inprogress

[jalview.git] / forester / java / src / org / forester / application / gsdi.java

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index 0ec4958..17dbf7e 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.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.application;
 
@@ -267,6 +267,9 @@ public final class gsdi {
         catch ( final IOException e ) {
             fatalError( "error", e.toString(), log_writer );
         }
+        catch ( final OutOfMemoryError e ) {
+            ForesterUtil.outOfMemoryError( e );
+        }
         catch ( final Exception e ) {
             e.printStackTrace();
             fatalError( "unexpected error", e.toString(), log_writer );
@@ -285,10 +288,7 @@ public final class gsdi {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
             if ( base_algorithm == ALGORITHM.GSDIR ) {
-                writer.toPhyloXML( out_file,
-                                   ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTrees(),
-                                   0,
-                                   ForesterUtil.LINE_SEPARATOR );
+                writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
             }
             else {
                 writer.toPhyloXML( out_file, gene_tree, 0 );