public List < Subunit > getAlignedSubunits2 ( ) { List < Subunit > aligned = new ArrayList < Subunit > ( subunitMap . size ( ) ) ; for ( Integer key : subunitMap . keySet ( ) ) aligned . ( subunits2 . get ( subunitMap . get ( key ) ) ) ; return aligned ; }
Return the aligned subunits of the second Subunit group in the alignment order .