added make.fastq command

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index a141988e51c90989515a5ec868319a94015a6e2d..ee16221903ce2ee738cd7b941ca90c5b57e05c04 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -21,8 +21,13 @@ 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();
        
@@ -34,13 +39,15 @@ private:
        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;
-       vector<string>  Estimators, Groups;
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
 
 };