X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.h;h=b7a494149249af486c2a8cb812b00316a42b241f;hb=44b464979e91c2a1f144ac45ca12c14fcf6579f0;hp=6e9d5cc3f498c96574d93321ecf2823edb0fa004;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 6e9d5cc..b7a4941 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -17,44 +17,40 @@
 #include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
-
-/* The collect.shared() command:
-	The collect command generates a collector's curve from the given file representing several groups.  
-	The collect.shared command can only be executed after a successful read.shared command. 
-	It outputs a file for each estimator you choose to use.  The collect.shared command parameters are label, line, freq, jumble and shared.  
-	No parameters are required, but you may not use both the line and label parameters at the same time. 
-	The collect.shared command should be in the following format: collect.shared(label=yourLabel, line=yourLines, 
-	freq=yourFreq,  jumble=yourJumble, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, 
-	shared=sharedChao-sharedAce-sharedJabund). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
-	freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-	The valid shared estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-	The label and line parameters are used to analyze specific lines in your input. */
-
+#include "sharedutilities.h"
 
 class GlobalData;
 
 class CollectSharedCommand : public Command {
 	
 public:
-	CollectSharedCommand();	
+	CollectSharedCommand(string);	
 	~CollectSharedCommand();
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
+	SharedUtil* util;
 	GroupMap* groupmap;
 	SharedListVector* SharedList;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	SharedOrderVector* order;
 	InputData* input;
 	ValidCalculators* validCalculator;
 	Collect* cCurve;
 	vector<Display*> cDisplays;
-	int freq;
+	float freq;
 	string format;
 
+	bool abort, allLines, all;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups, outputDir;
+	vector<string>  Estimators, Groups, outputNames;
+
+
 };
 
 #endif