changes while testing

[mothur.git] / fastamap.h

diff --git a/fastamap.h b/fastamap.h
index 355a8df51786bdac9c229aed9d4233bd46d41c3e..e1ff3dff2f9ceab1c663f0646141594fe1d20339 100644 (file)
--- a/fastamap.h
+++ b/fastamap.h
@@ -10,9 +10,8 @@
  *
  */
  
-using namespace std;
- 
 #include "mothur.h"
+#include "mothurout.h"
 
 
 /* This class represents the fasta file.  It reads a fasta file a populates the internal data structure "data".
@@ -23,30 +22,28 @@ a list of the sequences names who have the same sequence and a number of how man
 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, 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&);
+       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        - condensed representation of file
        map<string, string>  seqmap;  //name, sequence  -  uncondensed representation of file
-       map<string, group>::iterator it;
-       map<string, string>::iterator it2;
+       MothurOut* m;
 };
 
 #endif