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 vector<string> MergeFileCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"input", "output","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "MergeFileCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 MergeFileCommand::MergeFileCommand(){
  26         try {
  27                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["merge"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> MergeFileCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"input","output"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "MergeFileCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> MergeFileCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "MergeFileCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61
  62 MergeFileCommand::MergeFileCommand(string option)  {
  63         try {
  64                 abort = false;
  65
  66                 if(option == "help") {
  67                         help();
  68                         abort = true;
  69                 }
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"input", "output","outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["merge"] = tempOutNames;
  88
  89                         //if the user changes the input directory command factory will send this info to us in the output parameter
  90                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  91                         if (inputDir == "not found"){   inputDir = "";          }
  92
  93                         string fileList = validParameter.validFile(parameters, "input", false);
  94                         if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
  95                         else{   m->splitAtDash(fileList, fileNames);    }
  96
  97                         //if the user changes the output directory command factory will send this info to us in the output parameter
  98                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found")   {       outputDir = "";         }
  99
 100
 101                         numInputFiles = fileNames.size();
 102                         ifstream testFile;
 103                         if(numInputFiles == 0){
 104                                 m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
 105                                 abort=true;
 106                         }
 107                         else{
 108                                 for(int i=0;i<numInputFiles;i++){
 109                                         if (inputDir != "") {
 110                                                 string path = m->hasPath(fileNames[i]);
 111                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 112                                                 if (path == "") {       fileNames[i] = inputDir + fileNames[i];         }
 113                                         }
 114
 115                                         if(m->openInputFile(fileNames[i], testFile)){   abort = true;   }
 116                                         testFile.close();
 117                                 }
 118                         }
 119
 120                         outputFileName = validParameter.validFile(parameters, "output", false);
 121                         if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
 122                         else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
 123                 }
 124
 125         }
 126         catch(exception& e) {
 127                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
 128                 exit(1);
 129         }
 130 }
 131
 132 //**********************************************************************************************************************
 133
 134 MergeFileCommand::~MergeFileCommand()   {       /*      do nothing      */      }
 135
 136 //**********************************************************************************************************************
 137
 138 int MergeFileCommand::execute(){
 139         try {
 140                 if (abort == true) {    return 0;       }
 141
 142                 ofstream outputFile;
 143                 m->openOutputFile(outputFileName, outputFile);
 144
 145                 char c;
 146                 for(int i=0;i<numInputFiles;i++){
 147                         ifstream inputFile; //declaration must be inside for loop of windows throws an error
 148
 149                         m->openInputFile(fileNames[i], inputFile);
 150
 151                         while(!inputFile.eof()){
 152                                 if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
 153
 154                                 c = inputFile.get();
 155                                 //-1 is eof char
 156                                 if (int(c) != -1) { outputFile << c; }
 157                         }
 158
 159                         inputFile.close();
 160                 }
 161
 162                 outputFile.close();
 163
 164                 if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0;  }
 165
 166                 m->mothurOutEndLine();
 167                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 168                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
 169                 m->mothurOutEndLine();
 170
 171                 return 0;
 172         }
 173         catch(exception& e) {
 174                 m->errorOut(e, "MergeFileCommand", "execute");
 175                 exit(1);
 176         }
 177 }
 178
 179 //**********************************************************************************************************************
 180
 181 void MergeFileCommand::help(){
 182         try {
 183                 m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
 184         }
 185         catch(exception& e) {
 186                 m->errorOut(e, "MergeFileCommand", "help");
 187                 exit(1);
 188         }
 189 }
 190
 191 //**********************************************************************************************************************