import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
final static private String WWW = "www.phylosoft.org/forester/";
final static private boolean SPECIAL = false;
- public static void main( final String args[] ) {
+ public static void main( final String args[] ) throws PhyloXmlDataFormatException {
ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
CommandLineArguments cla = null;
try {
}
if ( field != null ) {
for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferNodeNameToField( phy, field );
+ PhylogenyMethods.transferNodeNameToField( phy, field, false );
}
}
if ( midpoint_reroot ) {
if ( order_subtrees ) {
for( final Phylogeny phy : phys ) {
PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY );
+ phy.externalNodesHaveChanged();
+ phy.clearHashIdToNodeMap();
+ phy.recalculateNumberOfExternalDescendants( true );
}
}
try {