setlogfilecommand.cpp

   1 /*
   2  *  setlogfilecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setlogfilecommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SetLogFileCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"name","append","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "SetLogFileCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 vector<string> SetLogFileCommand::getRequiredParameters(){
  26         try {
  27                 string Array[] =  {"name"};
  28                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "SetLogFileCommand", "getRequiredParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 vector<string> SetLogFileCommand::getRequiredFiles(){
  38         try {
  39                 vector<string> myArray;
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "SetLogFileCommand", "getRequiredFiles");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48
  49 SetLogFileCommand::SetLogFileCommand(string option)  {
  50         try {
  51                 abort = false; calledHelp = false;
  52
  53                 //allow user to run help
  54                 if(option == "help") { help(); abort = true; calledHelp = true; }
  55
  56                 else {
  57                         //valid paramters for this command
  58                         string Array[] =  {"name","append","outputdir","inputdir"};
  59                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  60
  61                         OptionParser parser(option);
  62                         map<string, string> parameters = parser.getParameters();
  63
  64                         ValidParameters validParameter;
  65                         //check to make sure all parameters are valid for command
  66                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  67                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  68                         }
  69
  70                         name = validParameter.validFile(parameters, "name", false);
  71                         if (name == "not found") {  m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; }
  72
  73                         string temp = validParameter.validFile(parameters, "append", false);            if (temp == "not found") {  temp = "F";  }
  74                         append = m->isTrue(temp);
  75                 }
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "SetLogFileCommand", "SetLogFileCommand");
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83
  84 void SetLogFileCommand::help(){
  85         try {
  86                 m->mothurOut("The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n");
  87                 m->mothurOut("The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n");
  88                 m->mothurOut("The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n");
  89                 m->mothurOut("Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n");
  90                 m->mothurOut("Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n");
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "SetLogFileCommand", "help");
  94                 exit(1);
  95         }
  96 }
  97 //**********************************************************************************************************************
  98
  99 SetLogFileCommand::~SetLogFileCommand(){}
 100
 101 //**********************************************************************************************************************
 102
 103 int SetLogFileCommand::execute(){
 104         try {
 105
 106                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 107
 108                 commandFactory = CommandFactory::getInstance();
 109
 110                 commandFactory->setLogfileName(name, append);
 111
 112                 return 0;
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "SetLogFileCommand", "execute");
 116                 exit(1);
 117         }
 118 }
 119 //**********************************************************************************************************************/