package org.forester.msa;
+import org.forester.sequence.Sequence;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
+
public class MsaCompactor {
- private calc
+ private DescriptiveStatistics[] calc() {
+ final double gappiness[] = calcGappiness();
+ final DescriptiveStatistics stats[] = new DescriptiveStatistics[ _msa.getNumberOfSequences() ];
+ for ( int row = 0; row < _msa.getNumberOfSequences(); ++row ) {
+ stats[ row ] = new BasicDescriptiveStatistics();
+ for( int col = 0; col < _msa.getLength(); ++col ) {
+ if ( _msa.getResidueAt( row, col ) != Sequence.GAP ) {
+ stats[ row ].addValue( gappiness[ col ] );
+
+ }
+ }
+ }
+ return stats;
+ }
private double[] calcGappiness() {
final double gappiness[] = new double[ _msa.getLength() ];