X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fastamap.h;h=e1ff3dff2f9ceab1c663f0646141594fe1d20339;hp=fbda6aee6cd6b383da0d577f3d1b98d8ec1614e7;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d

diff --git a/fastamap.h b/fastamap.h
index fbda6ae..e1ff3df 100644
--- 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