- if ( calculate_aln_mean_identity ) {
- _average_identity_ratio = MsaMethods.calculateIdentityRatio( 0, msa.getLength() - 1, msa ).arithmeticMean();
+ _avg_number_of_gaps = MsaMethods.calcNumberOfGapsStats( msa ).arithmeticMean();
+ if ( calculate_normalized_shannon_entropy ) {
+ _entropy7 = MsaMethods.calcNormalizedShannonsEntropy( 7, msa );
+ _entropy21 = MsaMethods.calcNormalizedShannonsEntropy( 21, msa );