added make.fastq command

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index d81ff6dc2d1c6588d86f9cccbb0251778bd85011..ee16221903ce2ee738cd7b941ca90c5b57e05c04 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -16,25 +16,18 @@
 #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 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, 
-        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. */
-
-
 class GlobalData;
 
 class RareFactSharedCommand : public Command {
        
 public:
-       RareFactSharedCommand(string);  
+       RareFactSharedCommand(string);
+       RareFactSharedCommand();
        ~RareFactSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -46,16 +39,15 @@ private:
        ValidCalculators* validCalculator;
        Rarefact* rCurve;
        vector<Display*> rDisplays;
-       int freq, nIters;
+       int nIters;
        string format;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort, allLines;
-       set<int> lines; //hold lines to be used
+       float freq;
+       
+       bool abort, allLines, jumble;
        set<string> labels; //holds labels to be used
-       string line, label, calc, groups;
-       vector<string>  Estimators, Groups;
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
 
 };