}
else {
ForesterUtil
- .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
+ .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
}
}
if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) {
System.out.println( "Usage" );
System.out.println();
System.out
- .println( PRG_NAME
- + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
+ .println( PRG_NAME
+ + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
System.out.println();
System.out.println( " Options" );
System.out.println( " -" + GT_FIRST + "=<first> : first gene tree to analyze (0-based index)" );
System.out.println( " -" + GT_LAST + "=<last> : last gene tree to analyze (0-based index)" );
System.out.println( " -" + REROOTING_OPT
- + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
+ + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
System.out.println( " or 'outgroup' (default: by minizming duplications)" );
System.out.println( " -" + OUTGROUP
- + "=<outgroup> : for rooting by outgroup, name of outgroup (external gene tree node)" );
+ + "=<outgroup> : for rooting by outgroup, name of outgroup (external gene tree node)" );
System.out
- .println( " -" + RETURN_SPECIES_TREE + "=<outfile> : to write the (stripped) species tree to file" );
+ .println( " -" + RETURN_SPECIES_TREE + "=<outfile> : to write the (stripped) species tree to file" );
System.out.println( " -" + RETURN_BEST_GENE_TREE
- + "=<outfile> : to write (one) minimal duplication gene tree to file" );
+ + "=<outfile> : to write (one) minimal duplication gene tree to file" );
System.out
- .println( " -"
- + TRANSFER_TAXONOMY_OPTION
- + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n"
- + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" );
+ .println( " -"
+ + TRANSFER_TAXONOMY_OPTION
+ + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n"
+ + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" );
System.out.println( " -" + USE_SDIR
- + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
+ + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
System.out.println( " disallowed, as are most options)" );
System.out.println();
System.out.println( " Formats" );
System.out
- .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," );
+ .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," );
System.out
- .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" );
+ .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" );
System.out
- .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" );
+ .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" );
System.out.println( " in the species tree." );
System.out.println();
System.out.println( " Examples" );