X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.h;h=7f7ad893b74140087248edfd7deb7b8c3441e671;hp=5429e77acf8411bd3836e3cc6fa3b1a23db24a5a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=d037597badc8d18e235c59f0c1114180edb7f98f

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 5429e77..7f7ad89 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -9,53 +9,66 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #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(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "parsimony";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	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;
 	
-	public:
-		ParsimonyCommand();	
-		~ParsimonyCommand() { delete pars; }
-		int execute();	
+	void printParsimonyFile();  
+	int printUSummaryFile();
+	void getUserInput();
+	int readNamesFile();
 	
-	private:
-		GlobalData* globaldata;
-		vector<Tree*> T;	   //user trees
-		Tree* randT;  //random tree
-		TreeMap* tmap;
-		Parsimony* pars;
-		string parsFile, sumFile, distFile;
-		int iters, randomtree, numGroups;
-		vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
-		vector<float> userTreeScores; //scores for users trees
-		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, float> validScores;  //contains scores from both user and random
-		map<int, float> rscoreFreq;  //pscore, number of random trees with that score.
-		map<int, float> uscoreFreq;  //pscore, number of user trees with that score.
-		map<int, float> rCumul;  //pscore, cumulative percentage of number of random trees with that score or lower.
-		map<int, float> uCumul;  //pscore, cumulative percentage of number of user trees with that score or lower .
-		map<int, float>::iterator it;
-		map<int, float>::iterator it2;
-		
-		ofstream out, outSum, outDist;
-		
-		void printParsimonyFile();  
-		void printUSummaryFile();
-		void getUserInput();
-		
 };