*
*/
-#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;
- int iters, numGroups;
+ vector<string> groupComb; // AB. AC, BC...
+ string parsFile, parsFileout, sumFile, randomtree;
+ int iters, numGroups, numComp, counter;
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
- vector<float> UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ 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
- map<int, float> validScores; //contains scores from both user and random
- map<int, float> rscoreFreq; //pscore, number of random trees with that score.
- map<int, float> uscoreFreq; //pscore, number of user trees with that score.
- map<int, float> rCumul; //pscore, cumulative percentage of number of random trees with that score or lower.
- map<int, float> uCumul; //pscore, cumulative percentage of number of user trees with that score or lower .
- map<int, float>::iterator it;
- map<int, float>::iterator it2;
+ 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.
+ vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+ map<int, double>::iterator it;
+ map<int, double>::iterator it2;
- ofstream out, outSum, outDist;
+ ofstream out, outSum;
+ ifstream inFile;
void printParsimonyFile();
void printUSummaryFile();
void getUserInput();
+ void setGroups();
+ void initFile(string);
+ void output(vector<double>);
+ void resetFile();
+
};