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_pairwisealigner.c
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7740 lines (7335 loc) · 267 KB
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/* Copyright 2018-2025 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"
#include <float.h>
#include <stdbool.h>
#include "_pairwisealigner.h"
#include "substitution_matrices/_arraycore.h"
static bool warned = false; // FIXME remove once Biopython 1.87 is out.
#define STARTPOINT 0x8
#define ENDPOINT 0x10
#define M_MATRIX 0x1
#define Ix_MATRIX 0x2
#define Iy_MATRIX 0x4
#define DONE 0x3
#define NONE 0x7
#define OVERFLOW_ERROR -1
#define MEMORY_ERROR -2
#define OTHER_ERROR -3
#define SAFE_ADD(t, s) \
{ if (s != OVERFLOW_ERROR) { \
term = t; \
if (term > PY_SSIZE_T_MAX - s) s = OVERFLOW_ERROR; \
else s += term; \
} \
}
static PyTypeObject *Array_Type = NULL;
/* this will be set when initializing the module */
#define ERR_UNEXPECTED_MODE \
PyErr_Format(PyExc_RuntimeError, "mode has unexpected value (in "__FILE__" on line %d)", __LINE__);
#define ERR_UNEXPECTED_ALGORITHM \
PyErr_Format(PyExc_RuntimeError, "algorithm has unexpected value (in "__FILE__" on line %d)", __LINE__);
typedef struct {
unsigned char trace : 5;
unsigned char path : 3;
} Trace;
typedef struct {
unsigned char Ix : 4;
unsigned char Iy : 4;
} TraceGapsGotoh;
typedef struct {
int* MIx;
int* IyIx;
int* MIy;
int* IxIy;
} TraceGapsWatermanSmithBeyer;
typedef struct {
PyObject_HEAD
Trace** M;
union { TraceGapsGotoh** gotoh;
TraceGapsWatermanSmithBeyer** waterman_smith_beyer; } gaps;
int nA;
int nB;
int iA;
int iB;
Mode mode;
Algorithm algorithm;
Py_ssize_t length;
unsigned char strand;
} PathGenerator;
static PyObject*
PathGenerator_create_path(PathGenerator* self, int i, int j) {
PyObject* tuple;
PyObject* target_row;
PyObject* query_row;
PyObject* value;
int path;
int k, l;
int n = 1;
int direction = 0;
Trace** M = self->M;
const unsigned char strand = self->strand;
k = i;
l = j;
while (1) {
path = M[k][l].path;
if (!path) break;
if (path != direction) {
n++;
direction = path;
}
switch (path) {
case HORIZONTAL: l++; break;
case VERTICAL: k++; break;
case DIAGONAL: k++; l++; break;
}
}
direction = 0;
tuple = PyTuple_New(2);
if (!tuple) return NULL;
target_row = PyTuple_New(n);
query_row = PyTuple_New(n);
PyTuple_SET_ITEM(tuple, 0, target_row);
PyTuple_SET_ITEM(tuple, 1, query_row);
if (target_row && query_row) {
k = 0;
switch (strand) {
case '+':
while (1) {
path = M[i][j].path;
if (path != direction) {
value = PyLong_FromLong(i);
if (!value) break;
PyTuple_SET_ITEM(target_row, k, value);
value = PyLong_FromLong(j);
if (!value) break;
PyTuple_SET_ITEM(query_row, k, value);
k++;
direction = path;
}
switch (path) {
case HORIZONTAL: j++; break;
case VERTICAL: i++; break;
case DIAGONAL: i++; j++; break;
default: return tuple;
}
}
break;
case '-': {
const int nB = self->nB;
while (1) {
path = M[i][j].path;
if (path != direction) {
value = PyLong_FromLong(i);
if (!value) break;
PyTuple_SET_ITEM(target_row, k, value);
value = PyLong_FromLong(nB-j);
if (!value) break;
PyTuple_SET_ITEM(query_row, k, value);
k++;
direction = path;
}
switch (path) {
case HORIZONTAL: j++; break;
case VERTICAL: i++; break;
case DIAGONAL: i++; j++; break;
default: return tuple;
}
}
break;
}
}
}
Py_DECREF(tuple); /* all references were stolen */
return PyErr_NoMemory();
}
static Py_ssize_t
PathGenerator_needlemanwunsch_length(PathGenerator* self)
{
int i;
int j;
int trace;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
Py_ssize_t term;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t temp;
Py_ssize_t* counts;
counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!counts) goto exit;
counts[0] = 1;
for (j = 1; j <= nB; j++) {
trace = M[0][j].trace;
count = 0;
if (trace & HORIZONTAL) SAFE_ADD(counts[j-1], count);
counts[j] = count;
}
for (i = 1; i <= nA; i++) {
trace = M[i][0].trace;
count = 0;
if (trace & VERTICAL) SAFE_ADD(counts[0], count);
temp = counts[0];
counts[0] = count;
for (j = 1; j <= nB; j++) {
trace = M[i][j].trace;
count = 0;
if (trace & HORIZONTAL) SAFE_ADD(counts[j-1], count);
if (trace & VERTICAL) SAFE_ADD(counts[j], count);
if (trace & DIAGONAL) SAFE_ADD(temp, count);
temp = counts[j];
counts[j] = count;
}
}
PyMem_Free(counts);
exit:
return count;
}
static Py_ssize_t
PathGenerator_smithwaterman_length(PathGenerator* self)
{
int i;
int j;
int trace;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
Py_ssize_t term;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t total = 0;
Py_ssize_t temp;
Py_ssize_t* counts;
counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!counts) goto exit;
counts[0] = 1;
for (j = 1; j <= nB; j++) counts[j] = 1;
for (i = 1; i <= nA; i++) {
temp = counts[0];
counts[0] = 1;
for (j = 1; j <= nB; j++) {
trace = M[i][j].trace;
count = 0;
if (trace & DIAGONAL) SAFE_ADD(temp, count);
if (M[i][j].trace & ENDPOINT) SAFE_ADD(count, total);
if (trace & HORIZONTAL) SAFE_ADD(counts[j-1], count);
if (trace & VERTICAL) SAFE_ADD(counts[j], count);
temp = counts[j];
if (count == 0 && (trace & STARTPOINT)) count = 1;
counts[j] = count;
}
}
count = total;
PyMem_Free(counts);
exit:
return count;
}
static Py_ssize_t
PathGenerator_gotoh_global_length(PathGenerator* self)
{
int i;
int j;
int trace;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
TraceGapsGotoh** gaps = self->gaps.gotoh;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t term;
Py_ssize_t M_temp;
Py_ssize_t Ix_temp;
Py_ssize_t Iy_temp;
Py_ssize_t* M_counts = NULL;
Py_ssize_t* Ix_counts = NULL;
Py_ssize_t* Iy_counts = NULL;
M_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!M_counts) goto exit;
Ix_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Ix_counts) goto exit;
Iy_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Iy_counts) goto exit;
M_counts[0] = 1;
Ix_counts[0] = 0;
Iy_counts[0] = 0;
for (j = 1; j <= nB; j++) {
M_counts[j] = 0;
Ix_counts[j] = 0;
Iy_counts[j] = 1;
}
for (i = 1; i <= nA; i++) {
M_temp = M_counts[0];
M_counts[0] = 0;
Ix_temp = Ix_counts[0];
Ix_counts[0] = 1;
Iy_temp = Iy_counts[0];
Iy_counts[0] = 0;
for (j = 1; j <= nB; j++) {
count = 0;
trace = M[i][j].trace;
if (trace & M_MATRIX) SAFE_ADD(M_temp, count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_temp, count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_temp, count);
M_temp = M_counts[j];
M_counts[j] = count;
count = 0;
trace = gaps[i][j].Ix;
if (trace & M_MATRIX) SAFE_ADD(M_temp, count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_counts[j], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_counts[j], count);
Ix_temp = Ix_counts[j];
Ix_counts[j] = count;
count = 0;
trace = gaps[i][j].Iy;
if (trace & M_MATRIX) SAFE_ADD(M_counts[j-1], count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_counts[j-1], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_counts[j-1], count);
Iy_temp = Iy_counts[j];
Iy_counts[j] = count;
}
}
count = 0;
if (M[nA][nB].trace) SAFE_ADD(M_counts[nB], count);
if (gaps[nA][nB].Ix) SAFE_ADD(Ix_counts[nB], count);
if (gaps[nA][nB].Iy) SAFE_ADD(Iy_counts[nB], count);
exit:
if (M_counts) PyMem_Free(M_counts);
if (Ix_counts) PyMem_Free(Ix_counts);
if (Iy_counts) PyMem_Free(Iy_counts);
return count;
}
static Py_ssize_t
PathGenerator_gotoh_local_length(PathGenerator* self)
{
int i;
int j;
int trace;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
TraceGapsGotoh** gaps = self->gaps.gotoh;
Py_ssize_t term;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t total = 0;
Py_ssize_t M_temp;
Py_ssize_t Ix_temp;
Py_ssize_t Iy_temp;
Py_ssize_t* M_counts = NULL;
Py_ssize_t* Ix_counts = NULL;
Py_ssize_t* Iy_counts = NULL;
M_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!M_counts) goto exit;
Ix_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Ix_counts) goto exit;
Iy_counts = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Iy_counts) goto exit;
M_counts[0] = 1;
Ix_counts[0] = 0;
Iy_counts[0] = 0;
for (j = 1; j <= nB; j++) {
M_counts[j] = 1;
Ix_counts[j] = 0;
Iy_counts[j] = 0;
}
for (i = 1; i <= nA; i++) {
M_temp = M_counts[0];
M_counts[0] = 1;
Ix_temp = Ix_counts[0];
Ix_counts[0] = 0;
Iy_temp = Iy_counts[0];
Iy_counts[0] = 0;
for (j = 1; j <= nB; j++) {
count = 0;
trace = M[i][j].trace;
if (trace & M_MATRIX) SAFE_ADD(M_temp, count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_temp, count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_temp, count);
if (count == 0 && (trace & STARTPOINT)) count = 1;
M_temp = M_counts[j];
M_counts[j] = count;
if (M[i][j].trace & ENDPOINT) SAFE_ADD(count, total);
count = 0;
trace = gaps[i][j].Ix;
if (trace & M_MATRIX) SAFE_ADD(M_temp, count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_counts[j], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_counts[j], count);
Ix_temp = Ix_counts[j];
Ix_counts[j] = count;
count = 0;
trace = gaps[i][j].Iy;
if (trace & M_MATRIX) SAFE_ADD(M_counts[j-1], count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_counts[j-1], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_counts[j-1], count);
Iy_temp = Iy_counts[j];
Iy_counts[j] = count;
}
}
count = total;
exit:
if (M_counts) PyMem_Free(M_counts);
if (Ix_counts) PyMem_Free(Ix_counts);
if (Iy_counts) PyMem_Free(Iy_counts);
return count;
}
static Py_ssize_t
PathGenerator_waterman_smith_beyer_global_length(PathGenerator* self)
{
int i;
int j;
int trace;
int* p;
int gap;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
TraceGapsWatermanSmithBeyer** gaps = self->gaps.waterman_smith_beyer;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t term;
Py_ssize_t** M_count = NULL;
Py_ssize_t** Ix_count = NULL;
Py_ssize_t** Iy_count = NULL;
M_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!M_count) goto exit;
Ix_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!Ix_count) goto exit;
Iy_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!Iy_count) goto exit;
for (i = 0; i <= nA; i++) {
M_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!M_count[i]) goto exit;
Ix_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Ix_count[i]) goto exit;
Iy_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Iy_count[i]) goto exit;
}
for (i = 0; i <= nA; i++) {
for (j = 0; j <= nB; j++) {
count = 0;
trace = M[i][j].trace;
if (trace & M_MATRIX) SAFE_ADD(M_count[i-1][j-1], count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_count[i-1][j-1], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_count[i-1][j-1], count);
if (count == 0) count = 1; /* happens at M[0][0] only */
M_count[i][j] = count;
count = 0;
p = gaps[i][j].MIx;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(M_count[i-gap][j], count);
p++;
}
}
p = gaps[i][j].IyIx;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(Iy_count[i-gap][j], count);
p++;
}
}
Ix_count[i][j] = count;
count = 0;
p = gaps[i][j].MIy;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(M_count[i][j-gap], count);
p++;
}
}
p = gaps[i][j].IxIy;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(Ix_count[i][j-gap], count);
p++;
}
}
Iy_count[i][j] = count;
}
}
count = 0;
if (M[nA][nB].trace)
SAFE_ADD(M_count[nA][nB], count);
if (gaps[nA][nB].MIx[0] || gaps[nA][nB].IyIx[0])
SAFE_ADD(Ix_count[nA][nB], count);
if (gaps[nA][nB].MIy[0] || gaps[nA][nB].IxIy[0])
SAFE_ADD(Iy_count[nA][nB], count);
exit:
if (M_count) {
if (Ix_count) {
if (Iy_count) {
for (i = 0; i <= nA; i++) {
if (!M_count[i]) break;
PyMem_Free(M_count[i]);
if (!Ix_count[i]) break;
PyMem_Free(Ix_count[i]);
if (!Iy_count[i]) break;
PyMem_Free(Iy_count[i]);
}
PyMem_Free(Iy_count);
}
PyMem_Free(Ix_count);
}
PyMem_Free(M_count);
}
return count;
}
static Py_ssize_t
PathGenerator_waterman_smith_beyer_local_length(PathGenerator* self)
{
int i;
int j;
int trace;
int* p;
int gap;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
TraceGapsWatermanSmithBeyer** gaps = self->gaps.waterman_smith_beyer;
Py_ssize_t term;
Py_ssize_t count = MEMORY_ERROR;
Py_ssize_t total = 0;
Py_ssize_t** M_count = NULL;
Py_ssize_t** Ix_count = NULL;
Py_ssize_t** Iy_count = NULL;
M_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!M_count) goto exit;
Ix_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!Ix_count) goto exit;
Iy_count = PyMem_Malloc((nA+1)*sizeof(Py_ssize_t*));
if (!Iy_count) goto exit;
for (i = 0; i <= nA; i++) {
M_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!M_count[i]) goto exit;
Ix_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Ix_count[i]) goto exit;
Iy_count[i] = PyMem_Malloc((nB+1)*sizeof(Py_ssize_t));
if (!Iy_count[i]) goto exit;
}
for (i = 0; i <= nA; i++) {
for (j = 0; j <= nB; j++) {
count = 0;
trace = M[i][j].trace;
if (trace & M_MATRIX) SAFE_ADD(M_count[i-1][j-1], count);
if (trace & Ix_MATRIX) SAFE_ADD(Ix_count[i-1][j-1], count);
if (trace & Iy_MATRIX) SAFE_ADD(Iy_count[i-1][j-1], count);
if (count == 0 && (trace & STARTPOINT)) count = 1;
M_count[i][j] = count;
if (M[i][j].trace & ENDPOINT) SAFE_ADD(count, total);
count = 0;
p = gaps[i][j].MIx;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(M_count[i-gap][j], count);
p++;
}
}
p = gaps[i][j].IyIx;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(Iy_count[i-gap][j], count);
p++;
}
}
Ix_count[i][j] = count;
count = 0;
p = gaps[i][j].MIy;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(M_count[i][j-gap], count);
p++;
}
}
p = gaps[i][j].IxIy;
if (p) {
while (1) {
gap = *p;
if (!gap) break;
SAFE_ADD(Ix_count[i][j-gap], count);
p++;
}
}
Iy_count[i][j] = count;
}
}
count = total;
exit:
if (M_count) {
if (Ix_count) {
if (Iy_count) {
for (i = 0; i <= nA; i++) {
if (!M_count[i]) break;
PyMem_Free(M_count[i]);
if (!Ix_count[i]) break;
PyMem_Free(Ix_count[i]);
if (!Iy_count[i]) break;
PyMem_Free(Iy_count[i]);
}
PyMem_Free(Iy_count);
}
PyMem_Free(Ix_count);
}
PyMem_Free(M_count);
}
return count;
}
static Py_ssize_t
PathGenerator_fogsaa_length(PathGenerator* self)
{
return 1;
}
static Py_ssize_t PathGenerator_length(PathGenerator* self) {
Py_ssize_t length = self->length;
if (length == 0) {
switch (self->algorithm) {
case NeedlemanWunschSmithWaterman:
switch (self->mode) {
case Global:
length = PathGenerator_needlemanwunsch_length(self);
break;
case Local:
length = PathGenerator_smithwaterman_length(self);
break;
default:
/* should not happen, but some compilers complain that
* that length can be used uninitialized.
*/
ERR_UNEXPECTED_MODE
return OTHER_ERROR;
}
break;
case Gotoh:
switch (self->mode) {
case Global:
length = PathGenerator_gotoh_global_length(self);
break;
case Local:
length = PathGenerator_gotoh_local_length(self);
break;
default:
/* should not happen, but some compilers complain that
* that length can be used uninitialized.
*/
ERR_UNEXPECTED_MODE
return OTHER_ERROR;
}
break;
case WatermanSmithBeyer:
switch (self->mode) {
case Global:
length = PathGenerator_waterman_smith_beyer_global_length(self);
break;
case Local:
length = PathGenerator_waterman_smith_beyer_local_length(self);
break;
default:
/* should not happen, but some compilers complain that
* that length can be used uninitialized.
*/
ERR_UNEXPECTED_MODE
return OTHER_ERROR;
}
break;
case FOGSAA:
if (self->mode != FOGSAA_Mode) {
ERR_UNEXPECTED_MODE
return OTHER_ERROR;
}
length = PathGenerator_fogsaa_length(self);
break;
case Unknown:
default:
ERR_UNEXPECTED_ALGORITHM
return OTHER_ERROR;
}
self->length = length;
}
switch (length) {
case OVERFLOW_ERROR:
PyErr_Format(PyExc_OverflowError,
"number of optimal alignments is larger than %zd",
PY_SSIZE_T_MAX);
break;
case MEMORY_ERROR:
PyErr_SetNone(PyExc_MemoryError);
break;
case OTHER_ERROR:
default:
break;
}
return length;
}
static void
PathGenerator_dealloc(PathGenerator* self)
{
int i;
const int nA = self->nA;
const Algorithm algorithm = self->algorithm;
Trace** M = self->M;
if (M) {
for (i = 0; i <= nA; i++) {
if (!M[i]) break;
PyMem_Free(M[i]);
}
PyMem_Free(M);
}
switch (algorithm) {
case NeedlemanWunschSmithWaterman:
case FOGSAA:
break;
case Gotoh: {
TraceGapsGotoh** gaps = self->gaps.gotoh;
if (gaps) {
for (i = 0; i <= nA; i++) {
if (!gaps[i]) break;
PyMem_Free(gaps[i]);
}
PyMem_Free(gaps);
}
break;
}
case WatermanSmithBeyer: {
TraceGapsWatermanSmithBeyer** gaps = self->gaps.waterman_smith_beyer;
if (gaps) {
int j;
const int nB = self->nB;
int* trace;
for (i = 0; i <= nA; i++) {
if (!gaps[i]) break;
for (j = 0; j <= nB; j++) {
trace = gaps[i][j].MIx;
if (trace) PyMem_Free(trace);
trace = gaps[i][j].IyIx;
if (trace) PyMem_Free(trace);
trace = gaps[i][j].MIy;
if (trace) PyMem_Free(trace);
trace = gaps[i][j].IxIy;
if (trace) PyMem_Free(trace);
}
PyMem_Free(gaps[i]);
}
PyMem_Free(gaps);
}
break;
}
case Unknown:
default:
PyErr_WriteUnraisable((PyObject*)self);
break;
}
Py_TYPE(self)->tp_free((PyObject*)self);
}
static PyObject* PathGenerator_next_needlemanwunsch(PathGenerator* self)
{
int i = 0;
int j = 0;
int path;
int trace = 0;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
path = M[i][j].path;
if (path == DONE) return NULL;
if (path == 0) {
/* Generate the first path. */
i = nA;
j = nB;
}
else {
/* We already have a path. Prune the path to see if there are
* any alternative paths. */
while (1) {
if (path == HORIZONTAL) {
trace = M[i][++j].trace;
if (trace & VERTICAL) {
M[--i][j].path = VERTICAL;
break;
}
if (trace & DIAGONAL) {
M[--i][--j].path = DIAGONAL;
break;
}
}
else if (path == VERTICAL) {
trace = M[++i][j].trace;
if (trace & DIAGONAL) {
M[--i][--j].path = DIAGONAL;
break;
}
}
else /* DIAGONAL */ {
i++;
j++;
}
path = M[i][j].path;
if (!path) {
/* we reached the end of the alignment without finding
* an alternative path */
M[0][0].path = DONE;
return NULL;
}
}
}
/* Follow the traceback until we reach the origin. */
while (1) {
trace = M[i][j].trace;
if (trace & HORIZONTAL) M[i][--j].path = HORIZONTAL;
else if (trace & VERTICAL) M[--i][j].path = VERTICAL;
else if (trace & DIAGONAL) M[--i][--j].path = DIAGONAL;
else break;
}
return PathGenerator_create_path(self, 0, 0);
}
static PyObject* PathGenerator_next_smithwaterman(PathGenerator* self)
{
int trace = 0;
int i = self->iA;
int j = self->iB;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
int path = M[0][0].path;
if (path == DONE || path == NONE) return NULL;
path = M[i][j].path;
if (path) {
/* We already have a path. Prune the path to see if there are
* any alternative paths. */
while (1) {
if (path == HORIZONTAL) {
trace = M[i][++j].trace;
if (trace & VERTICAL) {
M[--i][j].path = VERTICAL;
break;
}
else if (trace & DIAGONAL) {
M[--i][--j].path = DIAGONAL;
break;
}
}
else if (path == VERTICAL) {
trace = M[++i][j].trace;
if (trace & DIAGONAL) {
M[--i][--j].path = DIAGONAL;
break;
}
}
else /* DIAGONAL */ {
i++;
j++;
}
path = M[i][j].path;
if (!path) break;
}
}
if (path) {
trace = M[i][j].trace;
} else {
/* Find a suitable end point for a path.
* Only allow end points ending at the M matrix. */
while (1) {
if (j < nB) j++;
else if (i < nA) {
i++;
j = 0;
}
else {
/* we reached the end of the sequences without finding
* an alternative path */
M[0][0].path = DONE;
return NULL;
}
trace = M[i][j].trace;
if (trace & ENDPOINT) {
trace &= DIAGONAL; /* exclude paths ending in a gap */
break;
}
}
M[i][j].path = 0;
}
/* Follow the traceback until we reach the origin. */
while (1) {
if (trace & HORIZONTAL) M[i][--j].path = HORIZONTAL;
else if (trace & VERTICAL) M[--i][j].path = VERTICAL;
else if (trace & DIAGONAL) M[--i][--j].path = DIAGONAL;
else if (trace & STARTPOINT) {
self->iA = i;
self->iB = j;
return PathGenerator_create_path(self, i, j);
}
else {
PyErr_SetString(PyExc_RuntimeError,
"Unexpected trace in PathGenerator_next_smithwaterman");
return NULL;
}
trace = M[i][j].trace;
}
}
static PyObject* PathGenerator_next_gotoh_global(PathGenerator* self)
{
int i = 0;
int j = 0;
int m;
int path;
int trace = 0;
const int nA = self->nA;
const int nB = self->nB;
Trace** M = self->M;
TraceGapsGotoh** gaps = self->gaps.gotoh;
m = M_MATRIX;
path = M[i][j].path;
if (path == DONE) return NULL;
if (path == 0) {
i = nA;
j = nB;
}
else {
/* We already have a path. Prune the path to see if there are
* any alternative paths. */
while (1) {
path = M[i][j].path;
if (path == 0) {
switch (m) {
case M_MATRIX: m = Ix_MATRIX; break;
case Ix_MATRIX: m = Iy_MATRIX; break;
case Iy_MATRIX: m = 0; break;
}
break;
}
switch (path) {
case HORIZONTAL: trace = gaps[i][++j].Iy; break;
case VERTICAL: trace = gaps[++i][j].Ix; break;
case DIAGONAL: trace = M[++i][++j].trace; break;
}
switch (m) {
case M_MATRIX:
if (trace & Ix_MATRIX) {
m = Ix_MATRIX;
break;
}
case Ix_MATRIX:
if (trace & Iy_MATRIX) {
m = Iy_MATRIX;
break;
}
case Iy_MATRIX:
default:
switch (path) {
case HORIZONTAL: m = Iy_MATRIX; break;
case VERTICAL: m = Ix_MATRIX; break;
case DIAGONAL: m = M_MATRIX; break;
}
continue;
}
switch (path) {
case HORIZONTAL: j--; break;
case VERTICAL: i--; break;
case DIAGONAL: i--; j--; break;
}
M[i][j].path = path;
break;
}
}
if (path == 0) {
/* Generate a new path. */
switch (m) {
case M_MATRIX:
if (M[nA][nB].trace) {
/* m = M_MATRIX; */
break;
}
case Ix_MATRIX:
if (gaps[nA][nB].Ix) {
m = Ix_MATRIX;
break;
}
case Iy_MATRIX: