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

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
deleted file mode 100644 (file)
index 24062ba..0000000
--- a/removegroupscommand.h
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef REMOVEGROUPSCOMMAND_H
-#define REMOVEGROUPSCOMMAND_H
-
-/*
- *  removegroupscommand.h
- *  Mothur
- *
- *  Created by westcott on 11/10/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-#include "groupmap.h"
-
-class RemoveGroupsCommand : public Command {
-       
-public:
-       
-       RemoveGroupsCommand(string);    
-       RemoveGroupsCommand();
-       ~RemoveGroupsCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "remove.groups";                       }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
-       string getDescription()         { return "removes 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;
-       string accnosfile, fastafile, namefile, groupfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
-       bool abort;
-       vector<string> outputNames, Groups;
-       GroupMap* groupMap;
-       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
-       
-       
-       int readFasta();
-       int readShared();
-       int readName();
-       int readGroup();
-       void readAccnos();
-       int readList();
-       int readTax();
-       int fillNames();
-    int readDesign();
-       
-};
-
-#endif
-
-