1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
#ifndef PDSSparCC_runSparcc_h
#define PDSSparCC_runSparcc_h
//
// runSparcc.h
// PDSSparCC
//
// Created by Patrick Schloss on 10/31/12.
// Copyright (c) 2012 University of Michigan. All rights reserved.
//
/**************************************************************************************************/
//#include "sparcc.h"
#include "mothurout.h"
#include "utils.hpp"
/**************************************************************************************************/
class CalcSparcc {
public:
CalcSparcc(vector<vector<float> >, int, int, string);
vector<vector<float> > getRho() { return median; }
private:
MothurOut* m;
Utils util;
void addPseudoCount(vector<vector<float> >&);
vector<float> getLogFractions(vector<vector<float> >, string);
void getT_Matrix(vector<float>);
void getT_Vector();
void getD_Matrix();
vector<float> getBasisVariances();
vector<vector<float> > getBasisCorrelations(vector<float>);
float getExcludedPairs(vector<vector<float> >, int&, int&);
void excludeValues(int, int);
void getMedian(vector<vector<vector<float> > >);
vector<float> tMatrix;
vector<vector<float> > dMatrix;
vector<float> tVector;
vector<vector<int> > excluded;
vector<vector<float> > median;
int numOTUs;
int numGroups;
string normalizationMethod;
};
#endif
/**************************************************************************************************/
|
