X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryx.java;h=546a8c044b423fd66660c113578af58acbd9b5c2;hb=a3ab1c26605a4ffaaa5e8fd0927250c53c884bf9;hp=46ac48cc68b51ba1bfa143344341934728fdc998;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 46ac48c..546a8c0 100644
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -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;
@@ -125,14 +121,21 @@ 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 );
+        catch ( final OutOfMemoryError e ) {
+            AptxUtil.outOfMemoryError( e );
+        }
+        catch ( final Exception e ) {
+            AptxUtil.unexpectedException( e );
         }
-        catch ( final Error err ) {
-            AptxUtil.unexpectedError( err );
+        catch ( final Error e ) {
+            AptxUtil.unexpectedError( e );
         }
     }
 }
\ No newline at end of file