X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=6ec35412c3c82206bef933787c820ca36e2158d2;hb=29c0d3ec01be5372807eb86261100d77de253787;hp=a21167e3d07e2064c6e9a1dae736b0b1aeccf3a8;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index a21167e..6ec3541 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -14,7 +14,6 @@
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
-#include "parselistcommand.h"
 
 /* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single, 
 collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund 
@@ -33,18 +32,23 @@ class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-	ReadOtuCommand();
+	ReadOtuCommand(string);
 	~ReadOtuCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadOTUFile* 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