added chimera.uchime

[mothur.git] / indicatorcommand.h

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 0ec100aecba915fb304e72146d06cbe2376ce8aa..578aa95cbd6ebd773e6595c875ef487fe4a6861b 100644 (file)
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -13,7 +13,6 @@
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
-#include "globaldata.hpp"
 #include "sharedrabundvector.h"
 #include "sharedrabundfloatvector.h"
 #include "inputdata.h"
@@ -22,22 +21,24 @@ 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 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"; }
+       
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
-       string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
+       GroupMap* designMap;
+       string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
        bool abort;
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        vector<SharedRAbundVector*> lookup;
        vector<SharedRAbundFloatVector*> lookupFloat;