X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryx.java;h=7f96bdd1337bd5c5add0fe3f30d4190f7e7b4a5d;hb=ecfa899d355303acc65e93601e00922aad822883;hp=eddc9190cb597ed37ba29a4a03bcc637b21f0f2b;hpb=038c34792757a86f24296de5683e722fab3f9307;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index eddc919..7f96bdd 100644
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -68,7 +68,7 @@ public final class Archaeopteryx {
         try {
             int filename_index = 0;
             if ( args.length == 0 ) {
-                conf = new Configuration( null, false, false );
+                conf = new Configuration( null, false, false, true );
             }
             else if ( args.length > 0 ) {
                 // check for a config file
@@ -79,7 +79,7 @@ public final class Archaeopteryx {
                 if ( args[ 0 ].startsWith( "-open" ) ) {
                     filename_index += 1;
                 }
-                conf = new Configuration( config_filename, false, false );
+                conf = new Configuration( config_filename, false, false, true );
                 if ( args.length > filename_index ) {
                     f = new File( args[ filename_index ] );
                     final String err = ForesterUtil.isReadableFile( f );
@@ -125,14 +125,18 @@ public final class Archaeopteryx {
         if ( f != null ) {
             title = f.getName();
         }
+        File current_dir = null;
+        if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
+            current_dir = new File( "." );
+        }
         try {
-            MainFrameApplication.createInstance( phylogenies, conf, title );
+            MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
         }
         catch ( final Exception ex ) {
-            Util.unexpectedException( ex );
+            AptxUtil.unexpectedException( ex );
         }
         catch ( final Error err ) {
-            Util.unexpectedError( err );
+            AptxUtil.unexpectedError( err );
         }
     }
 }
\ No newline at end of file