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//
// sharedrabundvectors.hpp
// Mothur
//
// Created by Sarah Westcott on 5/15/17.
// Copyright © 2017 Schloss Lab. All rights reserved.
//
#ifndef sharedrabundvectors_hpp
#define sharedrabundvectors_hpp
#include "datavector.hpp"
#include "rabundvector.hpp"
#include "rabundfloatvector.hpp"
#include "sharedordervector.h"
#include "sharedrabundvector.hpp"
#include "sharedrabundfloatvector.hpp"
/* DataStructure for a shared file. */
//********************************************************************************************************************
inline bool compareRAbunds(SharedRAbundVector* left, SharedRAbundVector* right){ return (left->getGroup() < right->getGroup()); }
//********************************************************************************************************************
class SharedRAbundVectors : public DataVector {
public:
SharedRAbundVectors() : DataVector() { label = ""; numBins = 0; otuTag = "Otu"; }
SharedRAbundVectors(string oTag) : DataVector() { label = ""; numBins = 0; otuTag = oTag; }
SharedRAbundVectors(ifstream&, vector<string>& userGroups, string&, string&);
SharedRAbundVectors(SharedRAbundVectors& bv) : DataVector(bv), numBins(bv.numBins), otuTag(bv.otuTag) {
vector<SharedRAbundVector*> data = bv.getSharedRAbundVectors();
for (int i = 0; i < data.size(); i++) { push_back(data[i]); }
setLabels(bv.getLabel());
setOTUNames(bv.getOTUNames());
eliminateZeroOTUS();
}
~SharedRAbundVectors() { clear(); }
void setLabels(string l);
int getOTUTotal(int bin);
int getOTUTotal(string otuLabel); //returns 0 if otuLabel is not found
vector<int> getOTU(int bin);
int get(int bin, string group);
void set(int bin, int binSize, string group);
void setOTUNames(vector<string> names);
vector<string> getOTUNames();
string getOTUName(int);
void setOTUName(int, string);
int getNumBins() { return numBins; }
int getNumSeqsSmallestGroup();
vector<string> getNamesGroups(); //same order as Rabunds
int getNumGroups() { return (int)lookup.size(); }
int getNumSeqs(string); //group
int push_back(vector<int>, string binLabel=""); //add otu. mothur assumes abunds are in same order as groups.
int push_back(SharedRAbundVector*);
void eliminateZeroOTUS(); //run after push_backs if groups are chosen
int removeOTU(int bin);
int removeOTUs(vector<int>, bool sorted=false); //bins to remove, sorted or not
void removeGroups(vector<string> g);
int removeGroups(int minSize, bool silent=false); // removes any groups with numSeqs < minSize
int size() { return (int)lookup.size(); }
void resize(int n) { m->mothurOut("[ERROR]: can not use resize for SharedRAbundVectors.\n"); m->setControl_pressed(true); }
void clear() { for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != nullptr) { delete lookup[i]; lookup[i] = nullptr; } } lookup.clear(); groupNames.clear(); numBins = 0; }
void print(ostream&, bool&);
void printTidy(ostream&, bool&, bool);
RAbundVector getRAbundVector();
RAbundVector getRAbundVector(string); //group you want the rabund for
SAbundVector getSAbundVector();
SAbundVector getSAbundVector(string); //group you want the sabund for
OrderVector getOrderVector(map<string,int>*) { m->mothurOut("[ERROR]: can not convert SharedRAbundVectors to an ordervector, ordervectors assume no zero OTUS.\n"); m->setControl_pressed(true); OrderVector o; return o; }
SharedOrderVector getSharedOrderVector();
vector<SharedRAbundVector*> getSharedRAbundVectors();
vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors();
private:
void printHeaders(ostream&, bool&);
vector<SharedRAbundVector*> lookup;
vector<string> currentLabels;
map<string, int> groupNames;
int numBins;
string otuTag;
};
#endif /* sharedrabundvectors_hpp */
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