TreeMap* savetmap;
Parsimony* pars;
vector<string> groupComb; // AB. AC, BC...
- string sumFile, randomtree, allGroups;
+ string sumFile, randomtree, allGroups, outputDir;
int iters, numGroups, numComp, counter;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector< vector<float> > userTreeScores; //scores for users trees for each comb.
bool abort;
string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ vector<string> Groups, outputNames; //holds groups to be used
void printParsimonyFile();
- void printUSummaryFile();
+ int printUSummaryFile();
void getUserInput();
};