X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.h;h=2c36c35f6f3025bb3f07760055512b2e0e257914;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=05db05c414de9e0917c68050aebc655afe3aa846;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 05db05c..2c36c35 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -26,8 +26,11 @@ 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"; }
+
 	int execute();
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -37,6 +40,7 @@ private:
 	GroupMap* designMap;
 	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
 	bool abort;
+	int iters, processors;
 	vector<string> outputNames, Groups;
 	vector<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;
@@ -44,10 +48,18 @@ private:
 	int getShared();
 	int getSharedFloat();
 	int GetIndicatorSpecies(Tree*&);
+	int GetIndicatorSpecies();
 	set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
-	vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
-	vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
+	vector<float> getValues(vector< vector<SharedRAbundVector*> >&, map< vector<int>, vector<int> >);
+	vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&, map< vector<int>, vector<int> >);
 	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>);
+
 	
 };