X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.h;h=7f7ad893b74140087248edfd7deb7b8c3441e671;hp=274cac4e94f46b51aca95695f9fc4d7a4ba9c981;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 274cac4..7f7ad89 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -11,7 +11,7 @@
 
 #include "command.hpp"
 #include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
@@ -28,23 +28,24 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "parsimony";				}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
-	string getHelpString();	
 	
+	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:
-	ReadTree* read;
-	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, treefile, groupfile, namefile;
+	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.