X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=cd46b62b3462a4db2baa57865743d4bb37c198a7;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=3c250db030b04740e59df7ce24ba6b2752dc2023;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 3c250db..cd46b62 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,27 +13,35 @@
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 
-using namespace std;
-
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; }
-		int execute();	
+		UnifracUnweightedCommand(string);	
+		UnifracUnweightedCommand();
+		~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
+		int execute();
+		void help();	
 	
 	private:
 		GlobalData* globaldata;
+		SharedUtil* util;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
 		TreeMap* tmap;
 		Unweighted* unweighted;
-		string sumFile, unweightedFile, unweightedFileout;
+		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp, counter;
+		int iters, numGroups, numComp, counter, processors;
 		EstOutput userData;			//unweighted score info for user tree
 		EstOutput randomData;		//unweighted score info for random trees
 		vector< vector<float> > utreeScores; //scores for users trees for each comb.
@@ -41,22 +49,20 @@ class UnifracUnweightedCommand : public Command {
 		map<float, float>  validScores;  //map contains scores from random
 		vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
 		vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
-		map<float, float>::iterator it2;
-		map<float, float>::iterator it;
 		
+		bool abort, phylip, random, includeRoot;
+		string groups, itersString, outputDir, outputForm;
+		vector<string> Groups, outputNames; //holds groups to be used
+		map<string, vector<string> > outputTypes;
+
 		ofstream outSum, out;
 		ifstream inFile;
 		
-		void printUWSummaryFile();
+		void printUWSummaryFile(int);
 		void printUnweightedFile();
-		void setGroups();  
-		void initFile(string);
-		void output(vector<double>);
-		void resetFile();
- 
+		void createPhylipFile(int);
+		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif