X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=917255696166a505ae5734e20f0aaab47573876c;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=5e5484f4687474886730e437ea3d44d6aced3ccb;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 5e5484f..9172556 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -30,20 +30,18 @@ public:
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
 	string getHelpString();	
 	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:
-	ReadTree* read;
-	SharedUtil* util;
 	FileOutput* output;
 	vector<Tree*> T;	   //user trees
 	Tree* randT;  //random tree
 	Tree* copyUserTree; 
 	TreeMap* tmap; 
 	TreeMap* savetmap;
-	Parsimony* pars;
 	vector<string> groupComb; // AB. AC, BC...
 	string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
 	int iters, numGroups, numComp, counter, processors, numUniquesInName;