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#ifndef INPUTDATA_H
#define INPUTDATA_H
#include "mothur.h"
#include "ordervector.hpp"
#include "sharedlistvector.h"
#include "sharedordervector.h"
#include "listvector.hpp"
#include "sharedrabundvectors.hpp"
#include "sharedrabundfloatvectors.hpp"
#include "utils.hpp"
class InputData {
public:
InputData(string, string, vector<string>);
InputData(string, string, string);
~InputData();
ListVector* getListVector();
ListVector* getListVector(string); //pass the label you want
ListVector* getListVector(string, bool); //pass the label you want, reset filepointer
SharedListVector* getSharedListVector();
SharedListVector* getSharedListVector(string); //pass the label you want
OrderVector* getOrderVector();
OrderVector* getOrderVector(string); //pass the label you want
SharedOrderVector* getSharedOrderVector();
SharedOrderVector* getSharedOrderVector(string); //pass the label you want
SAbundVector* getSAbundVector();
SAbundVector* getSAbundVector(string); //pass the label you want
RAbundVector* getRAbundVector();
RAbundVector* getRAbundVector(string); //pass the label you want
SharedRAbundVectors* getSharedRAbundVectors();
SharedRAbundVectors* getSharedRAbundVectors(string); //pass the label you want
SharedRAbundFloatVectors* getSharedRAbundFloatVectors();
SharedRAbundFloatVectors* getSharedRAbundFloatVectors(string); //pass the label you want
SharedCLRVectors* getSharedCLRVectors();
SharedCLRVectors* getSharedCLRVectors(string); //pass the label you want
private:
Utils util;
string format;
ifstream fileHandle;
DataVector* input;
ListVector* list;
SharedListVector* SharedList;
OrderVector* output;
SharedOrderVector* SharedOrder;
SAbundVector* sabund;
RAbundVector* rabund;
map<string,int> orderMap;
string filename;
MothurOut* m;
vector<string> currentLabels;
vector<string> groups;
string nextDistanceLabel;
string otuTag;
};
#endif
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