );
+    }
+
     public static void main( final String args[] ) {
         Phylogeny[] phylogenies = null;
         String config_filename = null;
@@ -103,7 +108,7 @@ 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, "" );
                         }
                     }
                 }