catchallcommand.h

   1 #ifndef CATCHALLCOMMAND_H
   2 #define CATCHALLCOMMAND_H
   3
   4 /*
   5  *  catchallcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/11/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "readotu.h"
  16 #include "sabundvector.hpp"
  17
  18 /*
  19  citation goes here
  20  */
  21
  22 /****************************************************************************/
  23
  24 class CatchAllCommand : public Command {
  25
  26 public:
  27
  28         CatchAllCommand(string);
  29         CatchAllCommand();
  30         ~CatchAllCommand() {}
  31         vector<string> getRequiredParameters();
  32         vector<string> getValidParameters();
  33         vector<string> getRequiredFiles();
  34         map< string, vector<string> > getOutputFiles() { return outputTypes; }
  35         int execute();
  36         void help();
  37
  38 private:
  39
  40         GlobalData* globaldata;
  41
  42         string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path, savedOutputDir;
  43         bool abort, allLines;
  44         set<string> labels;
  45         vector<string> outputNames;
  46         map< string, vector<string> > outputTypes;
  47         vector<string> groups;
  48
  49         string process(SAbundVector*, string);
  50         int createSummaryFile(string, string, ofstream&);
  51         vector<string> parseSharedFile(string);
  52         string combineSummmary(vector<string>&);
  53 };
  54
  55 /****************************************************************************/
  56
  57 #endif
  58
  59