X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=2eee7c44e674073420c217f1b4d49aa4dc769497;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=b6aea7dad9215a131691019445c2f911c77084a4;hpb=f099fdc1e3a0d7b75d780a164e5bdb93496a7a1d;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index b6aea7d..2eee7c4 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -24,7 +24,12 @@ class UnifracWeightedCommand : public Command {
 	
 	public:
 		UnifracWeightedCommand(string);
+		UnifracWeightedCommand();
 		~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
 		int execute();	
 		void help();
 	
@@ -34,7 +39,7 @@ class UnifracWeightedCommand : public Command {
 			int num;
 			linePair(int i, int j) : start(i), num(j) {}
 		};
-		vector<linePair*> lines;
+		vector<linePair> lines;
 		
 		GlobalData* globaldata;
 		SharedUtil* util;
@@ -43,7 +48,6 @@ class UnifracWeightedCommand : public Command {
 		vector<double> utreeScores;  //user tree unweighted scores
 		vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
 		vector<string> groupComb; // AB. AC, BC...
-		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
 		string sumFile, outputDir;
@@ -56,9 +60,10 @@ class UnifracWeightedCommand : public Command {
 		vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c								
 		map<float, float>  validScores;  //map contains scores from random
 		
-		bool abort, phylip, random;
-		string groups, itersString;
+		bool abort, phylip, random, includeRoot;
+		string groups, itersString, outputForm;
 		vector<string> Groups, outputNames; //holds groups to be used
+		map<string, vector<string> > outputTypes;
 		int processors;
 
 		
@@ -70,8 +75,8 @@ class UnifracWeightedCommand : public Command {
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();
-		int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-		int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+		int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+		int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
 		
 };