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,true); parameters.push_back(pinput);
  16                 CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,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 MergeFileCommand::MergeFileCommand(){
  46         try {
  47                 abort = true; calledHelp = true;
  48                 setParameters();
  49                 vector<string> tempOutNames;
  50                 outputTypes["merge"] = tempOutNames;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 MergeFileCommand::MergeFileCommand(string option)  {
  60         try {
  61                 abort = false; calledHelp = false;
  62
  63                 if(option == "help") {
  64                         help();
  65                         abort = true; calledHelp = true;
  66                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  67                 else {
  68                         vector<string> myArray = setParameters();
  69
  70                         OptionParser parser(option);
  71                         map<string,string> parameters = parser.getParameters();
  72
  73                         ValidParameters validParameter;
  74
  75                         //check to make sure all parameters are valid for command
  76                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  77                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  78                         }
  79
  80                         //initialize outputTypes
  81                         vector<string> tempOutNames;
  82                         outputTypes["merge"] = tempOutNames;
  83
  84                         //if the user changes the input directory command factory will send this info to us in the output parameter
  85                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  86                         if (inputDir == "not found"){   inputDir = "";          }
  87
  88                         string fileList = validParameter.validFile(parameters, "input", false);
  89                         if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
  90                         else{   m->splitAtDash(fileList, fileNames);    }
  91
  92                         //if the user changes the output directory command factory will send this info to us in the output parameter
  93                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found")   {       outputDir = "";         }
  94
  95
  96                         numInputFiles = fileNames.size();
  97                         ifstream testFile;
  98                         if(numInputFiles == 0){
  99                                 m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
 100                                 abort=true;
 101                         }
 102                         else{
 103                                 for(int i=0;i<numInputFiles;i++){
 104                                         if (inputDir != "") {
 105                                                 string path = m->hasPath(fileNames[i]);
 106                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 107                                                 if (path == "") {       fileNames[i] = inputDir + fileNames[i];         }
 108                                         }
 109
 110                                         if(m->openInputFile(fileNames[i], testFile)){   abort = true;   }
 111                                         testFile.close();
 112                                 }
 113                         }
 114
 115                         outputFileName = validParameter.validFile(parameters, "output", false);
 116                         if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
 117                         else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
 118                 }
 119
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127
 128 int MergeFileCommand::execute(){
 129         try {
 130                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 131
 132                 m->mothurRemove(outputFileName);
 133                 for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
 134
 135                 if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
 136
 137                 m->mothurOutEndLine();
 138                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 139                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
 140                 m->mothurOutEndLine();
 141
 142                 return 0;
 143         }
 144         catch(exception& e) {
 145                 m->errorOut(e, "MergeFileCommand", "execute");
 146                 exit(1);
 147         }
 148 }
 149 //**********************************************************************************************************************