fixed some bugs and added scriptengine

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index cb2219fc7ec1897aa69d492f467bc0572a67354e..c7290f4d85ec4f8bd671d4df914cd2738dd3c4c0 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,27 +9,21 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "listvector.hpp"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
+#include "validcalculator.h"
 
 /* The rarefaction.shared() command:
        The rarefaction command generates a rarefaction curve from a given file representing several groups.  
        The rarefaction.shared command can only be executed after a successful read.shared command. It outputs a file for each estimator you choose to use.  
-       The rarefaction.shared command parameters are label, line, iters, jumble and sharedrarefaction.  
+       The rarefaction.shared command parameters are label, line, iters and sharedrarefaction.  
        No parameters are required, but you may not use both the line and label  parameters at the same time.  
        The rarefaction command should be in the following format: rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, 
-       jumble= yourJumble, sharedrarefaction=yourEstimators).  Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, 
-       jumble=1, sharedrarefaction =sharedobserved).  The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
+        sharedrarefaction=yourEstimators).  Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, 
+        sharedrarefaction =sharedobserved).  The default values for 
        iters is 1000 and sharedrarefaction is sharedobserved which calculates the shared rarefaction curve for the observed richness. 
         The valid sharedrarefaction estimator is sharedobserved. The label and line parameters are used to analyze specific lines in your input. */
 
@@ -39,21 +33,29 @@ class GlobalData;
 class RareFactSharedCommand : public Command {
        
 public:
-       RareFactSharedCommand();        
+       RareFactSharedCommand(string);  
        ~RareFactSharedCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
-       GroupMap* groupmap;
-       ListVector* list;
-       ReadMatrix* read;
-       SharedOrderVector* order;
+       ReadOTUFile* read;
+       vector<SharedRAbundVector*> lookup;
        InputData* input;
+       ValidCalculators* validCalculator;
        Rarefact* rCurve;
        vector<Display*> rDisplays;
        int freq, nIters;
+       string format;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label, calc, groups;
+       vector<string>  Estimators, Groups;
+
 
 };
 
-#endif
\ No newline at end of file
+#endif