// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.msa;
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++;
}
}
return gap_rows;
}
+ final public static Msa removeSequence( final Msa msa, final String to_remove_id ) {
+ final List<Sequence> seqs = new ArrayList<Sequence>();
+ for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {
+ if ( !to_remove_id.equals( msa.getIdentifier( row ) ) ) {
+ seqs.add( BasicSequence.copySequence( msa.getSequence( row ) ) );
+ }
+ }
+ if ( seqs.size() < 1 ) {
+ return null;
+ }
+ return BasicMsa.createInstance( seqs );
+ }
+
final public static Msa removeSequences( final Msa msa, final List<String> to_remove_ids ) {
final List<Sequence> seqs = new ArrayList<Sequence>();
for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {