X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.h;h=3c24dfb843e770567a1486436536b97fabfe12b5;hb=cc19310422f125d6628980bd1148e1e816792382;hp=aa3156298a1a729f416bb793e60b7739c39843d1;hpb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
index aa31562..3c24dfb 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -12,7 +12,7 @@
 
 #include "command.hpp"
 #include "readtree.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
@@ -26,6 +26,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "indicator";				}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
 	string getDescription()		{ return "calculate the indicator value for each OTU"; }
@@ -35,11 +36,11 @@ public:
 	
 private:
 	ReadTree* read;
-	TreeMap* treeMap;
+	CountTable* ct;
 	GroupMap* designMap;
 	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
 	bool abort;
-	int iters;
+	int iters, processors;
 	vector<string> outputNames, Groups;
 	vector<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;
@@ -54,6 +55,11 @@ private:
 	map<int, float> getDistToRoot(Tree*&);
 	map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundVector*> >&, int);
 	map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >&, int);
+	vector<float> driver(vector< vector<SharedRAbundFloatVector*> >&, map< vector<int>, vector<int> >, int, vector<float>, int);
+	vector<float> driver(vector< vector<SharedRAbundVector*> >&, map< vector<int>, vector<int> >, int, vector<float>, int);
+	vector<float> getPValues(vector< vector<SharedRAbundFloatVector*> >&, map< vector<int>, vector<int> >, int, vector<float>);
+	vector<float> getPValues(vector< vector<SharedRAbundVector*> >&, map< vector<int>, vector<int> >, int, vector<float>);
+
 	
 };