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::setParameters(){
  14         try {
  15                 CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
  16                 CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
  17                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  18                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  19
  20                 vector<string> myArray;
  21                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  22                 return myArray;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "MergeFileCommand", "setParameters");
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30 string MergeFileCommand::getHelpString(){
  31         try {
  32                 string helpString = "";
  33                 helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file.";
  34                 helpString += "The merge.file command parameters are input and output.";
  35                 helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
  36                 helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
  37                 return helpString;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "MergeFileCommand", "getHelpString");
  41                 exit(1);
  42         }
  43 }
  44
  45 //**********************************************************************************************************************
  46 MergeFileCommand::MergeFileCommand(){
  47         try {
  48                 abort = true; calledHelp = true;
  49                 setParameters();
  50                 vector<string> tempOutNames;
  51                 outputTypes["merge"] = tempOutNames;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59
  60 MergeFileCommand::MergeFileCommand(string option)  {
  61         try {
  62                 abort = false; calledHelp = false;
  63
  64                 if(option == "help") {
  65                         help();
  66                         abort = true; calledHelp = true;
  67                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  68                 else {
  69                         vector<string> myArray = setParameters();
  70
  71                         OptionParser parser(option);
  72                         map<string,string> parameters = parser.getParameters();
  73
  74                         ValidParameters validParameter;
  75
  76                         //check to make sure all parameters are valid for command
  77                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  78                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  79                         }
  80
  81                         //initialize outputTypes
  82                         vector<string> tempOutNames;
  83                         outputTypes["merge"] = tempOutNames;
  84
  85                         //if the user changes the input directory command factory will send this info to us in the output parameter
  86                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  87                         if (inputDir == "not found"){   inputDir = "";          }
  88
  89                         string fileList = validParameter.validFile(parameters, "input", false);
  90                         if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
  91                         else{   m->splitAtDash(fileList, fileNames);    }
  92
  93                         //if the user changes the output directory command factory will send this info to us in the output parameter
  94                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found")   {       outputDir = "";         }
  95
  96
  97                         numInputFiles = fileNames.size();
  98                         ifstream testFile;
  99                         if(numInputFiles == 0){
 100                                 m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
 101                                 abort=true;
 102                         }
 103                         else{
 104                                 for(int i=0;i<numInputFiles;i++){
 105                                         if (inputDir != "") {
 106                                                 string path = m->hasPath(fileNames[i]);
 107                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 108                                                 if (path == "") {       fileNames[i] = inputDir + fileNames[i];         }
 109                                         }
 110
 111                                         if(m->openInputFile(fileNames[i], testFile)){   abort = true;   }
 112                                         testFile.close();
 113                                 }
 114                         }
 115
 116                         outputFileName = validParameter.validFile(parameters, "output", false);
 117                         if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
 118                         else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
 119                 }
 120
 121         }
 122         catch(exception& e) {
 123                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
 124                 exit(1);
 125         }
 126 }
 127 //**********************************************************************************************************************
 128
 129 int MergeFileCommand::execute(){
 130         try {
 131                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 132
 133                 ofstream outputFile;
 134                 m->openOutputFile(outputFileName, outputFile);
 135
 136                 char c;
 137                 for(int i=0;i<numInputFiles;i++){
 138                         ifstream inputFile; //declaration must be inside for loop of windows throws an error
 139
 140                         m->openInputFile(fileNames[i], inputFile);
 141
 142                         while(!inputFile.eof()){
 143                                 if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); m->mothurRemove(outputFileName); return 0;  }
 144
 145                                 c = inputFile.get();
 146                                 //-1 is eof char
 147                                 if (int(c) != -1) { outputFile << c; }
 148                         }
 149
 150                         inputFile.close();
 151                 }
 152
 153                 outputFile.close();
 154
 155                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0;  }
 156
 157                 m->mothurOutEndLine();
 158                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 159                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
 160                 m->mothurOutEndLine();
 161
 162                 return 0;
 163         }
 164         catch(exception& e) {
 165                 m->errorOut(e, "MergeFileCommand", "execute");
 166                 exit(1);
 167         }
 168 }
 169 //**********************************************************************************************************************