changes while testing

[mothur.git] / fastamap.h

diff --git a/fastamap.h b/fastamap.h
index fbda6aee6cd6b383da0d577f3d1b98d8ec1614e7..e1ff3dff2f9ceab1c663f0646141594fe1d20339 100644 (file)
--- a/fastamap.h
+++ b/fastamap.h
@@ -10,40 +10,40 @@
  *
  */
  
-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() { 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&);
-       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
\ No newline at end of file
+#endif