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