X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=7da0b2f9f5301d80302d97f7da23d1cd8fee12c1;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=dce1a0d4862190c01bb2082f8506d3a505bad899;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index dce1a0d..7da0b2f 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -23,8 +23,13 @@ class GlobalData;
 class RareFactCommand : public Command {
 	
 public:
-	RareFactCommand(string);	
+	RareFactCommand(string);
+	RareFactCommand();	
 	~RareFactCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();	
 	
@@ -36,14 +41,16 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	Rarefact* rCurve;
-	int freq, nIters, abund;
-
+	int nIters, abund, processors;
+	float freq;
+	
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string label, calc;
 	vector<string>  Estimators;
-	vector<string> inputFileNames;
+	vector<string> inputFileNames, outputNames;
 	vector<string> groups;
+	map<string, vector<string> > outputTypes;
 	string outputDir;
 	
 	vector<string> parseSharedFile(string);