+ final public static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( int c = from; c <= to; ++c ) {
+ stats.addValue( calculateIdentityRatio( msa, c ) );
+ }
+ return stats;
+ }
+
+ final public static DescriptiveStatistics calculateEffectiveLengthStatistics( final Msa msa ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {
+ final Sequence s = msa.getSequence( row );
+ stats.addValue( s.getLength() - s.getNumberOfGapResidues() );
+ }
+ return stats;
+ }
+
+ final public static double calculateIdentityRatio( final Msa msa, final int column ) {