*
*/
-using namespace std;
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <map>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "mothurout.h"
+
+
+/* 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() { m = MothurOut::getInstance(); }
~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 clear();
- int size(); //returns number of unique sequences
- void print(ostream&);
+ 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.
- int groupnumber; //the number of sequences in that group.
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 - condensed representation of file
+ map<string, string> seqmap; //name, sequence - uncondensed representation of file
+ MothurOut* m;
};
-#endif
\ No newline at end of file
+#endif