int nb_cols_lfmm(char *file)
{
FILE *fp = fopen_read(file);
int cols = 0;
int c;
char *szbuff;
char *token;
c = fgetc(fp);
while ((c != EOF) && (c != 10) && (c!= 13)) {
// count only columns (no space or tab)
c = fgetc(fp);
cols++;
}
fclose(fp);
// open file
fp = fopen_read(file);
szbuff = (char *)calloc(2 * cols, sizeof(char));
// read first line
token = fgets(szbuff, 2 * cols, fp);
cols = 0;
// count for first line
token = strtok(szbuff, SEP);
while (token) {
cols++;
token = strtok(NULL, SEP);
}
fclose(fp);
free(szbuff);
return cols;
}
/*
* readfromfile()
*
* The read callback that this function may use can return a value larger than
* 'size' (which then this function returns) that indicates a problem and it
* must be properly dealt with
*/
static size_t readfromfile(struct Form *form, char *buffer,
size_t size)
{
size_t nread;
bool callback = (form->data->type == FORM_CALLBACK)?TRUE:FALSE;
if(callback) {
if(form->fread_func == ZERO_NULL)
return 0;
else
nread = form->fread_func(buffer, 1, size, form->data->line);
}
else {
if(!form->fp) {
/* this file hasn't yet been opened */
form->fp = fopen_read(form->data->line, "rb"); /* b is for binary */
if(!form->fp)
return (size_t)-1; /* failure */
}
nread = fread(buffer, 1, size, form->fp);
}
if(!nread) {
/* this is the last chunk from the file, move on */
if(form->fp) {
fclose(form->fp);
form->fp = NULL;
}
form->data = form->data->next;
}
return nread;
}
int nb_ind_ancestrymap(char *input_file)
{
FILE* File=NULL;
int max_char_per_line = 1000;
int nb = 0, diff = 0;
char szbuff[max_char_per_line];
char *token;
char tmp[512] = "";
// open input file
File = fopen_read(input_file);
// first line
token = fgets(szbuff, max_char_per_line, File);
token = strtok(szbuff, SEP);
strcpy(tmp,token);
// while still the same SNP, count
while (!feof(File) && !diff) {
token = fgets(szbuff, max_char_per_line, File);
token = strtok(szbuff, SEP);
// compare the current name with the first name
diff = strcmp(tmp,token) != 0;
nb ++;
}
// close file
fclose(File);
return nb;
}
void pki_x509req::fload(const QString fname)
{
FILE *fp = fopen_read(fname);
X509_REQ *_req;
int ret = 0;
if (fp != NULL) {
_req = PEM_read_X509_REQ(fp, NULL, NULL, NULL);
if (!_req) {
pki_ign_openssl_error();
rewind(fp);
_req = d2i_X509_REQ_fp(fp, NULL);
}
fclose(fp);
if (ret || pki_ign_openssl_error()) {
if (_req)
X509_REQ_free(_req);
throw errorEx(tr("Unable to load the certificate request in file %1. Tried PEM, DER and SPKAC format.").arg(fname));
}
} else {
fopen_error(fname);
return;
}
if (_req) {
X509_REQ_free(request);
request = _req;
}
autoIntName();
if (getIntName().isEmpty())
setIntName(rmslashdot(fname));
openssl_error(fname);
}
void read_ancestrymap (char* input_file, int N, int M, int* data)
{
FILE *File = NULL;
int i, j, allele;
char tmp[512] = "";
char ref[512] = "";
int max_char_per_line = 1000;
char szbuff[max_char_per_line];
int warning = 0;
// open input file
File = fopen_read(input_file);
j = 0;
i = 0;
// while not the end of the file
// or not too many SNPs (j < M-1)
// or last SNP but not too many ind (j == (M-1) && i< N))
while (fgets(szbuff,max_char_per_line, File) && (j < M-1 || (j == (M-1) && i< N))) {
// read line
read_line_ancestrymap(szbuff, &allele, tmp, i+1, j+1, input_file, &warning);
// first SNP, save SNP name
if (j == 0 && i == 0)
strcpy(ref, tmp);
// new SNP
if (strcmp(ref, tmp) != 0) {
// test if the number indiviual for the line is ok
test_column (input_file, File, i, j+1, N, NULL);
// new line
i = 0;
j++;
// save new SNP name
strcpy(ref, tmp);
}
// write genotype
data[i * M + j] = allele;
i++;
}
test_column (input_file, File, i, j+1, N, NULL);
// test the number of lines
test_line(input_file, File, j+1, M);
fclose(File);
}
void pki_multi::fload(const QString fname)
{
FILE * fp;
BIO *bio = NULL;
fp = fopen_read(fname);
if (!fp) {
fopen_error(fname);
return;
}
bio = BIO_new_fp(fp, BIO_CLOSE);
fromPEM_BIO(bio, fname);
BIO_free(bio);
};
int nb_cols_geno(char *file)
{
FILE *fp = fopen_read(file);
int cols = 0;
int c;
// count the number of elements until EOF or "\n"
c = fgetc(fp);
while ((c != EOF) && (c != 10) && (c != 13)) {
cols++;
c = fgetc(fp);
}
fclose(fp);
return cols;
}
int nb_lines(char *file, int M)
{
FILE *fp = fopen_read(file);
int lines = 0;
int max_char_per_line = 20 * M + 10;
char *szbuff = (char *)calloc(max_char_per_line, sizeof(char));
// while not end of file
while (fgets(szbuff, max_char_per_line, fp))
// count
lines++;
fclose(fp);
free(szbuff);
return lines;
}
int MainWindow::open_default_db()
{
if (!dbfile.isEmpty())
return 0;
FILE *fp = fopen_read(getUserSettingsDir() +
QDir::separator() + "defaultdb");
if (!fp)
return 0;
char buff[256];
size_t len = fread(buff, 1, 255, fp);
fclose(fp);
buff[len] = 0;
dbfile = filename2QString(buff).trimmed();
if (QFile::exists(dbfile))
return init_database();
dbfile = QString();
return 0;
}
void read_data_int(char *file_data, int N, int M, int *dat)
{
FILE *m_File = NULL;
int i = 0;
int j = 0;
int max_char_per_line = MAX_LENGTH_NB_INT * M + 20;
char *szbuff;
char *token;
// allocate memory
szbuff = (char *) malloc(max_char_per_line * sizeof(char));
// open file
m_File = fopen_read(file_data);
i = 0;
while (fgets(szbuff, max_char_per_line, m_File) && (i < N)) {
j = 0;
// cut line with split character SEP (" ")
token = strtok(szbuff, SEP);
// read elements and register them in dat
while (token && j < M) {
//printf("%s\n",token);
dat[i * M + j] = (int)atof(token);
// next elements
token = strtok(NULL, SEP);
j++;
}
i++;
// check the number of columns
test_column(file_data, m_File, j, i, M, token);
}
// check the number of lines
test_line(file_data, m_File, i, N);
// close file
fclose(m_File);
// free memory
free(szbuff);
}
