Interface MatrixAligner<S extends Sequence<C>,​C extends Compound>

    • Method Detail

      • getScoreMatrix

        int[][][] getScoreMatrix()
        Returns the entire score matrix built during alignment. The first dimension has the length of the first (query) sequence + 1; the second has the length of the second (target) sequence + 1; the third has length equal to the number of scores stored per pairing of an element from each Sequence.
        the score matrix
      • getScoreMatrixAsString

        String getScoreMatrixAsString()
        Returns a depiction of the score matrix as a String. This may include additional description such as labels for each dimension: element from query sequence, element from target sequence, and meaning of each score.
        the score matrix as a character sequence