}
final private void write( final File outfile, final double gr ) throws IOException {
- writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_" + gr + ".aln" );
+ writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_"
+ + ForesterUtil.roundToInt( gr * 100 ) + ".fasta" );
}
final private void writeMsa( final String outfile ) throws IOException {
final Writer w = ForesterUtil.createBufferedWriter( outfile );
- _msa.write( w, MSA_FORMAT.PHYLIP );
+ _msa.write( w, MSA_FORMAT.FASTA );
w.close();
}
final private DescriptiveStatistics[] calcStats() {
final DescriptiveStatistics stats[] = calc();
sort( stats );
- for( int i = 0; i < stats.length; ++i ) {
- final DescriptiveStatistics s = stats[ i ];
- // System.out.print( s.getDescription() );
- // System.out.print( "\t" );
- // System.out.print( s.arithmeticMean() );
- // System.out.print( "\t(" );
- // System.out.print( s.arithmeticMean() );
- // System.out.print( ")" );
- // System.out.print( "\t" );
- // System.out.print( s.getMin() );
- // System.out.print( "\t" );
- // System.out.print( s.getMax() );
- // System.out.println();
+ for( final DescriptiveStatistics s : stats ) {
}
return stats;
}