#include "parsimony.h"
#include "treemap.h"
#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
-using namespace std;
class GlobalData;
public:
ParsimonyCommand();
- ~ParsimonyCommand() { delete pars; }
+ ~ParsimonyCommand() { delete pars; delete util; delete output; }
int execute();
private:
GlobalData* globaldata;
+ SharedUtil* util;
+ FileOutput* output;
vector<Tree*> T; //user trees
Tree* randT; //random tree
Tree* copyUserTree;
TreeMap* savetmap;
Parsimony* pars;
vector<string> groupComb; // AB. AC, BC...
- string parsFile, parsFileout, sumFile, randomtree;
+ string sumFile, randomtree, allGroups;
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.
void printParsimonyFile();
void printUSummaryFile();
void getUserInput();
- void setGroups();
- void initFile(string);
- void output(vector<double>);
- void resetFile();
-
};