if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
printHelp();
}
- if ( ( args.length < 3 ) || ( args.length > 11 ) ) {
+ if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
System.out.println();
System.out.println( "error: incorrect number of arguments" );
System.out.println();
}
if ( return_gene_tree != null ) {
System.out.println( "Write best gene tree to : " + return_gene_tree );
+ System.out.println( "Transfer taxonomic data : " + transfer_taxonomy );
}
time = System.currentTimeMillis();
final ALGORITHM algorithm;
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
+ nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( p instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
nex.setReplaceUnderscores( false );
nex.setIgnoreQuotes( true );
- nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
+ nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else {
throw new RuntimeException( "unknown parser type: " + p );
writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" );
}
if ( return_gene_tree != null ) {
+ String tt = "";
+ if ( transfer_taxonomy ) {
+ tt = "(with transferred taxonomic data) ";
+ }
writeTree( rio.getMinDuplicationsGeneTree(),
return_gene_tree,
- "Wrote (one) minimal duplication gene tree to" );
+ "Wrote (one) minimal duplication gene tree " + tt + "to" );
}
final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: "