final static private String PRG_VERSION = "1.01";
final static private String PRG_DATE = "2012.06.07";
final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "www.phylosoft.org/forester/";
+ final static private String WWW = "www.phylosoft.org/forester";
public static void main( final String[] args ) {
try {
ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
+ " external node(s), aborting" );
}
- final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true );
+ final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true, false );
for( final String remove_me : not_found ) {
- //PhylogenyMethods.removeNode( phy.getNode( remove_me ), phy );
phy.deleteSubtree( phy.getNode( remove_me ), true );
}
+ phy.clearHashIdToNodeMap();
+ phy.externalNodesHaveChanged();
if ( phy.getNumberOfExternalNodes() < 2 ) {
ForesterUtil.fatalError( PRG_NAME,
"after removal of unresolvable external nodes, phylogeny has "