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//
// oligos.h
// Mothur
//
// Created by Sarah Westcott on 4/4/14.
// Copyright (c) 2014 Schloss Lab. All rights reserved.
//
#ifndef Mothur_oligos_h
#define Mothur_oligos_h
#include "mothurout.h"
/**************************************************************************************************/
class Oligos {
public:
Oligos(string);
Oligos();
~Oligos() = default;
int read(string);
int read(string, bool); //read without reversing the paired barcodes, for make.contigs.
bool hasPairedPrimers() { return hasPPrimers; }
bool hasPairedBarcodes() { return hasPBarcodes; }
//for processing with trimOligos class
map<int, oligosPair> getPairedPrimers() { return pairedPrimers; }
map<int, oligosPair> getPairedBarcodes() { return pairedBarcodes; }
map<int, oligosPair> getReorientedPairedPrimers();
map<int, oligosPair> getReorientedPairedBarcodes();
map<int, oligosPair> getReversedPairedPrimers();
map<int, oligosPair> getReversedPairedBarcodes();
map<string, int> getPrimers() { return primers; }
map<string, int> getBarcodes() { return barcodes; }
map<string, int> getReversedPrimers();
vector<string> getReversedReversePrimers();
map<string, int> getReorientedPrimers();
vector<string> getReorientedReversePrimers();
vector<string> getLinkers() { return linker; }
vector<string> getSpacers() { return spacer; }
vector<string> getReversePrimers() { return revPrimer; }
vector<string> getPrimerNames() { return primerNameVector; }
vector<string> getBarcodeNames() { return barcodeNameVector; }
vector<string> getGroupNames() { return Groups; }
vector<string> getSRAGroupNames();
//for printing and other formatting uses
vector<string> getBarcodes(string); //get barcodes for a group. For paired barcodes will return forward.reverse
vector<string> getPrimers(string); //get primers for a group. For paired primers will return forward.reverse
string getGroupName(int, int);
string getBarcodeName(int);
string getPrimerName(int);
protected:
set<string> uniqueNames;
vector<string> Groups;
vector<string> revPrimer;
map<string, vector<string> > Group2Barcode;
map<string, vector<string> > Group2Primer;
map<int, oligosPair> pairedBarcodes;
map<int, oligosPair> pairedPrimers;
map<string, int> primers;
map<string, int> barcodes;
vector<string> linker;
vector<string> spacer;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
bool hasPPrimers, hasPBarcodes, pairedOligos, reversePairs;
string oligosfile;
int numBarcodes, numFPrimers;
MothurOut* m;
int indexPrimer;
int indexBarcode;
int indexPairedPrimer;
int indexPairedBarcode;
int readOligos();
string reverseOligo(string);
void formatOligo(string&);
};
/**************************************************************************************************/
#endif
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