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

[mothur.git] / sequenceparser.h

diff --git a/sequenceparser.h b/sequenceparser.h
deleted file mode 100644 (file)
index 23fcb9e..0000000
--- a/sequenceparser.h
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef SEQUENCEPARSER_H
-#define SEQUENCEPARSER_H
-
-/*
- *  sequenceParser.h
- *  Mothur
- *
- *  Created by westcott on 9/9/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "mothur.h"
-#include "mothurout.h"
-#include "sequence.hpp"
-#include "groupmap.h"
-
-/* This class reads a fasta and group file with a namesfile as optional and parses the data by group. 
- 
-       Note: The sum of all the groups unique sequences will be larger than the original number of unique sequences. 
-       This is because when we parse the name file we make a unique for each group instead of 1 unique for all
-       groups. 
- 
- */
-
-class SequenceParser {
-       
-       public:
-       
-               SequenceParser(string, string);                 //group, fasta - file mismatches will set m->control_pressed = true
-               SequenceParser(string, string, string); //group, fasta, name  - file mismatches will set m->control_pressed = true
-               ~SequenceParser();
-               
-               //general operations
-               int getNumGroups();
-               vector<string> getNamesOfGroups();      
-               bool isValidGroup(string);  //return true if string is a valid group
-               string getGroup(string);        //returns group of a specific sequence
-               
-               int getNumSeqs(string);         //returns the number of unique sequences in a specific group
-               vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
-               map<string, string> getNameMap(string); //returns seqName -> namesOfRedundantSeqs separated by commas for a specific group - the name file format, but each line is parsed by group.
-               
-               int getSeqs(string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false
-               int getNameMap(string, string); //print seqName -> namesOfRedundantSeqs separated by commas for a specific group - group, filename
-               
-               map<string, string> getAllSeqsMap(){ return allSeqsMap; }  //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
-       private:
-       
-               GroupMap* groupMap;
-               MothurOut* m;
-       
-               int numSeqs;
-               map<string, string> allSeqsMap;
-               map<string, vector<Sequence> > seqs; //a vector for each group
-               map<string, map<string, string> > nameMapPerGroup; //nameMap for each group
-};
-
-#endif
-