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

Before Change


        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)

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 "
Italian Trulli
In pattern: SUPERPATTERN

Frequency: 3

Non-data size: 3

Instances


Project Name: biotite-dev/biotite
Commit Name: 2bc5d43310eeca5c0d00b115b6f73d464f9c5576
Time: 2017-08-10
Author: patrick.kunzm@gmail.com
File Name: src/biopython/sequence/align/matrix.py
Class Name: SubstitutionMatrix
Method Name: __init__


Project Name: dpressel/mead-baseline
Commit Name: 78eba7b3f82b8420deac3cd28318dbfead0f9b9e
Time: 2018-10-30
Author: dpressel@gmail.com
File Name: python/baseline/dy/seq2seq/model.py
Class Name: Seq2SeqModel
Method Name: decode


Project Name: hanxiao/bert-as-service
Commit Name: 11da992272f0b41f6672f5ff078894282e5bb393
Time: 2018-11-08
Author: hanhxiao@tencent.com
File Name: client_example.py
Class Name:
Method Name: