X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=indicatorcommand.h;h=1f46081dd464c32e599cf1d173d1eba60df3db46;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hp=0d924fd1ff0a1a17cfa51b6faa5de55dcd3bf186;hpb=8173238f9f94af9baab8471de58bed7c8830948d;p=mothur.git

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 0d924fd..1f46081 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -12,8 +12,7 @@
 
 #include "command.hpp"
 #include "readtree.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 #include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
@@ -22,32 +21,49 @@ class IndicatorCommand : public Command {
 public:
 	IndicatorCommand(string);
 	IndicatorCommand();
-	~IndicatorCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~IndicatorCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "indicator";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	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();
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	ReadTree* read;
-	TreeMap* treeMap;
-	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
-	bool abort, pickedGroups;
+	CountTable* ct;
+	GroupMap* designMap;
+	string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
+	bool abort;
+	int iters, processors;
 	vector<string> outputNames, Groups;
-	map<string, vector<string> > outputTypes;
 	vector<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;
 	
 	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*> >&);
-	map<int, float> getLengthToLeaf(Tree*&);
+	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>);
+
 	
 };