_seqs = msa.getNumberOfSequences();
}
+ public final double[] calcGappiness() {
+ final int length = getLength();
+ final double gappiness[] = new double[ length ];
+ final int seqs = getNumberOfSequences();
+ for( int row = 0; row < seqs; ++row ) {
+ for( int col = 0; col < length; ++col ) {
+ }
+ }
+ return gappiness;
+ }
+
+ public static int calcGapSumPerColumn( final Msa msa, final int col ) {
+ int gap_rows = 0;
+ for( int j = 0; j < msa.getNumberOfSequences(); ++j ) {
+ if ( msa.isGapAt( j, col ) ) {
+ gap_rows++;
+ }
+ }
+ return gap_rows;
+ }
+
public short determineMaxIdLength() {
short max = 0;
for( int row = 0; row < getNumberOfSequences(); ++row ) {