System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
System.out.println();
System.out
- .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
- + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
+ .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
+ + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
System.out
- .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
+ .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
System.out.println( " : -t=<d> threshold for similarity (0.0 to 1.0)" );
System.out.println( " : -n no branch lengths in outfile for evaluator phylogenies" );
System.out.println();
else {
if ( !branch_lengths_in_ev_out ) {
ForesterUtil.fatalError( count_support.PRG_NAME,
- "Cannot use -n option if no outfile for evaluators specified" );
+ "Cannot use -n option if no outfile for evaluators specified" );
}
}
Phylogeny p = null;
}
if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) {
ForesterUtil.fatalError( count_support.PRG_NAME,
- "support threshold has to be between 0.0 and 1.0 (inclusive)" );
+ "support threshold has to be between 0.0 and 1.0 (inclusive)" );
}
}
List<Phylogeny> evaluator_phylogenies_above_threshold = null;
if ( threshhold >= 0 ) {
count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() );
System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length
- + " evaluator phylogenies are above threshold of " + threshhold );
+ + " evaluator phylogenies are above threshold of " + threshhold );
}
try {
final PhylogenyWriter w = new PhylogenyWriter();
final PhylogenyWriter w = new PhylogenyWriter();
if ( evaluator_phylogenies_above_threshold != null ) {
System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size()
- + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
+ + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";"
+ ForesterUtil.getLineSeparator() );
}
else {
w.toNewHampshire( evaluator_phylogenies_above_threshold,
- true,
branch_lengths_in_ev_out,
evaluators_outfile,
";" + ForesterUtil.getLineSeparator() );
";" + ForesterUtil.getLineSeparator() );
}
else {
- w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
+ w.toNewHampshire( Arrays.asList( ev ), branch_lengths_in_ev_out, evaluators_outfile, ";"
+ ForesterUtil.getLineSeparator() );
}
}