void UniquePrimeFactors (void) // Version 2 (DP approach). Parameter is left void as the target struct is defined statically in the heap (not the stack). Simplified version of the main function in Problem 70.
{
int i, j;
void intcat(int *, int *);
int isPrime (long, int);
for (i = 0; i < MAXNUM; i ++) {
numlist[i].number = i;
numlist[i].DistinctPrimes = NULL;
if (isPrime(i, 5)) {
numlist[i].DistinctPrimes = malloc(sizeof(int));
*numlist[i].DistinctPrimes = i;
} else {
for (j = 0; prime[j] <= sqrt(i); j++) {
if (!(i % prime[j])) {
if (search(prime[j], numlist[i/prime[j]].DistinctPrimes))
numlist[i].DistinctPrimes = numlist[i/prime[j]].DistinctPrimes;
else {
numlist[i].DistinctPrimes = malloc(MAXFACTOR*sizeof(int));
*numlist[i].DistinctPrimes = prime[j];
intcat (numlist[i].DistinctPrimes, numlist[i/prime[j]].DistinctPrimes);
} break;
} else continue;
}
}
}
}
static PyObject *parseFasta(PyObject *self, PyObject *args) {
/* Parse sequences from *filename* into the memory pointed by the
Numpy array passed as Python object. */
char *filename;
PyArrayObject *msa;
PyObject *labels = PyList_New(0);
PyObject *mapping = PyDict_New();
if (!PyArg_ParseTuple(args, "sO", &filename, &msa))
return NULL;
if (!labels || !mapping)
return PyErr_NoMemory();
char *line = malloc((FASTALINELEN) * sizeof(char));
if (!line)
return PyErr_NoMemory();
char *data = (char *) PyArray_DATA(msa);
int aligned = 1;
char ch, errmsg[LENLABEL] = "failed to parse FASTA file at line ";
long index = 0, count = 0;
long iline = 0, i, seqlen = 0, curlen = 0;
FILE *file = fopen(filename, "rb");
while (fgets(line, FASTALINELEN, file) != NULL) {
iline++;
if (line[0] == '>') {
if (seqlen != curlen) {
if (seqlen) {
aligned = 0;
free(line);
free(data);
fclose(file);
PyErr_SetString(PyExc_IOError, intcat(errmsg, iline));
return NULL;
} else
seqlen = curlen;
}
// `line + 1` is to omit `>` character
count += parseLabel(labels, mapping, line + 1, FASTALINELEN);
curlen = 0;
} else {
for (i = 0; i < FASTALINELEN; i++) {
ch = line[i];
if (ch < 32)
break;
else {
data[index++] = ch;
curlen++;
}
}
}
}
fclose(file);
free(line);
if (aligned && seqlen != curlen) {
PyErr_SetString(PyExc_IOError, intcat(errmsg, iline));
return NULL;
}
npy_intp dims[2] = {index / seqlen, seqlen};
PyArray_Dims arr_dims;
arr_dims.ptr = dims;
arr_dims.len = 2;
PyArray_Resize(msa, &arr_dims, 0, NPY_CORDER);
PyObject *result = Py_BuildValue("(OOOi)", msa, labels, mapping, count);
Py_DECREF(labels);
Py_DECREF(mapping);
return result;
}
Token *build_type (typeID t, Token o, Token ret[])
{
/* XXX: elliptics */
if (is_reference (t))
t = ptrdown (dereference (t));
Token tmp [100], *dcls = &tmp [20], *dcle = dcls;
Token *st = open_typeID (t);
int i = 1, b = 0;
if (o) {
*(++dcle) = -1;
*dcls-- = o;
} else *dcls-- = -1;
for (;;i++) {
switch (st [i]) {
case '*':
*dcls-- = '*';
b = 1;
continue;
case '[':
if (b) *dcls-- = '(', *dcle++ = ')', b = 0;
*dcle++ = '['; *dcle++ = ']';
continue;
case '(':
if (b) *dcls-- = '(', *dcle++ = ')', b = 0;
*dcle++ = '(';
for (i++;;)
if (st [i] == B_ELLIPSIS) {
*dcle++ = ELLIPSIS;
break;
} else {
if (st [i] == INTERNAL_ARGEND) break;
Token arg [50];
intcpy (dcle, build_type (st [i++], 0, arg));
dcle += intlen (dcle);
*dcle++ = ',';
}
if (dcle [-1] == ',') --dcle;
*dcle++ = ')';
continue;
case -1: break;
default: PRINTF ("UNKNWOWN %i\n", st [i]);
}
break;
}
*dcle = -1;
if (st [0] >= 0)
if (ISSYMBOL (st [0])) sintprintf (ret, st [0], -1);
else sintprintf (ret, isunion (st [0]) ? RESERVED_union : iRESERVED_struct (st [0]),
name_of_struct (st [0]), -1);
else switch (st [0]) {
case B_UCHAR: sintprintf (ret, RESERVED_unsigned, RESERVED_char, -1);
ncase B_SCHAR: sintprintf (ret, RESERVED_char, -1);
ncase B_USINT: sintprintf (ret, RESERVED_unsigned, RESERVED_short, RESERVED_int, -1);
ncase B_SSINT: sintprintf (ret, RESERVED_short, RESERVED_int, -1);
ncase B_UINT: sintprintf (ret, RESERVED_unsigned, RESERVED_int, -1);
ncase B_SINT: sintprintf (ret, RESERVED_int, -1);
ncase B_ULONG: sintprintf (ret, RESERVED_unsigned, RESERVED_long, -1);
ncase B_SLONG: sintprintf (ret, RESERVED_long, -1);
ncase B_ULLONG: sintprintf (ret, RESERVED_unsigned, RESERVED_long, RESERVED_long, -1);
ncase B_SLLONG: sintprintf (ret, RESERVED_long, RESERVED_long, -1);
ncase B_FLOAT: sintprintf (ret, RESERVED_float, -1);
ncase B_DOUBLE: sintprintf (ret, RESERVED_double, -1);
ncase B_VOID: sintprintf (ret, RESERVED_void, -1);
}
intcat (ret, dcls + 1);
return ret;
}
static PyObject *parseSelex(PyObject *self, PyObject *args) {
/* Parse sequences from *filename* into the the memory pointed by the
Numpy array passed as Python object. */
char *filename;
PyArrayObject *msa;
if (!PyArg_ParseTuple(args, "sO", &filename, &msa))
return NULL;
long i = 0, beg = 0, end = 0;
long size = SELEXLINELEN + 1, iline = 0, seqlen = 0;
char errmsg[LENLABEL] = "failed to parse SELEX/Stockholm file at line ";
PyObject *labels = PyList_New(0), *mapping = PyDict_New();
if (!labels || !mapping)
return PyErr_NoMemory();
char *line = malloc(size * sizeof(char));
if (!line)
return PyErr_NoMemory();
char *data = (char *) PyArray_DATA(msa);
/* figure out where the sequence starts and ends in a line*/
FILE *file = fopen(filename, "rb");
while (fgets(line, size, file) != NULL) {
iline++;
if (line[0] == '#' || line[0] == '/' || line[0] == '%')
continue;
for (i = 0; i < size; i++)
if (line[i] == ' ')
break;
for (; i < size; i++)
if (line[i] != ' ')
break;
beg = i;
for (; i < size; i++)
if (line[i] < 32)
break;
end = i;
seqlen = end - beg;
break;
}
iline--;
fseek(file, - strlen(line), SEEK_CUR);
long index = 0, count = 0;
int space = beg - 1; /* index of space character before sequence */
while (fgets(line, size, file) != NULL) {
iline++;
if (line[0] == '#' || line[0] == '/' || line[0] == '%')
continue;
if (line[space] != ' ') {
free(line);
fclose(file);
PyErr_SetString(PyExc_IOError, intcat(errmsg, iline));
return NULL;
}
count += parseLabel(labels, mapping, line, space);
for (i = beg; i < end; i++)
data[index++] = line[i];
}
fclose(file);
free(line);
npy_intp dims[2] = {index / seqlen, seqlen};
PyArray_Dims arr_dims;
arr_dims.ptr = dims;
arr_dims.len = 2;
PyArray_Resize(msa, &arr_dims, 0, NPY_CORDER);
PyObject *result = Py_BuildValue("(OOOi)", msa, labels, mapping, count);
Py_DECREF(labels);
Py_DECREF(mapping);
return result;
}
