int
GPD_2DPrimPoly::load(istream &is, int binary)
{
int cnt;
char cflag;
if (binary)
{
char tflag;
if (!UTread(is, &tflag)) return -1;
if (!UTread(is, &nVtx)) return -1;
if (!UTread(is, &cflag)) return -1;
if (tflag == 1) trim();
else untrim();
}
else
{
char ttoken[GPD_BUFSIZ];
is >> ttoken;
is >> nVtx >> cflag;
if (!is) return -1;
if (!strcmp(ttoken, "trim")) trim();
else untrim();
}
if (cflag == '<') close();
else open();
vtxList = new GPD_2DVertex[nVtx];
if (loadPrivate(is,binary) < 0) return -1;
for (cnt = 0; cnt < nVtx; cnt++)
if (getParent()->loadVertex(is, vtxList[cnt], binary) < 0) return -1;
if (!binary) // Get junk at end of line:
is.ignore(GPD_BUFSIZ-1, '\n');
if (!is) return -1;
return 0;
}
void Sequence::readFile(char* filename, const int flags) {
FILE* file = fopen(filename, "rt");
fseek(file, 0L, SEEK_END);
long fileSize = ftell(file);
rewind(file);
char line[500];
fgets(line, sizeof(line), file);
char tmp[500];
sscanf(line, ">%s", tmp);
name = tmp;
char* tok=strtok(tmp, "|");
for (int i=1; i<4 && tok != NULL; i++) {
tok = strtok (NULL, "|");
}
if (tok == NULL) {
accession = name;
} else {
accession = tok;
}
data_vector.reserve(fileSize);
int i;
int pos=0;
char complement_map[256];
for (int i=0; i<256; i++) {
complement_map[i] = toupper(i);
}
if (flags & FLAG_COMPLEMENT) {
complement_map['A'] = complement_map['a'] = 'T';
complement_map['T'] = complement_map['t'] = 'A';
complement_map['C'] = complement_map['c'] = 'G';
complement_map['G'] = complement_map['g'] = 'C';
}
while ((i=fgetc(file)) != EOF) {
if (i == '\r' || i == '\n' || i == ' ') continue;
if ((flags & FLAG_CLEAR_N) && ((char)i == 'N' || (char)i == 'n')) continue;
pos++;
data_vector.push_back(complement_map[(char)i]);
}
this->original_len = data_vector.size();
data_vector.push_back((char)0);
original_forward_data = &data_vector[0];
// TODO otimizar usando cuda
original_reverse_data = (char*)malloc(this->original_len+1);
for (int i=0; i<this->original_len; i++) {
original_reverse_data[this->original_len-1-i] = original_forward_data[i];
}
original_reverse_data[this->original_len] = 0;
fclose(file);
if (flags & FLAG_REVERSE) {
char* temp = original_reverse_data;
original_reverse_data = original_forward_data;
original_forward_data = temp;
}
untrim();
}
