X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.h;h=7f7ad893b74140087248edfd7deb7b8c3441e671;hp=e093ceb2de8efbbacf2d58e4d46257563b0797c3;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb

diff --git a/parsimonycommand.h b/parsimonycommand.h
index e093ceb..7f7ad89 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -11,56 +11,64 @@
 
 #include "command.hpp"
 #include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
 
-using namespace std;
-
-class GlobalData;
 
 class ParsimonyCommand : public Command {
+
+public:
+	ParsimonyCommand(string);	
+	ParsimonyCommand();
+	~ParsimonyCommand(){}
 	
-	public:
-		ParsimonyCommand();	
-		~ParsimonyCommand() { delete pars; }
-		int execute();	
+	vector<string> setParameters();
+	string getCommandName()			{ return "parsimony";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
 	
-	private:
-		GlobalData* globaldata;
-		vector<Tree*> T;	   //user trees
-		Tree* randT;  //random tree
-		Tree* copyUserTree; 
-		TreeMap* tmap; 
-		TreeMap* savetmap;
-		Parsimony* pars;
-		vector<string> groupComb; // AB. AC, BC...
-		string parsFile, parsFileout, sumFile, randomtree;
-		int iters, numGroups, numComp, counter;
-		vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
-		vector< vector<float> > userTreeScores; //scores for users trees for each comb.
-		vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
-		EstOutput userData;			//pscore info for user tree
-		EstOutput randomData;		//pscore info for random trees
-		map<int, double>  validScores;  //map contains scores from both user and random
-		vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
-		vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
-		vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
-		vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
-		map<int, double>::iterator it;
-		map<int, double>::iterator it2;
-		
-		ofstream out, outSum;
-		ifstream inFile;
-		
-		void printParsimonyFile();  
-		void printUSummaryFile();
-		void getUserInput();
-		void setGroups();
-		void initFile(string);
-		void output(vector<double>);
-		void resetFile();
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
+	string getDescription()		{ return "generic test that describes whether two or more communities have the same structure"; }
 
-		
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
+	
+private:
+	FileOutput* output;
+	vector<Tree*> T;	   //user trees
+	Tree* randT;  //random tree
+	Tree* copyUserTree; 
+	CountTable* ct; 
+	CountTable* savect;
+	vector<string> groupComb; // AB. AC, BC...
+	string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile, countfile;
+	int iters, numGroups, numComp, counter, processors, numUniquesInName;
+	vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
+	vector< vector<float> > userTreeScores; //scores for users trees for each comb.
+	vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+	EstOutput userData;			//pscore info for user tree
+	EstOutput randomData;		//pscore info for random trees
+	map<int, double>  validScores;  //map contains scores from both user and random
+	vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
+	vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
+	vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
+	vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+	
+	ofstream outSum;
+	bool abort;
+	string groups, itersString;
+	vector<string> Groups, outputNames; //holds groups to be used
+	map<string, string> nameMap;
+	
+	void printParsimonyFile();  
+	int printUSummaryFile();
+	void getUserInput();
+	int readNamesFile();
+	
 };