// 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.io.parsers;
import org.forester.msa.Msa;
import org.forester.msa.MsaFormatException;
import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
public final class GeneralMsaParser {
}
else {
throw new MsaFormatException( "illegal msa format (line: " + line_counter + "):\n\"" + trim( line )
- + "\"" );
+ + "\"" );
}
if ( is_first ) {
is_first = false;
}
}
} // while ( ( line = reader.readLine() ) != null )
- final List<Sequence> seqs = new ArrayList<Sequence>();
+ final List<MolecularSequence> seqs = new ArrayList<MolecularSequence>();
for( int i = 0; i < names_in_order.size(); ++i ) {
seqs.add( BasicSequence.createAaSequence( names_in_order.get( i ), temp_msa.get( names_in_order.get( i ) )
- .toString() ) );
+ .toString() ) );
}
final Msa msa = BasicMsa.createInstance( seqs );
return msa;