fullmatrix.h

   1 #ifndef FULLMATRIX_H
   2 #define FULLMATRIX_H
   3 /*
   4  *  fullmatrix.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 3/6/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "mothur.h"
  13 #include "groupmap.h"
  14 #include "globaldata.hpp"
  15 #include "progress.hpp"
  16
  17 using namespace std;
  18
  19 class FullMatrix {
  20
  21         public:
  22                 FullMatrix(){};
  23                 FullMatrix(ifstream&);
  24                 ~FullMatrix(){};
  25
  26                 int getNumSeqs();
  27                 void printMatrix(ostream&);
  28
  29         private:
  30                 void sortGroups();  //this function sorts the sequences within the matrix.
  31                 void quicksort(int, int, int);//row of matrix, low, high and row number
  32                 void readSquareMatrix(ifstream&);
  33                 void readLTMatrix(ifstream&);
  34                 vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
  35                 map<int, string> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
  36                 GroupMap* groupmap;  //maps sequences to groups they belong to.
  37                 GlobalData* globaldata;
  38                 int numSeqs;
  39                 bool square;
  40
  41 };
  42
  43 #endif