X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.h;h=7f7ad893b74140087248edfd7deb7b8c3441e671;hp=04acd302891f36df23399ac9d9b1694535c7005e;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 04acd30..7f7ad89 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -11,40 +11,42 @@
 
 #include "command.hpp"
 #include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
+#include "readtree.h"
 
 
-class GlobalData;
-
 class ParsimonyCommand : public Command {
 
 public:
 	ParsimonyCommand(string);	
 	ParsimonyCommand();
-	~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; }  }
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~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:
-	GlobalData* globaldata;
-	SharedUtil* util;
 	FileOutput* output;
 	vector<Tree*> T;	   //user trees
 	Tree* randT;  //random tree
 	Tree* copyUserTree; 
-	TreeMap* tmap; 
-	TreeMap* savetmap;
-	Parsimony* pars;
+	CountTable* ct; 
+	CountTable* savect;
 	vector<string> groupComb; // AB. AC, BC...
-	string sumFile, randomtree, allGroups, outputDir;
-	int iters, numGroups, numComp, counter;
+	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.
@@ -57,16 +59,15 @@ private:
 	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, vector<string> > outputTypes;
-
+	map<string, string> nameMap;
+	
 	void printParsimonyFile();  
 	int printUSummaryFile();
 	void getUserInput();
+	int readNamesFile();
 	
 };