#include "command.hpp"
#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, sumFile, randomtree;
- int iters, numGroups, numComp;
+ 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.
vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
EstOutput userData; //pscore info for user tree
EstOutput randomData; //pscore info for random trees
- vector< map<int, double> > validScores; //map contains scores from both user and random
+ map<int, double> validScores; //map contains scores from both user and random
vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
map<int, double>::iterator it2;
ofstream out, outSum;
+ ifstream inFile;
void printParsimonyFile();
void printUSummaryFile();
void getUserInput();
- void setGroups();
};