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//
// sharedrabundvector.hpp
// Mothur
//
// Created by Sarah Westcott on 7/24/17.
// Copyright © 2017 Schloss Lab. All rights reserved.
//
#ifndef sharedrabundvector_hpp
#define sharedrabundvector_hpp
#include "datavector.hpp"
#include "ordervector.hpp"
#include "rabundvector.hpp"
#include "rabundfloatvector.hpp"
#include "sabundvector.hpp"
/* Data Structure for a rabund file.
This class is a child to datavector. It represents OTU information at a certain distance.
A rabundvector can be converted into and ordervector, listvector or sabundvector.
Each member of the internal container "data" represents an individual OTU.
So data[0] = 6, because there are six member in that OTU.
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
a,b,g,j,l = sample A
c,d,h,i = sample B
e,f,k,m = sample C
The sharedRabund class is very similar to rabund. SharedRabund allows for 0 otus in a sample, rabunds do not. SharedRabund also know their group. SharedRabunds are stored as floats, but printed as integers or floats depending on whether it represents a shared or relabund file.
sharedrabund = A 5 2 1 1 1 0
B 5 2 2 0 0 0
C 5 2 0 1 0 1
*/
//class RAbundFloatVector;
class OrderVector;
class SharedRAbundVector : public DataVector {
#ifdef UNIT_TEST
friend class TestSharedRabundVector;
#endif
public:
SharedRAbundVector();
SharedRAbundVector(int);
SharedRAbundVector(vector<int>, int, int, int);
SharedRAbundVector(vector<int>);
SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs), group(bv.group) { };
SharedRAbundVector(ifstream&);
SharedRAbundVector(ifstream& f, string l, string g, int); //filehandle, label, numBins
~SharedRAbundVector();
int getNumBins();
int getNumSeqs();
int getMaxRank();
void set(int, int);
int get(int);
vector<int> get() { return data; }
string getGroup() { return group; } //group = "" for rabunds without groupInfo
void setGroup(string g) { group = g; }
int increment(int); //add 1 to bin
void push_back(int);
void resize(int);
int size();
void clear();
int remove(int);
int remove(vector<int>);
void print(ostream&); //nonsorted
RAbundVector getRAbundVector();
RAbundFloatVector getRAbundFloatVector();
SAbundVector getSAbundVector();
OrderVector getOrderVector(map<string,int>*);
protected:
vector<int> data;
int maxRank;
int numBins;
int numSeqs;
string group;
};
#endif /* sharedrabundvector_hpp */
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