X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fastamap.h;fp=fastamap.h;h=e1ff3dff2f9ceab1c663f0646141594fe1d20339;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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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