public static int calcGapSumPerColumn( final Msa msa, final int col ) {
int gap_rows = 0;
for( int j = 0; j < msa.getNumberOfSequences(); ++j ) {
- if ( msa.getResidueAt( j, col ) == Sequence.GAP ) {
+ if ( msa.isGapAt( j, col ) ) {
gap_rows++;
}
}
public static SortedMap<Character, Integer> calculateResidueDestributionPerColumn( final Msa msa, final int column ) {
final SortedMap<Character, Integer> map = new TreeMap<Character, Integer>();
for( final Character r : msa.getColumnAt( column ) ) {
- if ( !map.containsKey( r ) ) {
- map.put( r, 1 );
- }
- else {
- map.put( r, map.get( r ) + 1 );
+ if ( r != Sequence.GAP ) {
+ if ( !map.containsKey( r ) ) {
+ map.put( r, 1 );
+ }
+ else {
+ map.put( r, map.get( r ) + 1 );
+ }
}
}
return map;