added modify names parameter to set.dir

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index b7a494149249af486c2a8cb812b00316a42b241f..868cd473b29cb97ba5ee38f847aab8343e06c3ac 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -12,45 +12,44 @@
 
 #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 {
        
 public:
        CollectSharedCommand(string);   
+       CollectSharedCommand(); 
        ~CollectSharedCommand();
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "collect.shared";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
+       string getDescription()         { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+       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;
-
-
 };
 
 #endif