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

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
deleted file mode 100644 (file)
index 238dfb6..0000000
--- a/catchallcommand.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef CATCHALLCOMMAND_H
-#define CATCHALLCOMMAND_H
-
-/*
- *  catchallcommand.h
- *  Mothur
- *
- *  Created by westcott on 5/11/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "inputdata.h"
-#include "sabundvector.hpp"
-
-/* 
- citation goes here
- */ 
-
-/****************************************************************************/
-
-class CatchAllCommand : public Command {
-
-public:
-
-       CatchAllCommand(string);
-       CatchAllCommand();
-       ~CatchAllCommand() {}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "catchall";                    }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
-       string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
-       string getDescription()         { return "estimate number of species"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
-       bool abort, allLines;
-       set<string> labels;
-       vector<string> outputNames;
-       vector<string> groups;
-       
-       string process(SAbundVector*, string);
-       int createSummaryFile(string, string, ofstream&); 
-       vector<string> parseSharedFile(string);
-       string combineSummmary(vector<string>&);
-};
-
-/****************************************************************************/
-
-#endif
-
-