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//
// sharedclrvectors.hpp
// Mothur
//
// Created by Sarah Westcott on 1/21/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#ifndef sharedclrvectors_hpp
#define sharedclrvectors_hpp
#include "datavector.hpp"
#include "sharedclrvector.hpp"
/* DataStructure for a clr relabund file.
The clr - log centered ratio - is the log (base 2) of a value divided by the geometric mean of the values across all OTUs for that sample. For example here are the counts for four OTUs in one sample...
> x <- c(10, 5, 3, 1)
> log2(x / prod(x)^(1/4))
[1] 1.5147234 0.5147234 -0.2222422 -1.8072047
*/
//********************************************************************************************************************
inline bool compareCLRVectors(SharedCLRVector* left, SharedCLRVector* right){ return (left->getGroup() < right->getGroup()); }
//********************************************************************************************************************
class SharedCLRVectors : public DataVector {
public:
SharedCLRVectors() : DataVector() { label = ""; numBins = 0; otuTag = "Otu"; }
SharedCLRVectors(ifstream&, vector<string>&, string&, string&);
SharedCLRVectors(SharedCLRVectors& bv) : DataVector(bv), numBins(bv.numBins), otuTag(bv.otuTag) {
vector<SharedCLRVector*> data = bv.getSharedCLRVectors();
for (int i = 0; i < data.size(); i++) { push_back(data[i]); }
setLabels(bv.getLabel());
setOTUNames(bv.getOTUNames());
//eliminateZeroOTUS();
}
~SharedCLRVectors() { clear(); }
vector<string> getNamesGroups();
void setLabels(string l);
float getOTUTotal(int bin);
vector<float> getOTU(int bin);
float removeOTU(int bin);
float removeOTUs(vector<int>, bool sorted=false); //bins to remove, sorted or not
float get(int bin, string group);
void set(int bin, float binSize, string group);
void setOTUNames(vector<string> names);
vector<string> getOTUNames();
string getOTUName(int);
void setOTUName(int, string);
int push_back(vector<float>, string binLabel=""); //add otu. mothur assumes abunds are in same order as groups.
int push_back(SharedCLRVector*);
void removeGroups(vector<string> g);
int removeGroups(int minSize, bool silent=false); // removes any groups with numSeqs < minSize
void resize(int n) { m->mothurOut("[ERROR]: can not use resize for SharedCLRVectors.\n"); }
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; currentLabels.clear(); }
int size() { return (int)lookup.size(); }
int getNumGroups() { return (int)lookup.size(); }
int getNumBins() { return numBins; }
float getNumSeqs(string); //group
float getNumSeqsSmallestGroup();
void print(ostream&, bool&);
vector<SharedCLRVector*> getSharedCLRVectors();
RAbundVector getRAbundVector() { m->mothurOut("[ERROR]: can not use getRAbundVector for SharedCLRVectors.\n"); RAbundVector r; return r; }
SAbundVector getSAbundVector() { m->mothurOut("[ERROR]: can not use getSAbundVector for SharedCLRVectors.\n"); SAbundVector s; return s; }
OrderVector getOrderVector(map<string,int>* hold = nullptr) { m->mothurOut("[ERROR]: can not use getOrderVector for SharedCLRVectors.\n"); OrderVector o; return o; }
private:
void printHeaders(ostream&, bool&);
vector<SharedCLRVector*> lookup;
vector<string> currentLabels;
map<string, int> groupNames;
int numBins;
string otuTag;
};
#endif /* sharedclrvectors_hpp */
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