removing chime source files from mother project.

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index a21167e3d07e2064c6e9a1dae736b0b1aeccf3a8..c6d65037516c495f391ceb983273b1b9a20010e1 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -10,41 +10,37 @@
  */
 
 #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();
-       ~ReadOtuCommand();
-       int execute();
+       ~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;
+       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