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#ifndef FULLMATRIX_H
#define FULLMATRIX_H
/*
* fullmatrix.h
* Mothur
*
* Created by Sarah Westcott on 3/6/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "mothur.h"
#include "groupmap.h"
#include "progress.hpp"
struct Names {
string seqName;
string groupName;
};
class FullMatrix {
public:
//FullMatrix(){ m = MothurOut::getInstance(); }
FullMatrix(ifstream&, GroupMap*, bool);
~FullMatrix(){};
int getNumSeqs();
vector<int> getSizes();
vector<string> getGroups();
void setGroups(vector<string> names) { groups = names; }
void setSizes(vector<int> s) { sizes = s; }
int getNumGroups();
void printMatrix(ostream&);
float get(int, int);
Names getRowInfo(int row) { return index[row]; }
private:
vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
int readSquareMatrix(ifstream&);
int readLTMatrix(ifstream&);
vector<Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
vector<int> sizes;
vector<string> groups;
void sortGroups(int, int); //this function sorts the sequences within the matrix.
void swapRows(int, int);
GroupMap* groupmap; //maps sequences to groups they belong to.
int numSeqs;
int numGroups;
int numUserGroups;
bool sim;
MothurOut* m;
};
#endif
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