pipelinepdscommand.h

   1 #ifndef PIPELINEPDSCOMMAND_H
   2 #define PIPELINEPDSCOMMAND_H
   3
   4 /*
   5  *  pipelinepdscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/5/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "commandfactory.hpp"
  16
  17 /****************************************************/
  18
  19 class PipelineCommand : public Command {
  20
  21 public:
  22         PipelineCommand(string);
  23         PipelineCommand() { abort = true; calledHelp = true; }
  24         ~PipelineCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; } //empty
  29         int execute();
  30         void help();
  31
  32 private:
  33         bool abort;
  34         CommandFactory* cFactory;
  35         vector<string> outputNames;
  36         map<string, vector<string> > outputTypes;
  37         vector<string> commands;
  38         string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
  39         int processors;
  40
  41         bool readUsersPipeline();
  42         int runUsersPipeline();
  43         void createPatsPipeline();
  44         bool parseCommand(string, string&, string&);
  45         bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
  46         bool fillInMothurMade(string&, map<string, vector<string> >&);
  47 };
  48
  49 /****************************************************/
  50
  51 #endif
  52