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 struct Names {
  20         string  groupname;
  21         string          seqName;
  22 };
  23
  24
  25 class FullMatrix {
  26
  27         public:
  28                 FullMatrix(){};
  29                 FullMatrix(ifstream&);
  30                 ~FullMatrix(){};
  31
  32                 int getNumSeqs();
  33                 void printMatrix(ostream&);
  34
  35         private:
  36                 void sortGroups(int, int);  //this function sorts the sequences within the matrix.
  37                 void readSquareMatrix(ifstream&);
  38                 void readLTMatrix(ifstream&);
  39                 vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
  40                 map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
  41                 GroupMap* groupmap;  //maps sequences to groups they belong to.
  42                 GlobalData* globaldata;
  43                 int numSeqs;
  44                 bool square;
  45
  46 };
  47
  48 #endif