rio

[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 46ac48c..91a8fd9 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -94,11 +94,7 @@ public final class Archaeopteryx {
                         final NHXParser nhx = ( NHXParser ) p;
                         nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
                         nhx.setIgnoreQuotes( false );
-                        PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
-                        if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
-                            te = PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
-                        }
-                        nhx.setTaxonomyExtraction( te );
+                        nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
                     }
                     else if ( p instanceof NexusPhylogeniesParser ) {
                         nhx_or_nexus = true;
@@ -125,8 +121,12 @@ 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 ) {
             AptxUtil.unexpectedException( ex );