final private double _gap_ratio;
final private int _length;
final private int _number_of_sequences;
+ final private double _avg_number_of_gaps;
final private String _removed_seq;
public MsaProperties( final int number_of_sequences,
final double gap_ratio,
final double entropy7,
final double entropy21,
+ final double avg_number_of_gaps,
final String removed_seq ) {
_number_of_sequences = number_of_sequences;
_length = length;
_gap_ratio = gap_ratio;
_entropy7 = entropy7;
_entropy21 = entropy21;
+ _avg_number_of_gaps = avg_number_of_gaps;
_removed_seq = removed_seq;
}
_length = msa.getLength();
_gap_ratio = MsaMethods.calcGapRatio( msa );
_removed_seq = removed_seq;
+ _avg_number_of_gaps = MsaMethods.calcNumberOfGapsStats( msa ).arithmeticMean();
if ( calculate_normalized_shannon_entropy ) {
_entropy7 = MsaMethods.calcNormalizedShannonsEntropy( 7, msa );
_entropy21 = MsaMethods.calcNormalizedShannonsEntropy( 21, msa );
return _gap_ratio;
}
+ public final double getAvgNumberOfGaps() {
+ return _avg_number_of_gaps;
+ }
+
public final int getLength() {
return _length;
}