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

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 327ce5d28832dbe7f25d69f6c0755f6e931c747d..d7f2f8f3d946208cee976595bf6d8113811e7094 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -12,16 +12,12 @@
 
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "sharedutilities.h"
 
-class GlobalData;
 
 class CollectSharedCommand : public Command {
        
@@ -29,34 +25,27 @@ public:
        CollectSharedCommand(string);   
        CollectSharedCommand(); 
        ~CollectSharedCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "collect.shared";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       SharedUtil* util;
-       GroupMap* groupmap;
-       SharedListVector* SharedList;
-       ReadOTUFile* read;
        SharedOrderVector* order;
        InputData* input;
-       ValidCalculators* validCalculator;
        Collect* cCurve;
        vector<Display*> cDisplays;
        float freq;
-       string format;
 
        bool abort, allLines, all;
        set<string> labels; //holds labels to be used
-       string label, calc, groups, outputDir;
+       string label, calc, groups, outputDir, sharedfile;
        vector<string>  Estimators, Groups, outputNames;
-       map<string, vector<string> > outputTypes;
-
-
 };
 
 #endif