X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=79613f560746e443697e4e92bfed755605a6fe4a;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=30c8332c8285466c7571c4ca275977e47f3469fe;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 30c8332..79613f5 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -28,22 +28,21 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "parsimony";				}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Parsimony"; }
-	
+	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;