X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=26d392e86acd94654ec3a5ec6351770e4efb995f;hb=51cf89e90eef8b300c2786eb1560dd89e6e83445;hp=5429e77acf8411bd3836e3cc6fa3b1a23db24a5a;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 5429e77..26d392e 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -9,14 +9,12 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "parsimony.h"
 #include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 using namespace std;
 
@@ -26,31 +24,37 @@ class ParsimonyCommand : public Command {
 	
 	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
-		TreeMap* tmap;
+		Tree* copyUserTree; 
+		TreeMap* tmap; 
+		TreeMap* savetmap;
 		Parsimony* pars;
-		string parsFile, sumFile, distFile;
-		int iters, randomtree, numGroups;
+		vector<string> groupComb; // AB. AC, BC...
+		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<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();