public double [ ] [ ] getScoreMatrix ( ) { double [ ] [ ] matrix = new double [ sequences . size ( ) ] [ sequences . size ( ) ] ; for ( int i = 0 , n = 0 ; i < matrix . length ; i ++ ) { matrix [ i ] [ i ] = scorers . get ( i ) . getMaxScore ( ) ; for ( int j = i + 1 ; j < matrix . length ; j ++ ) { matrix [ i ] [ j ] = matrix [ j ] [ i ] = scorers . get ( n ++ ) . getScore ( ) ; } } return matrix ; }
Returns the similarity matrix used to construct this guide tree . The scores have not been normalized .