*
*/
-using namespace std;
-
#include "mothur.h"
-#include "utilities.hpp"
+#include "mothurout.h"
/* This class represents the fasta file. It reads a fasta file a populates the internal data structure "data".
class FastaMap {
public:
- FastaMap() {};
+ 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 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 printCondensedFasta(ostream&); //produces a fasta file.
- void readFastaFile(ifstream&);
+ 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 sequence names with the same sequence.
string names; //the names of the sequence separated by ','.
};
- map<string, group> data; //sequence, groupinfo
- 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