X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.h;h=b099c8a44390ef361019de2e12dff6af71f1dc73;hb=4c8e0f463a145681fab553c7d46f3de8570586b3;hp=64362ef61cdfdc18da9cb5b170a88ff9713d93c9;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/collectcommand.h b/collectcommand.h
index 64362ef..b099c8a 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,16 +9,13 @@
  *
  */
 
-#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:
@@ -40,19 +37,27 @@ 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 freq, abund, size;
+
+	bool abort, allLines;
+	set<int> lines; //hold lines to be used
+	set<string> labels; //holds labels to be used
+	string line, label, calc;
+	vector<string>  Estimators;
+
 
 };