added modify names parameter to set.dir

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 3737c11196c48cd7fba5179ee311264f22b0e6ba..868cd473b29cb97ba5ee38f847aab8343e06c3ac 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -9,52 +9,47 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
-
-/* The collect.shared() command:
-       The collect command generates a collector's curve from the given file representing several groups.  
-       The collect.shared command can only be executed after a successful read.shared command. 
-       It outputs a file for each estimator you choose to use.  The collect.shared command parameters are label, line, freq, jumble and shared.  
-       No parameters are required, but you may not use both the line and label parameters at the same time. 
-       The collect.shared command should be in the following format: collect.shared(label=yourLabel, line=yourLines, 
-       freq=yourFreq,  jumble=yourJumble, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, 
-       shared=sharedChao-sharedAce-sharedJabund). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
-       freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-       The valid shared estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-       The label and line parameters are used to analyze specific lines in your input. */
+#include "validcalculator.h"
+#include "sharedutilities.h"
 
 
-class GlobalData;
-
 class CollectSharedCommand : public Command {
        
 public:
+       CollectSharedCommand(string);   
        CollectSharedCommand(); 
        ~CollectSharedCommand();
-       int execute();  
+       
+       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;
-       GroupMap* groupmap;
-       SharedListVector* SharedList;
-       ReadMatrix* read;
        SharedOrderVector* order;
        InputData* input;
        Collect* cCurve;
        vector<Display*> cDisplays;
-       int freq;
+       float freq;
 
+       bool abort, allLines, all;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups, outputDir, sharedfile;
+       vector<string>  Estimators, Groups, outputNames;
 };
 
-#endif
\ No newline at end of file
+#endif