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

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
deleted file mode 100644 (file)
index 5d0daa2..0000000
--- a/sharedcommand.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef SHAREDCOMMAND_H
-#define SHAREDCOMMAND_H
-/*
- *  sharedcommand.h
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/2/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "sharedlistvector.h"
-#include "inputdata.h"
-
-/* The shared() command:
-       The shared command can only be executed after a successful read.shared command.  
-       The shared command parses a .list file and separates it into groups.  
-       It outputs a .shared file containing the OTU information for each group.  
-       There are no shared command parameters.  The shared command should be in the following format: shared(). */
-
-
-class SharedCommand : public Command {
-       
-public:
-       SharedCommand(string);  
-       SharedCommand();
-       ~SharedCommand();
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "make.shared";                         }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
-       string getDescription()         { return "make a shared file from a list and group file"; }
-
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-       int createMisMatchFile(SharedListVector*, GroupMap*);
-       int readOrderFile();
-       bool isValidGroup(string, vector<string>);
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-       int ListGroupSameSeqs(vector<string>&, SharedListVector*);
-    int createSharedFromListGroup(string);
-    int createSharedFromBiom(string);
-    string getTag(string&);
-    vector<string> readRows(string, ifstream&, int&); 
-    int getDims(string, int&, int&);
-    vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
-       
-       vector<string> Groups, outputNames, order;
-       set<string> labels;
-       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
-       bool firsttime, pickedGroups, abort, allLines;
-       map<string, ofstream*> filehandles;
-       map<string, ofstream*>::iterator it3;
-
-};
-
-#endif