mergefilecommand.cpp

   1 /*
   2  *  mergefilecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/14/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "mergefilecommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 MergeFileCommand::MergeFileCommand(string option){
  15         try {
  16                 abort = false;
  17
  18                 if(option == "help") {
  19                         help();
  20                         abort = true;
  21                 }
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"input", "output"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         string fileList = validParameter.validFile(parameters, "input", false);
  38                         if(fileList == "not found") { mothurOut("you must enter two or more file names"); mothurOutEndLine();  abort=true;  }
  39                         else{   splitAtDash(fileList, fileNames);       }
  40
  41                         numInputFiles = fileNames.size();
  42                         ifstream testFile;
  43                         if(numInputFiles == 0){
  44                                 mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); mothurOutEndLine();
  45                                 abort=true;
  46                         }
  47                         else{
  48                                 for(int i=0;i<numInputFiles;i++){
  49                                         if(openInputFile(fileNames[i], testFile)){      abort = true;   }
  50                                         testFile.close();
  51                                 }
  52                         }
  53
  54                         outputFileName = validParameter.validFile(parameters, "output", false);
  55                         if (outputFileName == "not found") { mothurOut("you must enter an output file name"); mothurOutEndLine();  abort=true;  }
  56                 }
  57
  58         }
  59         catch(exception& e) {
  60                 errorOut(e, "MergeFileCommand", "MergeFileCommand");
  61                 exit(1);
  62         }
  63 }
  64
  65 //**********************************************************************************************************************
  66
  67 MergeFileCommand::~MergeFileCommand()   {       /*      do nothing      */      }
  68
  69 //**********************************************************************************************************************
  70
  71 int MergeFileCommand::execute(){
  72         try {
  73                 if (abort == true) {    return 0;       }
  74
  75                 ofstream outputFile;
  76                 openOutputFile(outputFileName, outputFile);
  77
  78                 char c;
  79                 for(int i=0;i<numInputFiles;i++){
  80                         ifstream inputFile; //declaration must be inside for loop of windows throws an error
  81
  82                         openInputFile(fileNames[i], inputFile);
  83
  84                         while(!inputFile.eof()){        c = inputFile.get(); outputFile << c;   }
  85
  86                         inputFile.close();
  87                 }
  88
  89                 outputFile.close();
  90                 return 0;
  91         }
  92         catch(exception& e) {
  93                 errorOut(e, "MergeFileCommand", "execute");
  94                 exit(1);
  95         }
  96 }
  97
  98 //**********************************************************************************************************************
  99
 100 void MergeFileCommand::help(){
 101         try {
 102                 mothurOut("The merge.file command..."); mothurOutEndLine();
 103         }
 104         catch(exception& e) {
 105                 errorOut(e, "MergeFileCommand", "help");
 106                 exit(1);
 107         }
 108 }
 109
 110 //**********************************************************************************************************************