X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.h;h=1f46081dd464c32e599cf1d173d1eba60df3db46;hb=e1de1a55a2a0f87bd8e2fbedc0b583aee04a4ba4;hp=9c8c6d437470588be099c656d89942ab8d78cc61;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 9c8c6d4..1f46081 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"
@@ -26,18 +26,22 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "indicator";				}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
-	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Indicator"; }
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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()); }	
 	
 private:
 	ReadTree* read;
-	TreeMap* treeMap;
+	CountTable* ct;
 	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;
@@ -45,10 +49,21 @@ 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*> >&, vector<string>&, map< vector<int>, vector<int> >);
+	vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&, vector<string>&, 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>);
+
 	
 };