X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=7da0b2f9f5301d80302d97f7da23d1cd8fee12c1;hb=f598bd8389840cf030d61f5da7d0b2c3e37c06ba;hp=28be17cf995f18ede3f851579b619862d0c82551;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 28be17c..7da0b2f 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -14,42 +14,48 @@
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
 
-/*The rarefaction() command:
-	The rarefaction command generates a rarefaction curve from a given file.  
-	The rarefaction command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
-	The rarefaction command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster. 
-	The rarefaction command outputs a file for each estimator you choose to use.  It is recommended to only use rarefaction estimator.  
-	The rarefaction command parameters are label, line, iters, freq, rarefaction.  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(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators). 
-	Example rarefaction(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson). 
-	The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness. 
-	The valid rarefaction estimators are: rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson.  
-	Rarefaction is the only recommended estimator.  The label and line parameters are used to analyze specific lines in your input. */
-	
-
 class GlobalData;
 
 class RareFactCommand : public Command {
 	
 public:
+	RareFactCommand(string);
 	RareFactCommand();	
 	~RareFactCommand();
-	int execute();	
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
 	
 private:
 	GlobalData* globaldata;
 	vector<Display*> rDisplays;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	OrderVector* order;
 	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, outputNames;
+	vector<string> groups;
+	map<string, vector<string> > outputTypes;
+	string outputDir;
+	
+	vector<string> parseSharedFile(string);
+
+
 };
 
 #endif