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

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 077181220a836f6b118f68008996b411f81822fa..3d177e7a71967225011f6077a6597b4ac3b2486c 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,23 +14,23 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class SummarySharedCommand : public Command {
 
 public:
        SummarySharedCommand(string);
        SummarySharedCommand();
-       ~SummarySharedCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SummarySharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.shared";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        struct linePair {
@@ -38,17 +38,13 @@ private:
                int end;
        };
        vector<linePair> lines;
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
-       ValidCalculators* validCalculator;
        
        bool abort, allLines, mult, all, createPhylip;
        set<string> labels; //holds labels to be used
-       string label, calc, groups;
+       string label, calc, groups, sharedfile;
        vector<string>  Estimators, Groups, outputNames;
-       map<string, vector<string> > outputTypes;
        vector<SharedRAbundVector*> lookup;
        string format, outputDir;
        int numGroups, processors;