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

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index d225109359d4950ad88be6a1ff41dd49cf062251..5535237c98f97d32cacf3f967cb2501199a76473 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -13,39 +13,34 @@
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class SummaryCommand : public Command {
 
 public:
        SummaryCommand(string);
        SummaryCommand();
-       ~SummaryCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SummaryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.single";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
-       ValidCalculators* validCalculator;
        SAbundVector* sabund;
        int abund, size;
 
        bool abort, allLines, groupMode;
        set<string> labels; //holds labels to be used
-       string label, calc, outputDir;
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
        vector<string> inputFileNames, outputNames;
-       map<string, vector<string> > outputTypes;
        vector<string> groups;
        
        vector<string> parseSharedFile(string);