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

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
deleted file mode 100644 (file)
index ecc7376..0000000
--- a/phylotypecommand.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef PHYLOTYPECOMMAND_H
-#define PHYLOTYPECOMMAND_H
-
-
-/*
- *  phylotypecommand.h
- *  Mothur
- *
- *  Created by westcott on 11/20/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "taxonomyequalizer.h"
-#include "command.hpp"
-
-/*************************************************************************/
-
-class PhylotypeCommand : public Command {
-       
-public:
-       PhylotypeCommand(string);       
-       PhylotypeCommand();
-       ~PhylotypeCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "phylotype";           }
-       string getCommandCategory()             { return "Clustering";          }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
-       string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
-
-       int execute();
-       void help() { m->mothurOut(getHelpString()); }
-       
-private:
-       bool abort, allLines;
-       string taxonomyFileName, label, outputDir, namefile;
-       set<string> labels; //holds labels to be used
-       int cutoff;
-       map<string, string> namemap;
-       vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-       
-       map<int, int> currentNodes;
-       map<int, int> parentNodes;
-       map<int, int>::iterator itCurrent;
-       
-       int readNamesFile();
-
-};
-
-
-/*************************************************************************/
-
-
-#endif
-
-
-