removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / indicatorcommand.h

diff --git a/indicatorcommand.h b/indicatorcommand.h
index ae7499764dd7f32206ad36c01fdbd98fff3d8592..05db05c414de9e0917c68050aebc655afe3aa846 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"
@@ -22,23 +21,23 @@ 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(); 
+       
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
        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;