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"
28 FullMatrix(ifstream&);
32 vector<int> getSizes();
33 vector<string> getGroups();
35 void printMatrix(ostream&);
39 vector< vector<float> > matrix; //a 2D distance matrix of all the sequences and their distances to eachother.
40 void readSquareMatrix(ifstream&);
41 void readLTMatrix(ifstream&);
42 vector<Names> index; // row in vector, sequence group. need to know this so when we sort it can be updated.
44 vector<string> groups;
45 void sortGroups(int, int); //this function sorts the sequences within the matrix.
48 GroupMap* groupmap; //maps sequences to groups they belong to.
52 GlobalData* globaldata;