working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / sequenceparser.h

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+#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.
+               
+       private:
+       
+               GroupMap* groupMap;
+               MothurOut* m;
+       
+               int numSeqs;
+               map<string, vector<Sequence> > seqs; //a vector for each group
+               map<string, map<string, string> > nameMapPerGroup; //nameMap for each group
+};
+
+#endif
+