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

[mothur.git] / metastatscommand.h

diff --git a/metastatscommand.h b/metastatscommand.h
index 8c633b5417cbe07dc96827cf80c8e0b5522c0fad..1380444dc25e4b0ade5afc240acb2c942b6abd57 100644 (file)
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -12,23 +12,22 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class MetaStatsCommand : public Command {
 
 public:
        MetaStatsCommand(string);
        MetaStatsCommand();
-       ~MetaStatsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~MetaStatsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "metastats";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        struct linePair {
@@ -38,16 +37,13 @@ private:
        };
        vector<linePair> lines;
        
-       GlobalData* globaldata;
        GroupMap* designMap;
-       ReadOTUFile* read;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
-       map<string, vector<string> > outputTypes;
-       
+               
        bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
-       string groups, label, outputDir, inputDir, designfile, sets;
+       string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
        vector<string> Groups, outputNames, Sets;
        vector< vector<string> > namesOfGroupCombos;
        int iters, processors;