added make.fastq command

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 2f7920e922cf8509487aa2ae7a3060075b0e90cd..ee16221903ce2ee738cd7b941ca90c5b57e05c04 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -10,48 +10,45 @@
  */
 
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
-#include "sharedutilities.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.  
-       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), 
-       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. */
-
 
 class GlobalData;
 
 class RareFactSharedCommand : public Command {
        
 public:
-       RareFactSharedCommand();        
+       RareFactSharedCommand(string);
+       RareFactSharedCommand();
        ~RareFactSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
-       SharedUtil* util;
-       SharedListVector* SharedList;
-       ReadMatrix* read;
-       SharedOrderVector* order;
+       ReadOTUFile* read;
+       vector<SharedRAbundVector*> lookup;
        InputData* input;
        ValidCalculators* validCalculator;
        Rarefact* rCurve;
        vector<Display*> rDisplays;
-       int freq, nIters;
+       int nIters;
        string format;
+       float freq;
+       
+       bool abort, allLines, jumble;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+
 
 };