public final class MsaProperties {
- final private double _average_identity_ratio;
+ final private double _entropy21;
+ final private double _entropy7;
final private double _gap_ratio;
final private int _length;
final private int _number_of_sequences;
+ final private String _removed_seq;
public MsaProperties( final int number_of_sequences,
final int length,
final double gap_ratio,
- final double average_identity_ratio ) {
+ final double entropy7,
+ final double entropy21,
+ final String removed_seq ) {
_number_of_sequences = number_of_sequences;
_length = length;
_gap_ratio = gap_ratio;
- _average_identity_ratio = average_identity_ratio;
+ _entropy7 = entropy7;
+ _entropy21 = entropy21;
+ _removed_seq = removed_seq;
}
- public MsaProperties( final Msa msa, final boolean calculate_aln_mean_identity ) {
+ public MsaProperties( final Msa msa, final String removed_seq, final boolean calculate_normalized_shannon_entropy ) {
_number_of_sequences = msa.getNumberOfSequences();
_length = msa.getLength();
_gap_ratio = MsaMethods.calcGapRatio( msa );
- if ( calculate_aln_mean_identity ) {
- _average_identity_ratio = MsaMethods.calculateIdentityRatio( 0, msa.getLength() - 1, msa ).arithmeticMean();
+ _removed_seq = removed_seq;
+ if ( calculate_normalized_shannon_entropy ) {
+ _entropy7 = MsaMethods.calcNormalizedShannonsEntropy( 7, msa );
+ _entropy21 = MsaMethods.calcNormalizedShannonsEntropy( 21, msa );
}
else {
- _average_identity_ratio = -1;
+ _entropy7 = -1;
+ _entropy21 = -1;
}
}
- public final double getAverageIdentityRatio() {
- return _average_identity_ratio;
+ public final double getEntropy21() {
+ return _entropy21;
+ }
+
+ public final double getEntropy7() {
+ return _entropy7;
}
public final double getGapRatio() {
public final int getNumberOfSequences() {
return _number_of_sequences;
}
+
+ public final String getRemovedSeq() {
+ return _removed_seq;
+ }
}