X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.h;h=10894e7218b5d2d607f2c0fa931f7c10a0f6146d;hb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63;hp=b92b35034466d1dd61f29a04d478d620c8bc4ef2;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/collectcommand.h b/collectcommand.h
index b92b350..10894e7 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,28 +9,26 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.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.  
-	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). 
-	example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack).  
-	The default values for  freq is 100, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
+	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. */
 
 
 
@@ -39,18 +37,26 @@ 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;
+	int freq, abund, size;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string label, calc;
+	vector<string>  Estimators;
+
 
 };