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
58
59
60
61
62
63
64
65
66
67
68
|
#ifndef CLUSTERCLASSIC_H
#define CLUSTERCLASSIC_H
#include "mothurout.h"
#include "listvector.hpp"
#include "rabundvector.hpp"
#include "nameassignment.hpp"
#include "counttable.h"
/*
* clusterclassic.h
* Mothur
*
* Created by westcott on 10/29/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
class ClusterClassic {
public:
ClusterClassic(float, string, bool);
int readPhylipFile(string, NameAssignment*);
int readPhylipFile(string, CountTable*);
void update(double&);
double getSmallDist() { return smallDist; }
int getNSeqs() { return nseqs; }
ListVector* getListVector() { return list; }
RAbundVector* getRAbundVector() { return rabund; }
string getTag() { return tag; }
void setMapWanted(bool m);
map<string, int> getSeqtoBin() { return seq2Bin; }
private:
double getSmallCell();
void clusterBins();
void clusterNames();
void updateMap();
void print();
struct colDist {
int col;
int row;
float dist;
colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
};
RAbundVector* rabund;
ListVector* list;
vector< vector<float> > dMatrix;
//vector<colDist> rowSmallDists;
int smallRow;
int smallCol, nseqs;
double smallDist;
bool mapWanted, sim;
double cutoff, aboveCutoff;
map<string, int> seq2Bin;
string method, tag;
MothurOut* m;
};
#endif
|
