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";
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ 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.PFAM_STYLE_RELAXED );
+ nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else {
throw new RuntimeException( "unknown parser type: " + p );
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 ) );