1 package org.forester.msa;
4 public class MsaCompactor {
6 final private Msa _msa;
8 public MsaCompactor( Msa msa ) {
17 private double[] calcGappiness() {
18 final double gappiness[] = new double[ _msa.getLength() ];
19 final int seqs = _msa.getNumberOfSequences();
20 for( int i = 0; i < gappiness.length; ++i ) {
21 gappiness[ i ] = ( double ) MsaMethods.calcGapSumPerColumn( _msa, i ) / _msa.getNumberOfSequences();