X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=2eee7c44e674073420c217f1b4d49aa4dc769497;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=751343b3f641d29799c8704d71f6684c04d504ac;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 751343b..2eee7c4 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -17,18 +17,30 @@
 #include "sharedutilities.h"
 #include "fileoutput.h"
 
-using namespace std;
 
 class GlobalData;
 
 class UnifracWeightedCommand : public Command {
 	
 	public:
-		UnifracWeightedCommand();	
-		~UnifracWeightedCommand() { delete weighted; delete util; }
+		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();
 	
 	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 +48,9 @@ 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 weightedFile, weightedFileout, 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
@@ -48,21 +59,25 @@ 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;
 		
-		ofstream outSum, out;
-		ifstream inFile;
+		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;
+
+		
+		ofstream outSum;
 		
 		void printWSummaryFile();
 		void printWeightedFile();  
+		void createPhylipFile();
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();
-		//void initFile(string);
-		//void output(vector<double>);
-		//void resetFile();
-
+		int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+		int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
+		
 };