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/* Copyright 2018-2019 by Michiel de Hoon. All rights reserved.
* This file is part of the Biopython distribution and governed by your
* choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
* Please see the LICENSE file that should have been included as part of this
* package.
*/
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define HORIZONTAL 0x1
#define VERTICAL 0x2
#define DIAGONAL 0x4
typedef enum {NeedlemanWunschSmithWaterman,
Gotoh,
WatermanSmithBeyer,
FOGSAA,
Unknown} Algorithm;
typedef enum {Global, Local, FOGSAA_Mode} Mode;
typedef struct {
PyObject_HEAD
Mode mode;
Algorithm algorithm;
double match;
double mismatch;
double epsilon;
double open_internal_insertion_score;
double extend_internal_insertion_score;
double open_left_insertion_score;
double extend_left_insertion_score;
double open_right_insertion_score;
double extend_right_insertion_score;
double open_internal_deletion_score;
double extend_internal_deletion_score;
double open_left_deletion_score;
double extend_left_deletion_score;
double open_right_deletion_score;
double extend_right_deletion_score;
bool open_internal_insertion_score_set;
bool extend_internal_insertion_score_set;
bool open_left_insertion_score_set;
bool extend_left_insertion_score_set;
bool open_right_insertion_score_set;
bool extend_right_insertion_score_set;
bool open_internal_deletion_score_set;
bool extend_internal_deletion_score_set;
bool open_left_deletion_score_set;
bool extend_left_deletion_score_set;
bool open_right_deletion_score_set;
bool extend_right_deletion_score_set;
PyObject* insertion_score_function;
PyObject* deletion_score_function;
Py_buffer substitution_matrix;
PyObject* alphabet;
int wildcard;
} Aligner;
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