fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / fastamap.h

diff --git a/fastamap.h b/fastamap.h
index fbda6aee6cd6b383da0d577f3d1b98d8ec1614e7..169974b27f107a00ba2a0f7738d7551160a37c62 100644 (file)
--- a/fastamap.h
+++ b/fastamap.h
@@ -12,13 +12,15 @@
  
 using namespace std;
  
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <map>
+#include "mothur.h"
 #include "utilities.hpp"
 
 
+/* 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:
@@ -32,7 +34,8 @@ public:
        void set(string, string, string); //sequencename, groupname, groupnumber, names.
        void clear();
        int size();                                     //returns number of unique sequences
-       void print(ostream&);
+       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&);
 
 private:
@@ -46,4 +49,4 @@ private:
        map<string, group>::iterator it;
 };
 
-#endif
\ No newline at end of file
+#endif