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#ifndef SHAREDLIST_H
#define SHAREDLIST_H
/*
* sharedlistvector.h
* Mothur
*
* Created by Sarah Westcott on 1/22/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "datavector.hpp"
#include "groupmap.h"
#include "counttable.h"
#include "sharedrabundvectors.hpp"
#include "sharedrabundfloatvectors.hpp"
#include "currentfile.h"
/* This class is a child to datavector. It represents OTU information at a certain distance.
A sharedlistvector can be converted into a sharedordervector, sharedrabundvector or sharedsabundvectorand
as well as an ordervector, rabundvector or sabundvector.
Each member of the internal container "data" represents an individual OTU.
Each individual in the OTU belongs to a group.
So data[0] = "a,b,c,d,e,f".
example: listvector = a,b,c,d,e,f g,h,i j,k l m
rabundvector = 6 3 2 1 1
sabundvector = 2 1 1 0 0 1
ordervector = 1 1 1 1 1 1 2 2 2 3 3 4 5 */
class SharedListVector : public DataVector {
public:
SharedListVector(ifstream&, vector<string>&, string&, string&);
SharedListVector(const SharedListVector& lv) : DataVector(lv.label), data(lv.data), maxRank(lv.maxRank), numBins(lv.numBins), numSeqs(lv.numSeqs), binLabels(lv.binLabels), groups(lv.groups), fillGroups(lv.fillGroups), groupMode(lv.groupMode), otuTag(lv.otuTag) { groupmap = nullptr; countTable = nullptr; };
~SharedListVector(){ if (groupmap != nullptr) { delete groupmap; } if (countTable != nullptr) { delete countTable; } };
int getNumBins() { return numBins; }
int getNumSeqs() { return numSeqs; }
int getMaxRank() { return maxRank; }
void set(int, string);
string get(int);
vector<string> getLabels();
void setLabels(vector<string>);
void push_back(string);
void resize(int);
void clear();
int size();
void print(ostream&);
RAbundVector getRAbundVector();
SAbundVector getSAbundVector();
OrderVector getOrderVector(map<string,int>*);
SharedOrderVector* getSharedOrderVector();
SharedRAbundVectors* getSharedRAbundVector(); //returns sharedRabundVectors for all the users groups
SharedRAbundFloatVectors* getSharedRAbundFloatVector(); //returns sharedRabundVectors for all the users groups
private:
vector<string> data; //data[i] is a list of names of sequences in the ith OTU.
GroupMap* groupmap;
CountTable* countTable;
vector<string> groups;
bool fillGroups;
int maxRank;
int numBins;
int numSeqs;
vector<string> binLabels;
string groupMode, otuTag;
};
#endif
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