fasta.hpp

#ifndef __FASTA_HPP__
#define __FASTA_HPP__

#include <string>
#include <vector>

using namespace std;

const long MAX_GENOME = 1000000000;
const long MAX_THREADCONTAINER = 10000000;
const	long MAX_PARTNUMBER = 500;
const long MAX_PARTNUMBERFORPERFECT = 40000;
const long PART_BASE = 1000000; // 1MB

// Clustering information.
struct hit
{
	long id;
	double identity;
	char strand;

};

// For single genome search.
struct Genome
{
	long size; //genome length
	long id; //index
	string descript; // genome name
	string cont; // genome content

};

// Total genomes info container.
struct GenomeClustInfo
{
	long size; //genome length
	long id; //index
	bool rep; // if it is representive of clustering
	double mumindex; //another index
	string descript; //genome name
	vector<hit> clusters, clusterunits;

};

void filter_n(string &seq_rc);

// Reverse complement sequence.
void reverse_complement(string &seq_rc, bool nucleotides_only);

// Trim sequence.
void trim(string &line, long &start, long &end);
void load_fasta(string filename, 
								string &S,
								vector<string> &descr,
								vector<long> &startpos);

void load_part_genomes(string filename, 
											 vector<Genome> &partgenomes,
											 vector<GenomeClustInfo> &totalgenomes,
											 long previous,
											 long number);

void load_part_genomes_internal(string filename, 
																vector<Genome> &partgenomes,
																vector<GenomeClustInfo> &totalgenomes,
																long previous,
																int &number,
																long totalsize,
																bool &ifend,
																int memiden);

void load_part_genomes_all(string filename, vector<Genome> &partgenomes);
// Load part genomes into memory between parts.
void load_part_genomes_mem(vector<Genome> &allpartgenomes, 
													 vector<Genome> &partgenomes,
													 vector<GenomeClustInfo> &totalgenomes,
													 long previous,
													 long number);

// Load part genomes into memory.
void load_part_genomes_internal_mem(vector<Genome> &allpartgenomes, 
																		vector<Genome> &partgenomes,
																		vector<GenomeClustInfo> &totalgenomes,
																		long previous,
																		int &number,
																		long totalsize,
																		bool &ifend,
																		int memiden);

void test_part(vector<Genome> &partgenomes);

// Make block for Suffix Array construction.
void make_block_ref(vector<Genome> &partgenomes,
										string &S,
										vector<GenomeClustInfo> &totalgenomes,
										vector<long> &descr,
										vector<long> &startpos);

// Load total genomes.
void load_total_genomes(string filename, vector<GenomeClustInfo> &totalgenomes);

#endif // __FASTA_HPP__