createdatabasecommand.cpp

   1 //
   2 //  createdatabasecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 3/28/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "createdatabasecommand.h"
  10 #include "sequence.hpp"
  11 #include "inputdata.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> CreateDatabaseCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
  18                 CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
  19                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "CreateDatabaseCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string CreateDatabaseCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The create.database command reads a listfile, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
  39                 helpString += "The create.database command parameters are repfasta, list, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required.  \n";
  40
  41         helpString += "The create.database command should be in the following format: \n";
  42                 helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
  43                 helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53
  54