void findDuplicate(std::string infile, std::string outfile, bool debug=false) {
std::vector<record> records;
readRecords(infile, records, debug);
sort(records, debug);
duplicate(outfile, records, debug);
}
bool TFastaFile::ReadFastaFile(char *fasta_filename, vector<Engine::SequenceManager::Sequence> &seq_list)
{
if( fasta_filename == NULL )
{
seq_list.clear() ;
std::cerr<<"Invalid file name" ;
return false;
}
string fn = string(fasta_filename);
readRecords(fn, seq_list, true);
return true ;
}
int main(int argc, char** argv) {
if(argc < 4) {
fprintf(stderr, "Usage: ./sHash search_2011 hash pagesize\n");
return 1;
}
// program arguments
char* search_file = argv[1];
char* hash_file = argv[2];
int pagesize = atoi(argv[3]);
if(pagesize <= 0) {
fprintf(stderr, "Pagesize must be greater than 0\n");
return 1;
}
// open search key / hash files
FILE *sf, *hf;
if(!openFile(search_file, &sf, "r")) {
fprintf(stderr, "Unable to open %s for reading\n", search_file);
return 1;
}
if(!openFile(hash_file, &hf, "rb")) {
fprintf(stderr, "Unable to open %s for reading\n", hash_file);
return 1;
}
// read in header data
unsigned char temp[sizeof(int)];
int pages;
int* record_count;
fread(temp, sizeof(int), 1, hf);
// number of pages
pages = hexToInt(temp, sizeof(int));
// number of records in each page
record_count = malloc(pages * sizeof(int));
if(record_count == NULL) {
fprintf(stderr, "memory allocation failed\n");
exit(1);
}
for(int i = 0; i < pages; i++) {
fread(temp, sizeof(int), 1, hf);
record_count[i] = hexToInt(temp, sizeof(int));
}
int hs = sizeof(int) * (pages+1);
unsigned int find_id, found, hash_id;
char line[MAX_LINE + 1];
Record** records = malloc(pagesize * sizeof(Record*));
if(records == NULL) {
fprintf(stderr, "memory allocation failed\n");
exit(1);
}
for(int i = 0; i < pagesize; i++) {
records[i] = calloc(1, sizeof(Record));
if(records[i] == NULL) {
fprintf(stderr, "memory allocation failed\n");
exit(1);
}
}
hrtime_t start, end;
start = gethrtime();
while(fgets(line, MAX_LINE + 1, sf) != NULL) {
find_id = atoi(line);
hash_id = find_id % pages;
found = 0;
// seek to the page given by the hash id
fseek(hf, hs + (RECORD_LEN * hash_id * pagesize), SEEK_SET);
// read in records from page
readRecords(hf, record_count[hash_id], records);
// check for an id match. if found, print record.
for(int i = 0; i < record_count[hash_id]; i++) {
if(records[i] && find_id == records[i]->id) {
printf("%s,%d,%d,%d,%s\n", records[i]->name, records[i]->race,
records[i]->class, records[i]->id,
records[i]->guild);
found = 1;
break;
}
}
if(!found)
fprintf(stderr, "%d: No match\n", find_id);
}
