fastamap.h

   1 #ifndef FASTAMAP_H
   2 #define FASTAMAP_H
   3
   4 /*
   5  *  fastamap.h
   6  *  mothur
   7  *
   8  *  Created by Sarah Westcott on 1/16/09.
   9  *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
  10  *
  11  */
  12
  13 using namespace std;
  14
  15 #include <iostream>
  16 #include <fstream>
  17 #include <string>
  18 #include <map>
  19 #include "utilities.hpp"
  20
  21
  22 class FastaMap  {
  23
  24 public:
  25         FastaMap() {};
  26         ~FastaMap() {};
  27
  28         string getGroupName(string);  //pass a sequence name get its group
  29         int getGroupNumber(string);  //pass a sequence name get number of sequence in its group
  30         string getNames(string);        //pass a sequence get the string of names in the group separated by ','s.
  31         void push_back(string, string); //sequencename, groupname
  32         void set(string, string, string); //sequencename, groupname, groupnumber, names.
  33         void clear();
  34         int size();                                     //returns number of unique sequences
  35         void print(ostream&);
  36         void readFastaFile(ifstream&);
  37
  38 private:
  39         struct group {
  40                 string groupname;                                       //the group name for identical sequences, will be set to the first sequence found.
  41                 int groupnumber;                                        //the number of sequence names with the same sequence.
  42                 string names;                                           //the names of the sequence separated by ','.
  43         };
  44
  45         map<string, group>  data;  //sequence, groupinfo
  46         map<string, group>::iterator it;
  47 };
  48
  49 #endif