public void apairs_from_seed ( int l , int i , int j ) { aligpath = new IndexPair [ l ] ; idx1 = new int [ l ] ; idx2 = new int [ l ] ; for ( int x = 0 ; x < l ; x ++ ) { idx1 [ x ] = i + x ; idx2 [ x ] = j + x ; aligpath [ x ] = new IndexPair ( ( short ) ( i + x ) , ( short ) ( j + x ) ) ; } }
Set apairs according to a seed position .