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                                 mothurOut("You must provide either an input or output for the set.outdir command."); mothurOutEndLine(); abort = true;
  43                         }
  44                 }
  45         }
  46         catch(exception& e) {
  47                 errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52
  53 void SetDirectoryCommand::help(){
  54         try {
  55                 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                 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                 mothurOut("The set.dir command parameter is output and is required.\n");
  58                 mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
  59                 mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
  60                 mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
  61                 mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
  62                 mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
  63         }
  64         catch(exception& e) {
  65                 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
  83                 //redirect output
  84                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
  85                 else {
  86                         //add / to name if needed
  87                         string lastChar = output.substr(output.length()-1);
  88                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  89                                 if (lastChar != "/") { output += "/"; }
  90                         #else
  91                                 if (lastChar != "\\") { output += "\\"; }
  92                         #endif
  93
  94                         //test to make sure directory exists
  95                         output = getFullPathName(output);
  96                         string outTemp = output + "temp";
  97                         ofstream out;
  98                         out.open(outTemp.c_str(), ios::trunc);
  99                         if(!out) {
 100                                 mothurOut(output + " directory does not exist or is not writable."); mothurOutEndLine();
 101                         }else{
 102                                 out.close();
 103                                 remove(outTemp.c_str());
 104                                 mothurOut("Changing output directory to " + output); mothurOutEndLine();
 105                                 commandFactory->setOutputDirectory(output);
 106                         }
 107                 }
 108
 109                 //redirect input
 110                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 111                 else {
 112                         //add / to name if needed
 113                         string lastChar = input.substr(input.length()-1);
 114                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 115                                 if (lastChar != "/") { input += "/"; }
 116                         #else
 117                                 if (lastChar != "\\") { input += "\\"; }
 118                         #endif
 119
 120                         //test to make sure directory exists
 121                         input = getFullPathName(input);
 122                         string inTemp = input + "temp";
 123                         ofstream in;
 124                         in.open(inTemp.c_str(), ios::trunc);
 125                         if(!in) {
 126                                 mothurOut(input + " directory does not exist or is not writable."); mothurOutEndLine();
 127                         }else{
 128                                 in.close();
 129                                 remove(inTemp.c_str());
 130                                 mothurOut("Changing input directory to " + input); mothurOutEndLine();
 131                                 commandFactory->setInputDirectory(input);
 132                         }
 133                 }
 134
 135                 return 0;
 136         }
 137         catch(exception& e) {
 138                 errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
 139                 exit(1);
 140         }
 141 }
 142 //**********************************************************************************************************************/