/
cpairwise2module.c
639 lines (572 loc) · 18.2 KB
/
cpairwise2module.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
/* Copyright 2002 by Jeffrey Chang. All rights reserved.
* This code is part of the Biopython distribution and governed by its
* license. Please see the LICENSE file that should have been included
* as part of this package.
*
* cpairwise2module.c
* Created 30 Sep 2001
*
* Optimized C routines that complement pairwise2.py.
*/
#include "Python.h"
#define _PRECISION 1000
#define rint(x) (int)((x)*_PRECISION+0.5)
/* Return a PyNumber as a double.
* Raises a TypeError if I can't do it.
*/
static double PyNumber_AsDouble(PyObject *py_num)
{
double val;
PyObject *floatobj;
if((floatobj = PyNumber_Float(py_num)) == NULL)
return(0.0);
val = PyFloat_AsDouble(floatobj);
Py_DECREF(floatobj);
return val;
}
/* Functions in this module. */
double calc_affine_penalty(int length, double open, double extend,
int penalize_extend_when_opening)
{
double penalty;
if(length <= 0)
return 0.0;
penalty = open + extend * length;
if(!penalize_extend_when_opening)
penalty -= extend;
return penalty;
}
struct IndexList {
int num_used;
int num_allocated;
int *indexes; /* Array of ints. Even ints are rows, odd ones are cols. */
};
static void IndexList_init(struct IndexList *il)
{
/* il->num_used = 0;
il->num_allocated = 0;
il->indexes = NULL; */
memset((void *)il, 0, sizeof(struct IndexList));
}
static void IndexList_free(struct IndexList *il)
{
if(il->indexes)
free(il->indexes);
IndexList_init(il);
}
static void IndexList_clear(struct IndexList *il)
{
il->num_used = 0;
}
static int IndexList_contains(struct IndexList *il,
const int row, const int col)
{
int i;
int stop;
stop = il->num_used*2;
for(i=0; i<stop; i+=2) {
if((il->indexes[i] == row) && (il->indexes[i+1] == col))
return 1;
}
return 0;
}
static int IndexList__verify_free_index(struct IndexList *il, int num_needed)
{
int *indexes;
int num_to_allocate;
int num_bytes;
if(il->num_allocated >= num_needed)
return 1;
/* Nearly all the cases are for list of length 1 or 2.
Empirically, the code seems to run fastest when I allocate the
exact amount for these. */
if(num_needed <= 2)
num_to_allocate = num_needed;
else
num_to_allocate = num_needed*2;
num_bytes = num_to_allocate*sizeof(int)*2;
if(!(indexes = realloc((void *)il->indexes, num_bytes))) {
PyErr_SetString(PyExc_MemoryError, "Out of memory");
return 0;
}
il->indexes = indexes;
il->num_allocated = num_to_allocate;
return 1;
}
static void IndexList_append(struct IndexList *il,
const int row, const int col)
{
int i;
if(!IndexList__verify_free_index(il, il->num_used+1))
return;
i=il->num_used*2;
il->indexes[i] = row;
il->indexes[i+1] = col;
il->num_used += 1;
}
static void IndexList_extend(struct IndexList *il1, struct IndexList *il2)
{
int i1, i2;
int stop;
if(!IndexList__verify_free_index(il1, il1->num_used+il2->num_used))
return;
stop=il2->num_used * 2;
for(i1=il1->num_used*2, i2=0; i2<stop; i1+=2, i2+=2) {
il1->indexes[i1] = il2->indexes[i2];
il1->indexes[i1+1] = il2->indexes[i2+1];
}
il1->num_used += il2->num_used;
}
/* static void IndexList_copy(struct IndexList *il1, struct IndexList *il2)
{
IndexList_clear(il1);
IndexList_extend(il1, il2);
} */
/* static void IndexList_assign(struct IndexList *il1, struct IndexList *il2)
{
if(il1->indexes)
free(il1->indexes);
il1->indexes = il2->indexes;
il1->num_used = il2->num_used;
il1->num_allocated = il2->num_allocated;
} */
double _get_match_score(PyObject *py_sequenceA, PyObject *py_sequenceB,
PyObject *py_match_fn, int i, int j,
char *sequenceA, char *sequenceB,
int use_sequence_cstring,
double match, double mismatch,
int use_match_mismatch_scores)
{
PyObject *py_A=NULL,
*py_B=NULL;
PyObject *py_arglist=NULL, *py_result=NULL;
double score = 0;
if(use_sequence_cstring && use_match_mismatch_scores) {
score = (sequenceA[i] == sequenceB[j]) ? match : mismatch;
return score;
}
/* Calculate the match score. */
if(!(py_A = PySequence_GetItem(py_sequenceA, i)))
goto _get_match_score_cleanup;
if(!(py_B = PySequence_GetItem(py_sequenceB, j)))
goto _get_match_score_cleanup;
if(!(py_arglist = Py_BuildValue("(OO)", py_A, py_B)))
goto _get_match_score_cleanup;
if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
goto _get_match_score_cleanup;
score = PyNumber_AsDouble(py_result);
_get_match_score_cleanup:
if(py_A) {
Py_DECREF(py_A);
}
if(py_B) {
Py_DECREF(py_B);
}
if(py_arglist) {
Py_DECREF(py_arglist);
}
if(py_result) {
Py_DECREF(py_result);
}
return score;
}
#if PY_MAJOR_VERSION >= 3
static PyObject* _create_bytes_object(PyObject* o) {
PyObject* b;
if (PyBytes_Check(o)) {
return o;
}
if (!PyUnicode_Check(o)) {
return NULL;
}
b = PyUnicode_AsASCIIString(o);
if (!b) {
PyErr_Clear();
return NULL;
}
return b;
}
#endif
/* This function is a more-or-less straightforward port of the
* equivalent function in pairwise2. Please see there for algorithm
* documentation.
*/
static PyObject *cpairwise2__make_score_matrix_fast(
PyObject *self, PyObject *args)
{
int i;
int row, col;
PyObject *py_sequenceA, *py_sequenceB, *py_match_fn;
#if PY_MAJOR_VERSION >= 3
PyObject *py_bytesA, *py_bytesB;
#endif
char *sequenceA=NULL, *sequenceB=NULL;
int use_sequence_cstring;
double open_A, extend_A, open_B, extend_B;
int penalize_extend_when_opening, penalize_end_gaps;
int align_globally, score_only;
PyObject *py_match=NULL, *py_mismatch=NULL;
double first_A_gap, first_B_gap;
double match, mismatch;
int use_match_mismatch_scores;
int lenA, lenB;
double *score_matrix = (double *)NULL;
struct IndexList *trace_matrix = (struct IndexList *)NULL;
PyObject *py_score_matrix=NULL, *py_trace_matrix=NULL;
double *row_cache_score = (double *)NULL,
*col_cache_score = (double *)NULL;
struct IndexList *row_cache_index = (struct IndexList *)NULL,
*col_cache_index = (struct IndexList *)NULL;
PyObject *py_retval = NULL;
if(!PyArg_ParseTuple(args, "OOOddddiiii", &py_sequenceA, &py_sequenceB,
&py_match_fn, &open_A, &extend_A, &open_B, &extend_B,
&penalize_extend_when_opening, &penalize_end_gaps,
&align_globally, &score_only))
return NULL;
if(!PySequence_Check(py_sequenceA) || !PySequence_Check(py_sequenceB)) {
PyErr_SetString(PyExc_TypeError,
"py_sequenceA and py_sequenceB should be sequences.");
return NULL;
}
/* Optimize for the common case. Check to see if py_sequenceA and
py_sequenceB are strings. If they are, use the c string
representation. */
#if PY_MAJOR_VERSION < 3
use_sequence_cstring = 0;
if(PyString_Check(py_sequenceA) && PyString_Check(py_sequenceB)) {
sequenceA = PyString_AS_STRING(py_sequenceA);
sequenceB = PyString_AS_STRING(py_sequenceB);
use_sequence_cstring = 1;
}
#else
py_bytesA = _create_bytes_object(py_sequenceA);
py_bytesB = _create_bytes_object(py_sequenceB);
if (py_bytesA && py_bytesB) {
sequenceA = PyBytes_AS_STRING(py_bytesA);
sequenceB = PyBytes_AS_STRING(py_bytesB);
use_sequence_cstring = 1;
}
else {
Py_XDECREF(py_bytesA);
Py_XDECREF(py_bytesB);
use_sequence_cstring = 0;
}
#endif
if(!PyCallable_Check(py_match_fn)) {
PyErr_SetString(PyExc_TypeError, "py_match_fn must be callable.");
return NULL;
}
/* Optimize for the common case. Check to see if py_match_fn is
an identity_match. If so, pull out the match and mismatch
member variables and calculate the scores myself. */
match = mismatch = 0;
use_match_mismatch_scores = 0;
if(!(py_match = PyObject_GetAttrString(py_match_fn, "match")))
goto cleanup_after_py_match_fn;
match = PyNumber_AsDouble(py_match);
if(PyErr_Occurred())
goto cleanup_after_py_match_fn;
if(!(py_mismatch = PyObject_GetAttrString(py_match_fn, "mismatch")))
goto cleanup_after_py_match_fn;
mismatch = PyNumber_AsDouble(py_mismatch);
if(PyErr_Occurred())
goto cleanup_after_py_match_fn;
use_match_mismatch_scores = 1;
cleanup_after_py_match_fn:
if(PyErr_Occurred())
PyErr_Clear();
if(py_match) {
Py_DECREF(py_match);
}
if(py_mismatch) {
Py_DECREF(py_mismatch);
}
/* Cache some commonly used gap penalties */
first_A_gap = calc_affine_penalty(1, open_A, extend_A,
penalize_extend_when_opening);
first_B_gap = calc_affine_penalty(1, open_B, extend_B,
penalize_extend_when_opening);
/* Allocate matrices for storing the results and initalize them. */
lenA = PySequence_Length(py_sequenceA);
lenB = PySequence_Length(py_sequenceB);
score_matrix = malloc(lenA*lenB*sizeof(*score_matrix));
trace_matrix = malloc(lenA*lenB*sizeof(*trace_matrix));
if(!score_matrix || !trace_matrix) {
PyErr_SetString(PyExc_MemoryError, "Out of memory");
goto _cleanup_make_score_matrix_fast;
}
for(i=0; i<lenA*lenB; i++) {
score_matrix[i] = 0;
IndexList_init(&trace_matrix[i]);
}
/* Initialize the first row and col of the score matrix. */
for(i=0; i<lenA; i++) {
double score = _get_match_score(py_sequenceA, py_sequenceB,
py_match_fn, i, 0,
sequenceA, sequenceB,
use_sequence_cstring,
match, mismatch,
use_match_mismatch_scores);
if(PyErr_Occurred())
goto _cleanup_make_score_matrix_fast;
if(penalize_end_gaps)
score += calc_affine_penalty(i, open_B, extend_B,
penalize_extend_when_opening);
score_matrix[i*lenB] = score;
}
for(i=0; i<lenB; i++) {
double score = _get_match_score(py_sequenceA, py_sequenceB,
py_match_fn, 0, i,
sequenceA, sequenceB,
use_sequence_cstring,
match, mismatch,
use_match_mismatch_scores);
if(PyErr_Occurred())
goto _cleanup_make_score_matrix_fast;
if(penalize_end_gaps)
score += calc_affine_penalty(i, open_A, extend_A,
penalize_extend_when_opening);
score_matrix[i] = score;
}
/* Now initialize the row and col cache. */
row_cache_score = malloc((lenA-1)*sizeof(*row_cache_score));
row_cache_index = malloc((lenA-1)* sizeof(*row_cache_index));
col_cache_score = malloc((lenB-1)*sizeof(*col_cache_score));
col_cache_index = malloc((lenB-1)* sizeof(*col_cache_index));
if(!row_cache_score || !row_cache_index ||
!col_cache_score || !col_cache_index) {
PyErr_SetString(PyExc_MemoryError, "Out of memory");
goto _cleanup_make_score_matrix_fast;
}
memset((void *)row_cache_score, 0, (lenA-1)*sizeof(*row_cache_score));
memset((void *)row_cache_index, 0, (lenA-1)*sizeof(*row_cache_index));
memset((void *)col_cache_score, 0, (lenB-1)*sizeof(*col_cache_score));
memset((void *)col_cache_index, 0, (lenB-1)*sizeof(*col_cache_index));
for(i=0; i<lenA-1; i++) {
row_cache_score[i] = score_matrix[i*lenB] + first_A_gap;
IndexList_append(&row_cache_index[i], i, 0);
}
for(i=0; i<lenB-1; i++) {
col_cache_score[i] = score_matrix[i] + first_B_gap;
IndexList_append(&col_cache_index[i], 0, i);
}
/* Fill in the score matrix. */
for(row=1; row<lenA; row++) {
for(col=1; col<lenB; col++) {
double nogap_score, row_score, col_score, best_score;
int best_score_rint;
struct IndexList *il;
double score, open_score, extend_score;
int open_score_rint, extend_score_rint;
/* Calculate the best score. */
nogap_score = score_matrix[(row-1)*lenB+col-1];
if(col > 1) {
row_score = row_cache_score[row-1];
} else {
row_score = nogap_score-1; /* Make sure it's not best score */
}
if(row > 1) {
col_score = col_cache_score[col-1];
} else {
col_score = nogap_score-1; /* Make sure it's not best score */
}
best_score = (row_score > col_score) ? row_score : col_score;
if(nogap_score > best_score)
best_score = nogap_score;
best_score_rint = rint(best_score);
/* Set the score and traceback matrices. */
score = best_score + _get_match_score(py_sequenceA, py_sequenceB,
py_match_fn, row, col,
sequenceA, sequenceB,
use_sequence_cstring,
match, mismatch,
use_match_mismatch_scores);
if(PyErr_Occurred())
goto _cleanup_make_score_matrix_fast;
if(!align_globally && score < 0)
score_matrix[row*lenB+col] = 0;
else
score_matrix[row*lenB+col] = score;
il = &trace_matrix[row*lenB+col];
if(best_score_rint == rint(nogap_score)) {
IndexList_append(il, row-1, col-1);
}
if(best_score_rint == rint(row_score)) {
IndexList_extend(il, &row_cache_index[row-1]);
}
if(best_score_rint == rint(col_score)) {
IndexList_extend(il, &col_cache_index[col-1]);
}
/* Update the cached column scores. */
open_score = score_matrix[(row-1)*lenB+col-1] + first_B_gap;
extend_score = col_cache_score[col-1] + extend_B;
open_score_rint = rint(open_score);
extend_score_rint = rint(extend_score);
if(open_score_rint > extend_score_rint) {
col_cache_score[col-1] = open_score;
IndexList_clear(&col_cache_index[col-1]);
IndexList_append(&col_cache_index[col-1], row-1, col-1);
} else if(extend_score_rint > open_score_rint) {
col_cache_score[col-1] = extend_score;
} else {
col_cache_score[col-1] = open_score;
if(!IndexList_contains(&col_cache_index[col-1], row-1, col-1))
IndexList_append(&col_cache_index[col-1], row-1, col-1);
}
/* Update the cached row scores. */
open_score = score_matrix[(row-1)*lenB+col-1] + first_A_gap;
extend_score = row_cache_score[row-1] + extend_A;
open_score_rint = rint(open_score);
extend_score_rint = rint(extend_score);
if(open_score_rint > extend_score_rint) {
row_cache_score[row-1] = open_score;
IndexList_clear(&row_cache_index[row-1]);
IndexList_append(&row_cache_index[row-1], row-1, col-1);
} else if(extend_score_rint > open_score_rint) {
row_cache_score[row-1] = extend_score;
} else {
row_cache_score[row-1] = open_score;
if(!IndexList_contains(&row_cache_index[row-1], row-1, col-1))
IndexList_append(&row_cache_index[row-1], row-1, col-1);
}
}
}
/* Save the score and traceback matrices into real python objects. */
if(!(py_score_matrix = PyList_New(lenA)))
goto _cleanup_make_score_matrix_fast;
if(!(py_trace_matrix = PyList_New(lenA)))
goto _cleanup_make_score_matrix_fast;
for(row=0; row<lenA; row++) {
PyObject *py_score_row, *py_trace_row;
if(!(py_score_row = PyList_New(lenB)))
goto _cleanup_make_score_matrix_fast;
PyList_SET_ITEM(py_score_matrix, row, py_score_row);
if(!(py_trace_row = PyList_New(lenB)))
goto _cleanup_make_score_matrix_fast;
PyList_SET_ITEM(py_trace_matrix, row, py_trace_row);
for(col=0; col<lenB; col++) {
int i;
PyObject *py_score, *py_indexlist;
int offset = row*lenB + col;
struct IndexList *il = &trace_matrix[offset];
/* Set py_score_matrix[row][col] to the score. */
if(!(py_score = PyFloat_FromDouble(score_matrix[offset])))
goto _cleanup_make_score_matrix_fast;
PyList_SET_ITEM(py_score_row, col, py_score);
if(score_only)
continue;
/* Set py_trace_matrix[row][col] to a list of indexes. On
the edges of the matrix (row or column is 0), the
matrix should be [None]. */
if(!row || !col) {
if(!(py_indexlist = PyList_New(1)))
goto _cleanup_make_score_matrix_fast;
Py_INCREF(Py_None);
PyList_SET_ITEM(py_indexlist, 0, Py_None);
}
else {
if(!(py_indexlist = PyList_New(il->num_used)))
goto _cleanup_make_score_matrix_fast;
for(i=0; i<il->num_used; i++) {
PyObject *py_index=NULL;
int row = il->indexes[i*2],
col = il->indexes[i*2+1];
if(!(py_index = Py_BuildValue("(ii)", row, col)))
goto _cleanup_make_score_matrix_fast;
PyList_SET_ITEM(py_indexlist, i, py_index);
}
}
PyList_SET_ITEM(py_trace_row, col, py_indexlist);
}
}
py_retval = Py_BuildValue("(OO)", py_score_matrix, py_trace_matrix);
_cleanup_make_score_matrix_fast:
if(score_matrix)
free(score_matrix);
if(trace_matrix) {
for(i=0; i<lenA*lenB; i++)
IndexList_free(&trace_matrix[i]);
free(trace_matrix);
}
if(row_cache_score)
free(row_cache_score);
if(col_cache_score)
free(col_cache_score);
if(row_cache_index) {
for(i=0; i<lenA-1; i++)
IndexList_free(&row_cache_index[i]);
free(row_cache_index);
}
if(col_cache_index) {
for(i=0; i<lenB-1; i++) {
IndexList_free(&col_cache_index[i]);
}
free(col_cache_index);
}
if(py_score_matrix) {
Py_DECREF(py_score_matrix);
}
if(py_trace_matrix) {
Py_DECREF(py_trace_matrix);
}
#if PY_MAJOR_VERSION >= 3
if (py_bytesA != NULL && py_bytesA != py_sequenceA) Py_DECREF(py_bytesA);
if (py_bytesB != NULL && py_bytesB != py_sequenceB) Py_DECREF(py_bytesB);
#endif
return py_retval;
}
static PyObject *cpairwise2_rint(
PyObject *self, PyObject *args, PyObject *keywds)
{
double x;
int precision = _PRECISION;
int rint_x;
static char *kwlist[] = {"x", "precision", NULL};
if(!PyArg_ParseTupleAndKeywords(args, keywds, "d|l", kwlist,
&x, &precision))
return NULL;
rint_x = (int)(x * precision + 0.5);
#if PY_MAJOR_VERSION >= 3
return PyLong_FromLong((long)rint_x);
#else
return PyInt_FromLong((long)rint_x);
#endif
}
/* Module definition stuff */
static PyMethodDef cpairwise2Methods[] = {
{"_make_score_matrix_fast",
(PyCFunction)cpairwise2__make_score_matrix_fast, METH_VARARGS, ""},
{"rint", (PyCFunction)cpairwise2_rint, METH_VARARGS|METH_KEYWORDS, ""},
{NULL, NULL, 0, NULL}
};
static char cpairwise2__doc__[] =
"XXX document here\n\
\n\
";
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef moduledef = {
PyModuleDef_HEAD_INIT,
"cpairwise2",
cpairwise2__doc__,
-1,
cpairwise2Methods,
NULL,
NULL,
NULL,
NULL
};
PyObject *
PyInit_cpairwise2(void)
#else
void
initcpairwise2(void)
#endif
{
#if PY_MAJOR_VERSION >= 3
PyObject* module = PyModule_Create(&moduledef);
if (module==NULL) return NULL;
return module;
#else
(void) Py_InitModule3("cpairwise2", cpairwise2Methods, cpairwise2__doc__);
#endif
}