X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=7da0b2f9f5301d80302d97f7da23d1cd8fee12c1;hb=995238e9aa4455e3b59053e3dfe497b89caed79e;hp=1bcb0cf490dda8358a6ba55f042e689abc51bf69;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 1bcb0cf..7da0b2f 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -18,27 +18,18 @@
 #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(string);
+	RareFactCommand();	
 	~RareFactCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();	
 	
@@ -50,13 +41,20 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	Rarefact* rCurve;
-	int freq, nIters, abund;
-
+	int nIters, abund, processors;
+	float freq;
+	
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string line, label, calc;
+	string label, calc;
 	vector<string>  Estimators;
+	vector<string> inputFileNames, outputNames;
+	vector<string> groups;
+	map<string, vector<string> > outputTypes;
+	string outputDir;
+	
+	vector<string> parseSharedFile(string);
+
 
 };