static bool
stream_next_seq(
panda_seq_identifier *id,
panda_qual **forward,
size_t *forward_length,
panda_qual **reverse,
size_t *reverse_length,
struct fastq_data *data) {
panda_seq_identifier rid;
char buffer[BUFFER_SIZE];
size_t fsize;
size_t rsize;
int fdir;
int rdir;
*forward = NULL;
*reverse = NULL;
if (!read_line(buffer, BUFFER_SIZE, &data->forward, &fsize)) {
return false;
}
if ((fdir = panda_seqid_parse(id, &buffer[1], data->policy)) == 0) {
LOGV(PANDA_DEBUG_FILE, PANDA_CODE_ID_PARSE_FAILURE, "%s", buffer);
return false;
}
if (!read_line(buffer, BUFFER_SIZE, &data->reverse, &rsize)) {
return false;
}
if ((rdir = panda_seqid_parse(&rid, &buffer[1], data->policy)) == 0) {
LOGV(PANDA_DEBUG_FILE, PANDA_CODE_ID_PARSE_FAILURE, "%s", buffer);
return false;
}
if (!panda_seqid_equal(id, &rid)) {
LOG(PANDA_DEBUG_FILE, PANDA_CODE_NOT_PAIRED);
return false;
}
if (!read_seq(id, data->forward_seq, PANDA_MAX_LEN, &data->forward, iupac_forward, data, forward_length)) {
*forward_length = 0;
*reverse_length = 0;
LOG(PANDA_DEBUG_FILE, PANDA_CODE_PARSE_FAILURE);
return false;
}
if (!read_seq(id, data->reverse_seq, PANDA_MAX_LEN, &data->reverse, iupac_reverse, data, reverse_length)) {
*forward_length = 0;
*reverse_length = 0;
LOG(PANDA_DEBUG_FILE, PANDA_CODE_PARSE_FAILURE);
return false;
}
*forward = data->forward_seq;
*reverse = data->reverse_seq;
return true;
}
/*--------------------------------------------------------------------------*/
sequ *input(int argc, char **argv)
{
sequ *sq;
int istty;
istty=isatty(fileno(stdout))&&isatty(fileno(stdin));
if(istty)
{
sq=lies_seq(stdin);
}
else
{
sq=read_seq(stdin);
}
return(sq);
}
int main(int argc, char *argv[])
{
vector<HeuristicChooseReversal *> hcr_seq;
/* Set random seed */
unsigned long seed = mix(clock(), time(NULL), getpid());
/* Set random seed */
srand(seed);
/* Exact Unitaty Parameters */
ofstream fout;
/* Time results */
timestamp_t time_begin;
timestamp_t time_end;
time_begin = get_timestamp();
/* Log result file */
ostream *logOut = NULL;
ostream *logTime = NULL;
/* Check essential parameters */
// TODO: start to use parameter names instead of parameter sequence, ex: -p 1,2,4...
if (argc < 7) {
printf("Usage:\n");
printf("lwr_test_metaheuristic permutation number_of_iteration inversion_limit frame_limit is_signed cost_function {-r=[[...]]}.\n\n");
printf("Parameters description:\n");
printf(" 1. permutation: the input permutation.\n\n");
printf(" 2. number_of_iteration: number of iterations that will\n");
printf("be performed by the Metaheuristic.\n\n");
printf(" 3. inversion_limit: limit (upper bound) for the number of inversions\n");
printf("that will be selected at each iteration of the heuristic for building solutions.\n\n");
printf(" 4. frame_limit: percentege (in the interval (0,100]) of frames that \n");
printf("will be selected at each iteration of the Metaheuristic.\n\n");
printf(" 5. is_signed: 1 if the input permutation is signed, 0 otherwise.\n\n");
printf(" 6. cost_function: 1 for linear function, 2 for quadratic function and 3 logaritmic function.\n\n");
printf(" 7. -r=[[...]]: Optional parameter to give a seed solution as a input parameter\n");
return 0;
}
/* Seed result */
Result seed_result;
/* Permutation parameters */
parameter perm_param;
/* Exact Unitary parameters */
parameter exactP;
/* Improve parameters */
parameter improveP;
/* ChooseHeuristic parameters*/
parameter hcrP;
/* list of solvers for choose reversals */
vector<Solver *> solver_hcr;
string intervalMethod = "WINDOW";
string heuristicReversalsName = "BenefitLoss";
/* -------------------Read the parameters From terminal----------------- */
int p_read = 1;
// Read the permutation's sequence
vector<ll> perm_seq = read_seq(argv[p_read++]);
int num_it;
sscanf(argv[p_read++], "%d", &num_it);
int inv_limit;
sscanf(argv[p_read++], "%d", &inv_limit);
double frame_limit;
sscanf(argv[p_read++], "%lf", &frame_limit);
int is_signed;
sscanf(argv[p_read++], "%d", &is_signed);
int cost_function;
sscanf(argv[p_read++], "%d", &cost_function);
/* Construct the permutation */
if (is_signed) {
perm_param = getSignedParameters();
} else {
perm_param = getUnsignedGraspParameters();
}
Permutation perm = Permutation(perm_param, perm_seq);
// makes a copy from the original input permutation and set the normal mode
Permutation perm_orig = perm;
// Look for a input solution
Result input_seed_result;
bool has_input_seed_result = false;
if (p_read < argc) {
string solution = string(argv[p_read++]);
if (solution.substr(0, 2) == "-r") {
// in this caseheuristicName is supposed to be like -r=[[...]]
string str_result = solution.substr(3);
// Alterado por Ulisses
input_seed_result = Util::getResultFromStr(str_result.c_str(), cost_function);
has_input_seed_result = true;
Permutation perm_copy = perm;
bool valid = Solver::validateResult(perm_copy, input_seed_result, cout);
if (!valid) {
cout<<"Invalid input solution."<<endl;
exit(1);
}
}
}
/* -------------Check if the permutation is already sorted--------------- */
if (perm.isSorted(1, perm.size())) {
Result::printResult(seed_result, cout);
cout<<endl;
return 0;
}
/* ----------------------- Set Default Parameters ----------------------- */
parameter default_parameters = getDefaultParameters();
/* Set the output for results logging */
if (p_read < argc) {
logOut = new ofstream(argv[p_read++], std::ofstream::out|ofstream::app);
}
if (p_read < argc) {
logTime = new ofstream(argv[p_read++], std::ofstream::out|ofstream::app);
}
/* Look for Parameters */
string type;
parameter::iterator it;
for (it = default_parameters.begin(); it != default_parameters.end(); it++) {
pair<string, string> p = getParameterPair(it->F);
string type = p.F;
string name = p.S;
double value = it->S;
// get Num selected rev
if (type == "HCR") {
hcrP[name] = value;
} else if (type == "IMP") {
improveP[name] = value;
} else if (type == "BUILD_SOLUTION") {
exactP[name] = value;
}
p_read++;
}
/* Look for the unsigned mode */
improveP["UNSIGNED"] = !is_signed;
/* Create log file */
//ofstream log_out("log_test_signed.txt",ios_base::app);
/* ----------------------Set Parameters from terminal---------------------- */
hcrP["COST_FUNCTION"] = cost_function;
improveP["COST_FUNCTION"] = cost_function;
exactP["COST_FUNCTION"] = cost_function;
improveP["NUM_ROUND"] = num_it;
exactP["NUM_SELECTED_REV"] = inv_limit;
if (frame_limit <= 0 || frame_limit > 100) {
cerr<<"Error: frame_limit must be in the interval (0, 100]"<<endl;
exit(1);
}
improveP["ROLETTE_PERCENT_DISCARD"] = (100.0 - frame_limit);
/*---------------- Build the Choosen reversal Heuristic -------------------*/
hcr_seq = build_hcr_seq(
intervalMethod,
improveP,
hcrP,
exactP,
heuristicReversalsName
);
if (improveP["EXACT_UNITATY_LS"]) {
solver_hcr.push_back(new ExactUnitary(exactP, hcr_seq));
} else if (improveP["GRASP_HEURISTIC_LS"]) {
solver_hcr.push_back(new GRASPHeuristic(exactP, hcr_seq));
}
/*---------------------- Build The seed solution -------------------------*/
if (has_input_seed_result) {
seed_result = input_seed_result;
} else if (is_signed){
// Alterado por Ulisses
seed_result = sortByGRIMM(perm, true, cost_function);
} else {
seed_result = sortByGRIMMUnsigned(perm, NUM_IT_GRIMM_UNSIGNED, true, cost_function);
}
/*--------------------- Build Improvement Metaheuristic ------------------*/
ImproveReversals * ir = new ImproveReversals(
solver_hcr,
intervalMethod,
improveP,
logOut
);
/*-------------------------- Try improve the result ----------------------*/
Result r_improved = tryImprove(
seed_result,
ir,
perm_orig,
cost_function
);
/*----------------------- Validate result --------------------------------*/
bool valid = Solver::validateResult(perm_orig, r_improved, cout);
Result seedR = seed_result;
//seedR.reversals = seed_result;
seedR = Solver::calcTotalCost(seedR, cost_function);
/*------------------------- Print the result -----------------------------*/
if (valid) {
Result::printResult(r_improved, cout);
cout<<endl;
} else {
cout<<"ERROR";
return 1;
}
/*------------------------- Print time -----------------------------------*/
time_end = get_timestamp();
double time_sec = get_interval_time(time_begin, time_end);
if (logTime != NULL)
*(logTime)<<time_sec<<endl;
/* Clean all resources */
for (size_t i = 0; i < solver_hcr.size(); i++) {
delete solver_hcr[i];
}
solver_hcr.clear();
if (logOut != NULL)
delete logOut;
delete ir;
cleanResources();
return valid;
}
void Forwarder::read_seq(const std::string &seq_filename, const size_t alphabet_size, const size_t min_no_eval) {
std::vector<size_t> nStatesSave;
read_seq(seq_filename, alphabet_size, nStatesSave, min_no_eval);
}
