moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
deleted file mode 100644 (file)
index 224f4f0..0000000
--- a/getgroupscommand.h
+++ /dev/null
@@ -1,62 +0,0 @@
-#ifndef GETGROUPSCOMMAND_H
-#define GETGROUPSCOMMAND_H
-
-/*
- *  getgroupscommand.h
- *  Mothur
- *
- *  Created by westcott on 11/10/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-#include "groupmap.h"
-
-class GetGroupsCommand : public Command {
-       
-public:
-       
-       GetGroupsCommand(string);       
-       GetGroupsCommand();
-       ~GetGroupsCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "get.groups";                          }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
-       string getDescription()         { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
-
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-       
-private:
-       set<string> names;
-       map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
-                                                                                  //then the other files need to change the unique name in their file to match.
-                                                                                  //only add the names that need to be changed to keep the map search quick
-       string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
-       bool abort;
-       vector<string> outputNames, Groups;
-       GroupMap* groupMap;
-       
-       int readFasta();
-       int readName();
-       int readGroup();
-       void readAccnos();
-       int readList();
-       int readTax();
-       int fillNames();
-       int readShared();
-    int readDesign();
-       
-};
-
-#endif
-
-
-