X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=cd46b62b3462a4db2baa57865743d4bb37c198a7;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=3c031c66c1da524e5b7f3177cfca7d0743573a7a;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 3c031c6..cd46b62 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -23,7 +23,12 @@ class UnifracUnweightedCommand : public Command {
 	
 	public:
 		UnifracUnweightedCommand(string);	
-		~UnifracUnweightedCommand() { delete unweighted; delete util; }
+		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();	
 	
@@ -36,7 +41,7 @@ class UnifracUnweightedCommand : public Command {
 		Unweighted* unweighted;
 		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.
@@ -44,25 +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;
 		
-		OptionParser* parser;
-		map<string, string> parameters;
-		map<string, string>::iterator it4;
-		bool abort;
-		string groups, itersString;
-		vector<string> Groups; //holds groups to be used
+		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(int);
 		void printUnweightedFile();
+		void createPhylipFile(int);
 		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif