X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=7317c8a43092a5712a06dda00589d1eb4528c649;hb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;hp=2d78d57fe827a0678421f39a44c0d2e6fe4cedf0;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 2d78d57..7317c8a 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -23,12 +23,19 @@ class GlobalData;
 class UnifracWeightedCommand : public Command {
 	
 	public:
-		UnifracWeightedCommand(string);	
-		~UnifracWeightedCommand() { delete weighted; delete util; }
+		UnifracWeightedCommand(string);
+		~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
 		int execute();	
 		void help();
 	
 	private:
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+		
 		GlobalData* globaldata;
 		SharedUtil* util;
 		FileOutput* output;
@@ -36,10 +43,9 @@ 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;
+		string sumFile, outputDir;
 		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//weighted score info for user tree
 		EstOutput randomData;		//weighted score info for random trees
@@ -48,25 +54,23 @@ class UnifracWeightedCommand : public Command {
 		vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
 		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
-		map<float, float>::iterator it2;
-		map<float, float>::iterator it;
 		
-		OptionParser* parser;
-		map<string, string> parameters;
-		map<string, string>::iterator it4;
-		bool abort;
+		bool abort, phylip, random;
 		string groups, itersString;
-		vector<string> Groups; //holds groups to be used
+		vector<string> Groups, outputNames; //holds groups to be used
+		int processors;
 
 		
-		ofstream outSum, out;
-		ifstream inFile;
+		ofstream outSum;
 		
 		void printWSummaryFile();
 		void printWeightedFile();  
+		void createPhylipFile();
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();
+		int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
+		int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
 		
 };