using namespace std;
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <map>
-#include "utilities.hpp"
+#include "mothur.h"
/* This class represents the fasta file. It reads a fasta file a populates the internal data structure "data".
string getGroupName(string); //pass a sequence name get its group
int getGroupNumber(string); //pass a sequence name get number of sequence in 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, groupname
- void set(string, string, string); //sequencename, groupname, groupnumber, names.
- void clear();
- int size(); //returns number of unique sequences
- void print(ostream&); //produces a 2 column file with the groupname in the first column and the names in the second column.
+ void push_back(string, string); //sequencename, sequence
+ int sizeUnique(); //returns number of unique sequences
+ void printNamesFile(ostream&); //produces a 2 column file with the groupname in the first column and the names in the second column - a names file.
+ void printCondensedFasta(ostream&); //produces a fasta file.
void readFastaFile(ifstream&);
+ string getSequence(string); //pass it a name of a sequence, it returns the sequence.
private:
struct group {
string names; //the names of the sequence separated by ','.
};
- map<string, group> data; //sequence, groupinfo
+ map<string, group> data; //sequence, groupinfo - condensed representation of file
+ map<string, string> seqmap; //name, sequence - uncondensed representation of file
map<string, group>::iterator it;
+ map<string, string>::iterator it2;
};
#endif