moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / fastamap.h

diff --git a/fastamap.h b/fastamap.h
deleted file mode 100644 (file)
index e1ff3df..0000000
--- a/fastamap.h
+++ /dev/null
@@ -1,49 +0,0 @@
-#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