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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.
+ *
+ */
+ 
+#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() { m = MothurOut::getInstance(); }
+       ~FastaMap() {};
+       
+       string getGroupName(string);  //pass a sequence name get 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, 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.
+               string names;                                           //the names of the sequence separated by ','.
+       };
+
+       map<string, group>  data;  //sequence, groupinfo        - condensed representation of file
+       map<string, string>  seqmap;  //name, sequence  -  uncondensed representation of file
+       MothurOut* m;
+};
+
+#endif