getgroupcommand.cpp

   1 /*
   2  *  getgroupcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 2/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getgroupcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetgroupCommand::setParameters(){
  14         try {
  15                 CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
  16                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  17                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  18
  19                 vector<string> myArray;
  20                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  21                 return myArray;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "GetgroupCommand", "setParameters");
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 string GetgroupCommand::getHelpString(){
  30         try {
  31                 string helpString = "";
  32                 helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
  33                 //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
  34                 helpString += "You may not use any parameters with the get.group command.\n";
  35                 helpString += "The get.group command should be in the following format: \n";
  36                 helpString += "get.group()\n";
  37                 helpString += "Example get.group().\n";
  38                 return helpString;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "GetgroupCommand", "getHelpString");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 GetgroupCommand::GetgroupCommand(){
  47         try {
  48                 abort = true; calledHelp = true;
  49                 setParameters();
  50                 vector<string> tempOutNames;
  51                 outputTypes["bootgroup"] = tempOutNames;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59 GetgroupCommand::GetgroupCommand(string option)  {
  60         try {
  61                 abort = false; calledHelp = false;
  62
  63                 //allow user to run help
  64                 if(option == "help") { help(); abort = true; calledHelp = true; }
  65                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  66
  67                 else {
  68                         vector<string> myArray = setParameters();
  69
  70                         OptionParser parser(option);
  71                         map<string,string> parameters = parser.getParameters();
  72                         map<string,string>::iterator it;
  73
  74                         ValidParameters validParameter;
  75                         //check to make sure all parameters are valid for command
  76                         for (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["bootgroup"] = 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                         else {
  88                                 string path;
  89                                 it = parameters.find("shared");
  90                                 //user has given a template file
  91                                 if(it != parameters.end()){
  92                                         path = m->hasPath(it->second);
  93                                         //if the user has not given a path then, add inputdir. else leave path alone.
  94                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
  95                                 }
  96                         }
  97
  98                         //get shared file
  99                         sharedfile = validParameter.validFile(parameters, "shared", true);
 100                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 101                         else if (sharedfile == "not found") {
 102                                 //if there is a current shared file, use it
 103                                 sharedfile = m->getSharedFile();
 104                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 105                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 106                         }else { m->setSharedFile(sharedfile); }
 107
 108
 109                         //if the user changes the output directory command factory will send this info to us in the output parameter
 110                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 111                 }
 112         }
 113         catch(exception& e) {
 114                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 115                 exit(1);
 116         }
 117 }
 118 //**********************************************************************************************************************
 119
 120 int GetgroupCommand::execute(){
 121         try {
 122
 123                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 124
 125                 //open shared file
 126                 m->openInputFile(sharedfile, in);
 127
 128                 //open output file
 129                 outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
 130                 m->openOutputFile(outputFile, out);
 131
 132                 int num, inputData, count;
 133                 count = 0;
 134                 string holdLabel, nextLabel, groupN, label;
 135
 136                 //read in first row since you know there is at least 1 group.
 137                 in >> label >> groupN >> num;
 138                 holdLabel = label;
 139
 140                 //output first group
 141                 m->mothurOut(groupN); m->mothurOutEndLine();
 142                 out << groupN << '\t' << groupN << endl;
 143
 144                 //get rest of line
 145                 for(int i=0;i<num;i++){
 146                         in >> inputData;
 147                 }
 148
 149                 if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 150
 151                 if (in.eof() != true) { in >> nextLabel; }
 152
 153                 //read the rest of the groups info in
 154                 while ((nextLabel == holdLabel) && (in.eof() != true)) {
 155                         if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 156
 157                         in >> groupN >> num;
 158                         count++;
 159
 160                         //output next group
 161                         m->mothurOut(groupN); m->mothurOutEndLine();
 162                         out << groupN << '\t' << groupN << endl;
 163
 164                         //fill vector.
 165                         for(int i=0;i<num;i++){
 166                                 in >> inputData;
 167                         }
 168
 169                         if (in.eof() != true) { in >> nextLabel; }
 170                 }
 171
 172                 in.close();
 173                 out.close();
 174
 175                 if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
 176
 177                 m->mothurOutEndLine();
 178                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 179                 m->mothurOut(outputFile); m->mothurOutEndLine();        outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
 180                 m->mothurOutEndLine();
 181
 182                 return 0;
 183         }
 184
 185         catch(exception& e) {
 186                 m->errorOut(e, "GetgroupCommand", "execute");
 187                 exit(1);
 188         }
 189 }
 190
 191