X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=eb0ca8f7832e5f1877a172fa0449a3ae29e5416f;hb=09ce41fb228c00d0f49896c66b2f2c5760914769;hp=a21167e3d07e2064c6e9a1dae736b0b1aeccf3a8;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index a21167e..eb0ca8f 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -14,37 +14,33 @@
 #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 
-upon completion of the cluster command or you may use your own. The read.otu command parameter options are 
-listfile, rabundfile, sabundfile, groupfile and orderfile. The reaad.otu command can be used in two ways. 
-The first is to read a listfile, rabundfile or sabundfile and run the collect.single, rarefaction.single or summary.single. 
-For this use the read.otu command should be in the following format: read.otu(listfile=yourListFile, orderfile=yourOrderFile). 
-The listfile, rabundfile or sabundfile parameter is required, but you may only use one of them. 
-The second way to use the read.otu command is to read a listfile and a groupfile so you can use the collect.shared, 
-rarefaction.shared or summary.shared commands. In this case the read.otu command should be in the following format: 
-read.otu(listfile=yourListFile, groupfile=yourGroupFile). The listfile parameter and groupfile paramaters are required. 
-When using the command the second way read.otu command parses the .list file and separates it into groups. 
-It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. */
 
 class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
+	ReadOtuCommand(string);
 	ReadOtuCommand();
 	~ReadOtuCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadOTUFile* read;
 	InputData* input;
 	Command* shared;
-	Command* parselist;
 	GroupMap* groupMap;
-	string filename;
+	string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+	vector<string> Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+
 };
 
 #endif