import java.io.File;
import java.io.IOException;
+import java.math.RoundingMode;
import java.util.ArrayList;
import java.util.List;
final static private String PRG_NAME = "rio";
final static private String PRG_VERSION = "4.000 beta 10";
- final static private String PRG_DATE = "130325";
+ final static private String PRG_DATE = "140211";
final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
final static private String HELP_OPTION_1 = "help";
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: "
+ df.format( stats.sampleStandardDeviation() ) + ") ("
- + df.format( 100.0 * stats.arithmeticMean() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+ + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
if ( stats.getN() > 3 ) {
System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " ("
- + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+ + df.format( ( 100.0 * stats.median() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
}
System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " ("
- + df.format( 100.0 * stats.getMin() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+ + df.format( ( 100.0 * stats.getMin() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " ("
- + df.format( 100.0 * stats.getMax() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+ + df.format( ( 100.0 * stats.getMax() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
System.out.println( "Gene tree internal nodes : " + rio.getIntNodesOfAnalyzedGeneTrees() );
System.out.println( "Gene tree external nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() );
}
private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m )
throws IOException {
final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile );
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" );
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
df.setDecimalSeparatorAlwaysShown( false );
+ df.setRoundingMode( RoundingMode.HALF_UP );
for( int i = 0; i < m.size(); ++i ) {
w.print( "\t" );
w.print( m.getLabel( i ) );