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") { cout << "you must enter two or more file names" << endl;  abort=true;  }
  39                         else{   splitAtDash(fileList, fileNames);       }
  40
  41                         numInputFiles = fileNames.size();
  42                         ifstream testFile;
  43                         if(numInputFiles == 0){
  44                                 cout << "you must enter two or more file names and you entered " << fileNames.size() <<  " file names" << endl;
  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") { cout << "you must enter an output file name" << endl;  abort=true;  }
  56                 }
  57
  58         }
  59         catch(exception& e) {
  60                 cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  61                 exit(1);
  62         }
  63         catch(...) {
  64                 cout << "An unknown error has occurred in the MergeFileCommand class function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67 }
  68
  69 //**********************************************************************************************************************
  70
  71 MergeFileCommand::~MergeFileCommand()   {       /*      do nothing      */      }
  72
  73 //**********************************************************************************************************************
  74
  75 int MergeFileCommand::execute(){
  76         try {
  77                 if (abort == true) {    return 0;       }
  78
  79                 ofstream outputFile;
  80                 openOutputFile(outputFileName, outputFile);
  81
  82                 ifstream inputFile;
  83                 char c;
  84                 for(int i=0;i<numInputFiles;i++){
  85                         openInputFile(fileNames[i], inputFile);
  86
  87                         while(!inputFile.eof()){        c = inputFile.get(); outputFile << c;   }
  88
  89                         inputFile.close();
  90                 }
  91                 return 0;
  92         }
  93         catch(exception& e) {
  94                 cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  95                 exit(1);
  96         }
  97         catch(...) {
  98                 cout << "An unknown error has occurred in the BinSeqCommand class function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  99                 exit(1);
 100         }
 101
 102 }
 103
 104 //**********************************************************************************************************************
 105
 106 void MergeFileCommand::help(){
 107         try {
 108                 cout << "The merge.file command..." << endl;
 109         }
 110         catch(exception& e) {
 111                 cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114         catch(...) {
 115                 cout << "An unknown error has occurred in the MergeFileCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 116                 exit(1);
 117         }
 118
 119 }
 120
 121 //**********************************************************************************************************************