*
*/
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
#include "command.hpp"
#include "parsimony.h"
#include "treemap.h"
GlobalData* globaldata;
vector<Tree*> T; //user trees
Tree* randT; //random tree
+ Tree* copyUserTree;
TreeMap* tmap;
TreeMap* savetmap;
Parsimony* pars;
- string parsFile, sumFile, distFile, randomtree;
+ string parsFile, sumFile, randomtree;
int iters, numGroups;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector<float> userTreeScores; //scores for users trees
map<int, float>::iterator it;
map<int, float>::iterator it2;
- ofstream out, outSum, outDist;
+ ofstream out, outSum;
void printParsimonyFile();
void printUSummaryFile();
void getUserInput();
+ void setGroups();
};