minor bugs fixes and added line and label options to read.otu's parselist and shared...

[mothur.git] / fastamap.h

diff --git a/fastamap.h b/fastamap.h
index bd262c4d0660671899d7d576327e3065051a04aa..8ba2fc6ec3e9507a018084080d6dd6275b1203d1 100644 (file)
--- a/fastamap.h
+++ b/fastamap.h
@@ -19,30 +19,37 @@ using namespace std;
 #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:
        FastaMap() {};
-       FastaMap(ifstream&);
        ~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 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:
        struct group {
                string groupname;                                       //the group name for identical sequences, will be set to the first sequence found.
-               int groupnumber;                                        //the number of sequences in that group.
+               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, group
-       map<string, group>::iterator it;        
+       map<string, group>  data;  //sequence, groupinfo
+       map<string, group>::iterator it;
 };
 
-#endif
\ No newline at end of file
+#endif