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[mothur.git] / fastamap.h

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+#ifndef FASTAMAP_H
+#define FASTAMAP_H
+
+/*
+ *  fastamap.h
+ *  mothur
+ *
+ *  Created by Sarah Westcott on 1/16/09.
+ *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
+ *
+ */
+ 
+using namespace std;
+ 
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <map>
+#include "utilities.hpp"
+
+
+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 clear();
+       int size();                                     //returns number of unique sequences
+       void print(ostream&);
+
+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.
+               string names;                                           //the names of the sequence separated by ','.
+       };
+
+       map<string, group>  data;  //sequence, group
+       map<string, group>::iterator it;        
+};
+
+#endif
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