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","outputdir","inputdir"};
  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                         //if the user changes the input directory command factory will send this info to us in the output parameter
  38                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  39                         if (inputDir == "not found"){   inputDir = "";          }
  40
  41                         string fileList = validParameter.validFile(parameters, "input", false);
  42                         if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
  43                         else{   splitAtDash(fileList, fileNames);       }
  44
  45                         //if the user changes the output directory command factory will send this info to us in the output parameter
  46                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found")   {       outputDir = "";         }
  47
  48
  49                         numInputFiles = fileNames.size();
  50                         ifstream testFile;
  51                         if(numInputFiles == 0){
  52                                 m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
  53                                 abort=true;
  54                         }
  55                         else{
  56                                 for(int i=0;i<numInputFiles;i++){
  57                                         if (inputDir != "") {
  58                                                 string path = hasPath(fileNames[i]);
  59                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  60                                                 if (path == "") {       fileNames[i] = inputDir + fileNames[i];         }
  61                                         }
  62
  63                                         if(openInputFile(fileNames[i], testFile)){      abort = true;   }
  64                                         testFile.close();
  65                                 }
  66                         }
  67
  68                         outputFileName = validParameter.validFile(parameters, "output", false);
  69                         if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
  70                         else if (outputDir != "") { outputFileName = outputDir + getSimpleName(outputFileName); }
  71                 }
  72
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
  76                 exit(1);
  77         }
  78 }
  79
  80 //**********************************************************************************************************************
  81
  82 MergeFileCommand::~MergeFileCommand()   {       /*      do nothing      */      }
  83
  84 //**********************************************************************************************************************
  85
  86 int MergeFileCommand::execute(){
  87         try {
  88                 if (abort == true) {    return 0;       }
  89
  90                 ofstream outputFile;
  91                 openOutputFile(outputFileName, outputFile);
  92
  93                 char c;
  94                 for(int i=0;i<numInputFiles;i++){
  95                         ifstream inputFile; //declaration must be inside for loop of windows throws an error
  96
  97                         openInputFile(fileNames[i], inputFile);
  98
  99                         while(!inputFile.eof()){
 100                                 if (m->control_pressed) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
 101
 102                                 c = inputFile.get();
 103                                 //-1 is eof char
 104                                 if (int(c) != -1) { outputFile << c; }
 105                         }
 106
 107                         inputFile.close();
 108                 }
 109
 110                 outputFile.close();
 111
 112                 if (m->control_pressed) { remove(outputFileName.c_str()); return 0;  }
 113
 114                 m->mothurOutEndLine();
 115                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 116                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 117                 m->mothurOutEndLine();
 118
 119                 return 0;
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "MergeFileCommand", "execute");
 123                 exit(1);
 124         }
 125 }
 126
 127 //**********************************************************************************************************************
 128
 129 void MergeFileCommand::help(){
 130         try {
 131                 m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
 132         }
 133         catch(exception& e) {
 134                 m->errorOut(e, "MergeFileCommand", "help");
 135                 exit(1);
 136         }
 137 }
 138
 139 //**********************************************************************************************************************