X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryx.java;h=8cbf8cad3c36cf27d5e932b81665a5cbec312bd0;hb=26d8d47ed32a0eb9bd43c409d0e26ff13570b246;hp=546a8c044b423fd66660c113578af58acbd9b5c2;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 546a8c0..8cbf8ca 100644
--- 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 ) {
@@ -50,6 +44,12 @@ public final class Archaeopteryx {
         return createApplication( phylogenies, "", "" );
     }
 
+    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 MainFrame createApplication( final Phylogeny[] phylogenies ) {
         return createApplication( phylogenies, "", "" );
     }
@@ -84,11 +84,11 @@ public final class Archaeopteryx {
                     f = new File( args[ filename_index ] );
                     final String err = ForesterUtil.isReadableFile( f );
                     if ( !ForesterUtil.isEmpty( err ) ) {
-                        ForesterUtil.fatalError( Constants.PRG_NAME, err );
+                        ForesterUtil.fatalError( AptxConstants.PRG_NAME, err );
                     }
                     boolean nhx_or_nexus = false;
                     final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
-                            .isValidatePhyloXmlAgainstSchema() );
+                                                                                           .isValidatePhyloXmlAgainstSchema() );
                     if ( p instanceof NHXParser ) {
                         nhx_or_nexus = true;
                         final NHXParser nhx = ( NHXParser ) p;
@@ -108,14 +108,14 @@ 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, "" );
                         }
                     }
                 }
             }
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( Constants.PRG_NAME, "failed to start: " + e.getLocalizedMessage() );
+            ForesterUtil.fatalError( AptxConstants.PRG_NAME, "failed to start: " + e.getLocalizedMessage() );
         }
         String title = "";
         if ( f != null ) {