X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fdom_dup.java;h=7981966512211a65a5bbb02e2776d64cf9822284;hb=efaea5057ced91f5d162cebb6459d206da1d3c82;hp=64b4640b0e7716be1387daf9ab200f6120f8ff17;hpb=c244a8d7a48af45dce446f57a4d7a24ea3a8c912;p=jalview.git

diff --git a/forester/java/src/org/forester/application/dom_dup.java b/forester/java/src/org/forester/application/dom_dup.java
index 64b4640..7981966 100644
--- a/forester/java/src/org/forester/application/dom_dup.java
+++ b/forester/java/src/org/forester/application/dom_dup.java
@@ -30,7 +30,7 @@ import org.forester.util.ForesterUtil;
 public class dom_dup {
 
     // HUMAN MOUSE
-    // ARATH SOYBN VOLCA CYAME PARTE THAPS EMIHU NAEGR 
+    // ARATH SOYBN VOLCA CYAME PARTE THAPS EMIHU NAEGR
     final static private String HELP_OPTION_1 = "help";
     final static private String HELP_OPTION_2 = "h";
     final static private String PRG_NAME      = "dom_dup";
@@ -51,7 +51,7 @@ public class dom_dup {
             final File intree_file = cla.getFile( 2 );
             final File species_groups_file = cla.getFile( 1 );
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny phy = factory.create( intree_file, new PhyloXmlParser() )[ 0 ];
+            final Phylogeny phy = factory.create( intree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
             ForesterUtil.programMessage( PRG_NAME, "Pattern string: " + pattern_str );
             final Pattern pattern = Pattern.compile( pattern_str );
             ForesterUtil.programMessage( PRG_NAME, "Pattern is: " + pattern );
@@ -192,7 +192,7 @@ public class dom_dup {
         System.out.println( " example: " );
         System.out.println();
         System.out
-                .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" );
+        .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" );
         System.out.println();
         System.out.println();
     }