WWW,
ForesterUtil.getForesterLibraryInformation() );
System.out.println( "Input MSA : " + in );
- System.out.println( " MSA length : " + msa.getLength() );
- System.out.println( " Number of sequences : " + msa.getNumberOfSequences() );
- System.out.println( " Median sequence length : " + NF_1.format( initial_msa_stats.median() ) );
- System.out.println( " Mean sequence length : "
+ System.out.println( "MSA length : " + msa.getLength() );
+ System.out.println( "Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( "Median sequence length : " + NF_1.format( initial_msa_stats.median() ) );
+ System.out.println( "Mean sequence length : "
+ NF_1.format( initial_msa_stats.arithmeticMean() ) );
- System.out.println( " Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) );
- System.out.println( " Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) );
- System.out.println( " Gap ratio : "
+ System.out.println( "Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) );
+ System.out.println( "Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) );
+ System.out.println( "Gap ratio : "
+ NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
- System.out.println( " Mean gap count per 100 residues : "
+ System.out.println( "Mean gap count per 100 residues : "
+ NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean() ) );
- System.out.println( " Normalized Shannon Entropy (entn7) : "
+ System.out.println( "Normalized Shannon Entropy (entn7) : "
+ NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) );
- System.out.println( " Normalized Shannon Entropy (entn21): "
+ System.out.println( "Normalized Shannon Entropy (entn21): "
+ NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
}