X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=e07dadc1713989455a7fa1f35b6cdaa6767abf6c;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=f00369ba8f4116db8d8e5dee015f60fa52f2a432;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index f00369b..e07dadc 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,10 +9,8 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
@@ -35,18 +33,24 @@ class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-	ReadOtuCommand();
+	ReadOtuCommand(string);
 	~ReadOtuCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	//ReadOTUFile* read;
 	InputData* input;
 	Command* shared;
 	Command* parselist;
 	GroupMap* groupMap;
-	string filename;
+	string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+
+	bool abort, allLines;
+	set<int> lines; //hold lines to be used
+	set<string> labels; //holds labels to be used
+
 };
 
 #endif