- log( "Gene trees analyzed range : " + first + "-" + last );
- }
- log( "Gene trees analyzed : " + _duplications_stats.getN() );
- log( "Mean number of duplications : " + df.format( _duplications_stats.arithmeticMean() )
- + " (sd: " + df.format( _duplications_stats.sampleStandardDeviation() ) + ")" + " ("
- + df.format( ( 100.0 * _duplications_stats.arithmeticMean() ) / getIntNodesOfAnalyzedGeneTrees() )
- + "%)" );
- if ( _duplications_stats.getN() > 3 ) {
- log( "Median number of duplications : " + df.format( _duplications_stats.median() )
- + " (" + df.format( ( 100.0 * _duplications_stats.median() ) / getIntNodesOfAnalyzedGeneTrees() )
- + "%)" );
- }
- log( "Minimum duplications : " + ( int ) _duplications_stats.getMin() + " ("
- + df.format( ( 100.0 * _duplications_stats.getMin() ) / getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
- log( "Maximum duplications : " + ( int ) _duplications_stats.getMax() + " ("
- + df.format( ( 100.0 * _duplications_stats.getMax() ) / getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
- log( "Gene tree internal nodes : " + getIntNodesOfAnalyzedGeneTrees() );
- log( "Gene tree external nodes : " + getExtNodesOfAnalyzedGeneTrees() );
+ log( "Gene trees analyzed range :\t" + first + "-" + last );
+ }
+ log( "Gene tree internal nodes :\t" + getIntNodesOfAnalyzedGeneTrees() );
+ log( "Gene tree external nodes :\t" + getExtNodesOfAnalyzedGeneTrees() );
+ log( "Removed ext gene tree nodes :\t" + getRemovedGeneTreeNodes().size() );
+ log( "Spec tree ext nodes (after strip) :\t" + species_tree.getNumberOfExternalNodes() );
+ log( "Spec tree polytomies (after strip) :\t" + PhylogenyMethods.countNumberOfPolytomies( species_tree ) );
+ log( "Taxonomy linking based on :\t" + getGSDIRtaxCompBase() );
+ log( "Mean number of duplications :\t" + df.format( getDuplicationsStatistics().arithmeticMean() )
+ + "\t"
+ + df.format( ( 100.0 * getDuplicationsStatistics().arithmeticMean() )
+ / getIntNodesOfAnalyzedGeneTrees() )
+ + "%\t(sd: " + df.format( getDuplicationsStatistics().sampleStandardDeviation() ) + ")" );
+ if ( getDuplicationsStatistics().getN() > 3 ) {
+ log( "Median number of duplications :\t" + df.format( median ) + "\t"
+ + df.format( ( 100.0 * median ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ }
+ log( "Minimum duplications :\t" + min + "\t"
+ + df.format( ( 100.0 * min ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ log( "Maximum duplications :\t" + ( int ) max + "\t"
+ + df.format( ( 100.0 * max ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ log( "Gene trees with median duplications :\t" + median_count + "\t" + df.format( median_count_percentage )
+ + "%" );
+ log( "Gene trees with minimum duplications:\t" + min_count + "\t" + df.format( min_count_percentage ) + "%" );
+ log( "Gene trees with maximum duplications:\t" + max_count + "\t" + df.format( max_count_percentage ) + "%" );