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";
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 );
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();
}