X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryx.java;h=a15ef512581fea65d9315b8dd236a5c4f502622e;hb=fbb463a0dc277aa6efa5231f6db554de3696b194;hp=6a28ef731ced083e296c966492de9a54a2b867e3;hpb=1a6e8795d5cd4c9b137069cc47121689b83377ed;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 6a28ef7..a15ef51 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;
 
@@ -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 ) {
@@ -94,11 +88,7 @@ public final class Archaeopteryx {
                         final NHXParser nhx = ( NHXParser ) p;
                         nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
                         nhx.setIgnoreQuotes( false );
-                        NHXParser.TAXONOMY_EXTRACTION te = NHXParser.TAXONOMY_EXTRACTION.NO;
-                        if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
-                            te = NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
-                        }
-                        nhx.setTaxonomyExtraction( te );
+                        nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
                     }
                     else if ( p instanceof NexusPhylogeniesParser ) {
                         nhx_or_nexus = true;
@@ -112,7 +102,7 @@ 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, "" );
                         }
                     }
                 }
@@ -132,11 +122,14 @@ public final class Archaeopteryx {
         try {
             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