X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=unifracunweightedcommand.h;h=3961e53cb68c96e70dd5bcd55449ed5d72346cd9;hp=ecf78f58a981e1f95602ed4e10973bcf7695cf14;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=fb5a52d8d7896ba00c9ccc6add22ed89c5fb2ad7

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index ecf78f5..3961e53 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -10,55 +10,61 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "unweighted.h"
-#include "treemap.h"
-
-using namespace std;
-
-class GlobalData;
+#include "counttable.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; }
-		int execute();	
+		UnifracUnweightedCommand(string);	
+		UnifracUnweightedCommand();
+		~UnifracUnweightedCommand() {}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "unifrac.unweighted";		}
+		string getCommandCategory()		{ return "Hypothesis Testing";		}
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
+		string getDescription()		{ return "generic tests that describes whether two or more communities have the same structure"; }
+
+		int execute();
+		void help() { m->mothurOut(getHelpString()); }
+	
 	
 	private:
-		GlobalData* globaldata;
+		FileOutput* output;
 		vector<Tree*> T;	   //user trees
-		vector<float> utreeScores;  //user tree unweighted scores
-		vector<float> UWScoreSig;  //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
-		Tree* randT;  //random tree
-		TreeMap* tmap;
-		Unweighted* unweighted;
-		string sumFile, distFile, unweightedFile;
-		int iters;
-		EstOutput userData;			//unweighted score info for user tree
-		EstOutput randomData;		//unweighted score info for random trees
-		map<float, float> validScores;  //contains scores from both user and random
-		map<float, float> rscoreFreq;  //unweighted score, number of random trees with that score.
-		map<float, float> uscoreFreq;  //unweighted, number of user trees with that score.
-		map<float, float> totalrscoreFreq;  //unweighted score, number of random trees with that score.
-		map<float, float> rCumul;		//unweighted score, cumulative percentage of number of random trees with that score or higher.
-		map<float, float> uCumul;  //unweighted, cumulative percentage of number of user trees with that score or higher .
-		map<float, float>::iterator it;
-		map<float, float>::iterator it2;
+		CountTable* ct;
+		string sumFile, allGroups;
+		vector<string> groupComb; // AB. AC, BC...
+		int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
+		vector< vector<float> > utreeScores; //scores for users trees for each comb.
+		vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
+		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.
 		
-		ofstream outSum, outDist, out;
+		bool abort, phylip, random, includeRoot, consensus, subsample;
+		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
+		vector<string> Groups, outputNames; //holds groups to be used
+
+		ofstream outSum, out;
+		ifstream inFile;
 		
-		void printUWSummaryFile();
+        int runRandomCalcs(Tree*, vector<double>);
+		void printUWSummaryFile(int);
 		void printUnweightedFile();
-		void saveRandomScores();    
+		void createPhylipFile(int);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif