using namespace std;
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <map>
+#include "mothur.h"
#include "utilities.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() {};
- FastaMap(ifstream&);
~FastaMap() {};
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&);
+ void print(ostream&); //produces a 2 column file with the groupname in the first column and the names in the second column.
+ void printCondensedFasta(ostream&); //produces a fasta file.
+ void readFastaFile(ifstream&);
private:
struct group {
string groupname; //the group name for identical sequences, will be set to the first sequence found.
- int groupnumber; //the number of sequences in that group.
+ int groupnumber; //the number of sequence names with the same sequence.
string names; //the names of the sequence separated by ','.
};
- map<string, group> data; //sequence, group
- map<string, group>::iterator it;
+ map<string, group> data; //sequence, groupinfo
+ map<string, group>::iterator it;
};
-#endif
\ No newline at end of file
+#endif