main.cpp
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#include <iostream>
#include <string>
#include <vector>
#include <unordered_map>
// import
#include "Importer/fasta.h"
#include "multithread/broadcaster.h"
// multithread
#include "multithread/buffer.h"
// Feature
#include "feature.h"
#include "feature_maker.h"
// callable
#include "feature_callable.h"
// Storage
#include "data/storage_buffer_flow.h"
#include "data/data_store_map.h"
// Data
#include "Importer/entry.h"
using namespace std;
void create_feature_maker(feature::Feature_callable *c,
string id,
data::Data_Store *ds,
multithread::Broadcaster *re);
std::vector<multithread::Buffer<data::Data_basic*>*> data_buffers;
std::vector<feature::Feature_maker*> feature_makers;
std::vector<feature::Feature_callable*> callable_entry;
std::unordered_map<std::string,data::Data_Store*> ds;
int main(int argc, char* argv[])
{
string input_file = string(argv[1]);
cout << input_file << endl;
string output = string(argv[2]);
cout << output << endl;
multithread::Buffer<data::Data_basic*> *fasta_out = new multithread::Buffer<data::Data_basic*>(THREAD_NB*BUFFER_SIZE);
fasta_out->close();
data_buffers.push_back(fasta_out);
multithread::Broadcaster re(fasta_out);
data::Data_Store_Map *tmp_ds;
/* ************** KMER ******************/
feature::Feature_callable *kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(3));
tmp_ds = new data::Data_Store_Map(output+"KMER3.txt");
ds["KMER3"] = tmp_ds;
create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6));
tmp_ds = new data::Data_Store_Map(output+"KMER6.txt");
ds["KMER6"] = tmp_ds;
create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
/* *********** ORF *********************/
/* ORF callable */
feature::Feature_callable *orf = static_cast<feature::Feature_callable*>(feature::ORF::get_callable());
tmp_ds = new data::Data_Store_Map(output+"ORF.txt");
ds["ORF"] = tmp_ds;
create_feature_maker(orf,feature::ORF::TYPE,tmp_ds,&re);
/* *********** Codon Position ***************/
feature::Feature_callable *cp = static_cast<feature::Feature_callable*>(feature::CodonPosition::get_callable());
tmp_ds = new data::Data_Store_Map(output+"CP.txt");
ds["CP"] = tmp_ds;
create_feature_maker(cp,feature::CodonPosition::TYPE,tmp_ds,&re);
/* *********** Fasta reader *************/
import::Fasta reader(fasta_out,input_file);
re.start();
reader.start();
/* **** join process ******/
reader.join();
re.join();
// shutdown pointer
while(!feature_makers.empty()){
feature::Feature_maker *fm = feature_makers.back();
feature_makers.pop_back();
delete fm;
}
while(!data_buffers.empty()){
multithread::Buffer<data::Data_basic*> *tmp_dk = data_buffers.back();
data_buffers.pop_back();
delete tmp_dk;
}
while(!callable_entry.empty()){
feature::Feature_callable *tmp_dk = callable_entry.back();
callable_entry.pop_back();
delete tmp_dk;
}
auto it = ds.begin();
while(it != ds.end()){
delete it->second;
++it;
}
return 0;
}
void create_feature_maker(feature::Feature_callable *c,
string id,
data::Data_Store *ds,
multithread::Broadcaster *re){
callable_entry.push_back(c);
multithread::Buffer<data::Data_basic*> *buf = new multithread::Buffer<data::Data_basic*>(THREAD_NB*BUFFER_SIZE);
data_buffers.push_back(buf);
feature::Feature_maker *fm = new feature::Feature_maker(c,buf,ds,id);
feature_makers.push_back(fm);
re->add_worker(buf);
}