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//
// biom.hpp
// Mothur
//
// Created by Sarah Westcott on 10/26/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#ifndef biom_hpp
#define biom_hpp
#include "utils.hpp"
#include "mothurout.h"
#include "sharedrabundfloatvectors.hpp"
#include "sharedrabundvectors.hpp"
#include "phylosummary.h"
#include "taxonomy.hpp"
#include "picrust.hpp"
//http://biom-format.org
//http://biom-format.org/documentation/format_versions/biom-1.0.html
//http://biom-format.org/documentation/format_versions/biom-2.1.html
/**************************************************************************************************/
class Biom {
public:
Biom();
Biom(string); //version
virtual ~Biom();
virtual void read(string) = 0;
virtual void load(SharedRAbundVectors* s, vector<Taxonomy> c);
virtual void load(SharedRAbundFloatVectors* s, vector<Taxonomy> c);
virtual void fillHeading(string mv, string sfn) { mothurVersion = mv; sharedFileName = sfn; }
virtual void print(string, vector<string>, Picrust*) { } //hdf5 print
virtual string getVersion() { return version; }
virtual string getMatrixElementType() { return matrixElementType; }
virtual SharedRAbundVectors* getSharedRAbundVectors() { return shared; }
virtual SharedRAbundFloatVectors* getSharedRAbundFloatVectors() { return sharedFloat; }
//otu taxonomies
virtual vector<Taxonomy> getConsTaxonomies() { return consTax; }
//sample taxonomies
virtual map<string, string> getGroupTaxonomies() { return groupTaxonomies; }
protected:
MothurOut* m;
Utils util;
string matrixFormat, tableType; //examples: tableType = "OTU table", matrixFormat = "sparse" or "dense"
string version, formatURL, label, matrixElementType; //version = simple or hdf5, set by child. matrixElementType = "int" or "float"
string tableID, mothurVersion, sharedFileName;
int maxLevel;
SharedRAbundVectors* shared; //always created with read
SharedRAbundFloatVectors* sharedFloat; //only created if the matrixElementType is float
vector<Taxonomy> consTax;
map<string, string> groupTaxonomies;
};
/**************************************************************************************************/
#endif /* biom_hpp */
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