X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=c6d65037516c495f391ceb983273b1b9a20010e1;hb=e339f9008daa7d37c9a9034829565620a6abe783;hp=586e6ef36e5ca3ab015db96b493c191612a9330a;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index 586e6ef..c6d6503 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -10,47 +10,35 @@
  */
 
 #include "command.hpp"
-#include "readotu.h"
 #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();
-	int execute();
-	void help();
+	ReadOtuCommand();
+	~ReadOtuCommand() {}
+	
+	vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+	string getCommandName()			{ return "read.otu";	}
+	string getCommandCategory()		{ return "Hidden";	}
+	string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }	
+	string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
+	string getDescription()		{ return "read.otu"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	InputData* input;
 	Command* shared;
-	Command* parselist;
 	GroupMap* groupMap;
-	string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+	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<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
 
 };