setdircommand.cpp

   1 /*
   2  *  setoutdircommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 1/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setdircommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"output","input","outputdir","inputdir"};
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         OptionParser parser(option);
  27                         map<string, string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30                         //check to make sure all parameters are valid for command
  31                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  32                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  33                         }
  34
  35                         output = validParameter.validFile(parameters, "output", false);
  36                         if (output == "not found") {  output = "";  }
  37
  38                         input = validParameter.validFile(parameters, "input", false);
  39                         if (input == "not found") {  input = "";  }
  40
  41                         if ((input == "") && (output == "")) {
  42                                 m->mothurOut("You must provide either an input or output for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  43                         }
  44                 }
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52
  53 void SetDirectoryCommand::help(){
  54         try {
  55                 m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
  56                 m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
  57                 m->mothurOut("The set.dir command parameter is output and is required.\n");
  58                 m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
  59                 m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
  60                 m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
  61                 m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
  62                 m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "SetDirectoryCommand", "help");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 SetDirectoryCommand::~SetDirectoryCommand(){}
  72
  73 //**********************************************************************************************************************
  74
  75 int SetDirectoryCommand::execute(){
  76         try {
  77
  78                 if (abort == true) { return 0; }
  79
  80                 commandFactory = CommandFactory::getInstance();
  81
  82                 //redirect output
  83                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
  84                 else {
  85                         //add / to name if needed
  86                         string lastChar = output.substr(output.length()-1);
  87                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  88                                 if (lastChar != "/") { output += "/"; }
  89                         #else
  90                                 if (lastChar != "\\") { output += "\\"; }
  91                         #endif
  92
  93                         //test to make sure directory exists
  94                         output = getFullPathName(output);
  95                         string outTemp = output + "temp";
  96                         ofstream out;
  97                         out.open(outTemp.c_str(), ios::trunc);
  98                         if(!out) {
  99                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 100                         }else{
 101                                 out.close();
 102                                 remove(outTemp.c_str());
 103                                 m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
 104                                 commandFactory->setOutputDirectory(output);
 105                         }
 106                 }
 107
 108                 //redirect input
 109                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 110                 else {
 111                         //add / to name if needed
 112                         string lastChar = input.substr(input.length()-1);
 113                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 114                                 if (lastChar != "/") { input += "/"; }
 115                         #else
 116                                 if (lastChar != "\\") { input += "\\"; }
 117                         #endif
 118
 119                         //test to make sure directory exists
 120                         input = getFullPathName(input);
 121                         string inTemp = input + "temp";
 122                         ofstream in;
 123                         in.open(inTemp.c_str(), ios::trunc);
 124                         if(!in) {
 125                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 126                         }else{
 127                                 in.close();
 128                                 remove(inTemp.c_str());
 129                                 m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 130                                 commandFactory->setInputDirectory(input);
 131                         }
 132                 }
 133
 134                 return 0;
 135         }
 136         catch(exception& e) {
 137                 m->errorOut(e, "SetDirectoryCommand", "execute");
 138                 exit(1);
 139         }
 140 }
 141 //**********************************************************************************************************************/