X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.h;h=773bdae5c1d0b71bdad01e4403d3af3702274e70;hb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;hp=9c24339d3d3745a1b2a6591af023c0fbb7ab3901;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git

diff --git a/collectcommand.h b/collectcommand.h
index 9c24339..773bdae 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -12,23 +12,23 @@
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
-//#include "groupmap.h"
+#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
 /*The collect() command:
 	The collect command generates a collector's curve from the given file.  
 	The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
 	The collect command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.  
-	The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, line, freq, single, abund.  
-	No parameters are required, but you may not use both the line and label  parameters at the same time.  
-	The collect command should be in the following format: collect(label=yourLabel, line=yourLines, freq=yourFreq, single=yourEstimators, abund=yourAbund). 
-	example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack).  
+	The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, freq, single, abund.  
+	No parameters are required.  
+	The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund). 
+	example collect(label=unique-.01-.03, freq=10, single=collect-chao-ace-jack).  
 	The default values for  freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
 	The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. 
-	The label and line parameters are used to analyze specific lines in your input. */
+	The label parameter is used to analyze specific labels in your input. */
 
 
 
@@ -37,19 +37,31 @@ class GlobalData;
 class CollectCommand : public Command {
 	
 public:
-	CollectCommand();	
+	CollectCommand(string);	
 	~CollectCommand();
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	OrderVector* order;
 	InputData* input;
 	Collect* cCurve;
 	ValidCalculators* validCalculator;
 	vector<Display*> cDisplays;
-	int freq, abund;
+	int abund, size;
+	float freq;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string label, calc, outputDir;
+	vector<string>  Estimators;
+	vector<string> inputFileNames;
+	vector<string> groups;
+	
+	vector<string> parseSharedFile(string);
+
 
 };