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

[mothur.git] / pipelinepdscommand.h

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
deleted file mode 100644 (file)
index 8abe0ea..0000000
--- a/pipelinepdscommand.h
+++ /dev/null
@@ -1,56 +0,0 @@
-#ifndef PIPELINEPDSCOMMAND_H
-#define PIPELINEPDSCOMMAND_H
-
-/*
- *  pipelinepdscommand.h
- *  Mothur
- *
- *  Created by westcott on 10/5/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-#include "commandfactory.hpp"
-
-/****************************************************/
-
-class PipelineCommand : public Command {
-       
-public:
-       PipelineCommand(string);
-       PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
-       ~PipelineCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "pipeline.pds";        }
-       string getCommandCategory()             { return "Hidden";                      }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
-       string getDescription()         { return "pat's pipeline"; }
-
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       bool abort;
-       CommandFactory* cFactory;
-       vector<string> outputNames;
-       vector<string> commands;
-       string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
-       int processors;
-       
-       bool readUsersPipeline();
-       int runUsersPipeline();
-       void createPatsPipeline();
-       bool parseCommand(string, string&, string&);
-       bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
-       bool fillInMothurMade(string&, map<string, vector<string> >&);
-};
-
-/****************************************************/
-
-#endif
-