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[mothur.git] / indicatorcommand.h

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+#ifndef INDICATORCOMMAND_H
+#define INDICATORCOMMAND_H
+
+/*
+ *  indicatorcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "readtree.h"
+#include "treemap.h"
+#include "sharedrabundvector.h"
+#include "sharedrabundfloatvector.h"
+#include "inputdata.h"
+
+class IndicatorCommand : public Command {
+public:
+       IndicatorCommand(string);
+       IndicatorCommand();
+       ~IndicatorCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "indicator";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       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()); }  
+       
+private:
+       ReadTree* read;
+       TreeMap* treeMap;
+       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;
+       
+       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*> >&, 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>);
+
+       
+};
+
+
+#endif
+