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