public void addAlignedSequence ( S sequence ) { if ( length == null ) { length = sequence . getLength ( ) ; } if ( sequence . getLength ( ) != length ) { throw new IllegalArgumentException ( sequence . getAccession ( ) + " length = " + sequence . getLength ( ) + " not equal to MSA length = " + length ) ; } sequences . add ( sequence ) ; }
A sequence that has been aligned to other sequences will have inserts .