7 * Created by Sarah Westcott on 3/6/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "globaldata.hpp"
15 #include "progress.hpp"
26 FullMatrix(){ m = MothurOut::getInstance(); }
27 FullMatrix(ifstream&);
31 vector<int> getSizes();
32 vector<string> getGroups();
33 void setGroups(vector<string> names) { groups = names; }
34 void setSizes(vector<int> s) { sizes = s; }
36 void printMatrix(ostream&);
38 Names getRowInfo(int row) { return index[row]; }
41 vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
42 int readSquareMatrix(ifstream&);
43 int readLTMatrix(ifstream&);
44 vector<Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
46 vector<string> groups;
48 void sortGroups(int, int); //this function sorts the sequences within the matrix.
49 void swapRows(int, int);
51 GroupMap* groupmap; //maps sequences to groups they belong to.
55 GlobalData* globaldata;