2bc5d43310eeca5c0d00b115b6f73d464f9c5576,src/biopython/sequence/align/matrix.py,SubstitutionMatrix,__init__,#SubstitutionMatrix#Any#Any#Any#,13

Before Change

        self._alph2 = alphabet2
        if isinstance(matrix, dict):
            self._matrix = np.full(( len(alphabet1), len(alphabet2) ), np.nan)
            for key, value in matrix.items():
                i = alphabet1.encode(key[0])
                j = alphabet2.encode(key[1])
                self._matrix[i,j] = value
        elif isinstance(matrix, np.ndarray):
            self._matrix = np.copy(matrix)
        else:
            raise TypeError("Matrix must be either a dictionary "

After Change

        if isinstance(matrix, dict):
            matrix_dict = matrix
            self._matrix = np.full(( len(alphabet1), len(alphabet2) ), np.nan)
            for i in range(len(alphabet1)):
                for j in range(len(alphabet2)):
                    sym1 = alphabet1.decode(i)
                    sym2 = alphabet2.decode(j)
                    try:
                        self._matrix[i,j] = matrix_dict[sym1, sym2]
                    except KeyError:
                        pass
        elif isinstance(matrix, np.ndarray):
            self._matrix = np.copy(matrix)
        else:
            raise TypeError("Matrix must be either a dictionary "

Instances