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#ifndef FASTAMAP_H
#define FASTAMAP_H
/*
* fastamap.h
* mothur
*
* Created by Sarah Westcott on 1/16/09.
* Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
*
*/
#include "mothurout.h"
#include "utils.hpp"
/* This class represents the fasta file. It reads a fasta file a populates the internal data structure "data".
Data is a map where the key is the sequence and the value is a struct containing the sequences groupname,
a list of the sequences names who have the same sequence and a number of how many sequence names there are. */
class FastaMap {
public:
FastaMap() { m = MothurOut::getInstance(); }
~FastaMap() = default;;
string getGroupName(string); //pass a sequence name get its group
string getNames(string); //pass a sequence get the string of names in the group separated by ','s.
void push_back(string, string); //sequencename, sequence
int sizeUnique(); //returns number of unique sequences
void printNamesFile(string); //produces a 2 column file with the groupname in the first column and the names in the second column - a names file.
void printCondensedFasta(string); //produces a fasta file.
void readFastaFile(string);
void readFastaFile(string, string);
string getSequence(string); //pass it a name of a sequence, it returns the sequence.
private:
struct group {
string groupname; //the group name for identical sequences, will be set to the first sequence found.
string names; //the names of the sequence separated by ','.
};
map<string, group> data; //sequence, groupinfo - condensed representation of file
map<string, string> seqmap; //name, sequence - uncondensed representation of file
MothurOut* m;
Utils util;
};
#endif
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