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::getValidParameters(){
  14         try {
  15                 string Array[] =  {"outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetgroupCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 GetgroupCommand::GetgroupCommand(){
  26         try {
  27                 abort = true; calledHelp = true;
  28                 vector<string> tempOutNames;
  29                 outputTypes["bootgroup"] = tempOutNames;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 vector<string> GetgroupCommand::getRequiredParameters(){
  38         try {
  39                 vector<string> myArray;
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "GetgroupCommand", "getRequiredParameters");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 vector<string> GetgroupCommand::getRequiredFiles(){
  49         try {
  50                 string Array[] =  {"shared"};
  51                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  52                 return myArray;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetgroupCommand", "getRequiredFiles");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 GetgroupCommand::GetgroupCommand(string option)  {
  61         try {
  62                 globaldata = GlobalData::getInstance();
  63                 abort = false; calledHelp = false;
  64
  65                 //allow user to run help
  66                 if(option == "help") { help(); abort = true; calledHelp = true; }
  67
  68                 else {
  69                         //valid paramters for this command
  70                         string Array[] =  {"outputdir","inputdir"};
  71                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  72
  73                         OptionParser parser(option);
  74                         map<string,string> parameters = parser.getParameters();
  75
  76                         ValidParameters validParameter;
  77                         //check to make sure all parameters are valid for command
  78                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  79                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  80                         }
  81
  82                         //initialize outputTypes
  83                         vector<string> tempOutNames;
  84                         outputTypes["bootgroup"] = tempOutNames;
  85
  86                         //if the user changes the output directory command factory will send this info to us in the output parameter
  87                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = "";         }
  88
  89                         if ((globaldata->getSharedFile() == "")) { m->mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); m->mothurOutEndLine(); abort = true; }
  90
  91                         if (abort == false) {
  92                                 //open shared file
  93                                 sharedfile = globaldata->getSharedFile();
  94                                 m->openInputFile(sharedfile, in);
  95
  96                                 //open output file
  97                                 if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
  98                                 outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
  99                                 m->openOutputFile(outputFile, out);
 100
 101                         }
 102                 }
 103         }
 104         catch(exception& e) {
 105                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 106                 exit(1);
 107         }
 108 }
 109 //**********************************************************************************************************************
 110
 111 void GetgroupCommand::help(){
 112         try {
 113                 m->mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
 114                 //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");
 115                 m->mothurOut("You may not use any parameters with the get.group command.\n");
 116                 m->mothurOut("The get.group command should be in the following format: \n");
 117                 m->mothurOut("get.group()\n");
 118                 m->mothurOut("Example get.group().\n");
 119
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "GetgroupCommand", "help");
 123                 exit(1);
 124         }
 125 }
 126
 127 //**********************************************************************************************************************
 128
 129 GetgroupCommand::~GetgroupCommand(){
 130 }
 131
 132 //**********************************************************************************************************************
 133
 134 int GetgroupCommand::execute(){
 135         try {
 136
 137                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 138
 139                 int num, inputData, count;
 140                 count = 0;
 141                 string holdLabel, nextLabel, groupN, label;
 142
 143                 //read in first row since you know there is at least 1 group.
 144                 in >> label >> groupN >> num;
 145                 holdLabel = label;
 146
 147                 //output first group
 148                 m->mothurOut(groupN); m->mothurOutEndLine();
 149                 out << groupN << '\t' << groupN << endl;
 150
 151                 //get rest of line
 152                 for(int i=0;i<num;i++){
 153                         in >> inputData;
 154                 }
 155
 156                 if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 157
 158                 if (in.eof() != true) { in >> nextLabel; }
 159
 160                 //read the rest of the groups info in
 161                 while ((nextLabel == holdLabel) && (in.eof() != true)) {
 162                         if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 163
 164                         in >> groupN >> num;
 165                         count++;
 166
 167                         //output next group
 168                         m->mothurOut(groupN); m->mothurOutEndLine();
 169                         out << groupN << '\t' << groupN << endl;
 170
 171                         //fill vector.
 172                         for(int i=0;i<num;i++){
 173                                 in >> inputData;
 174                         }
 175
 176                         if (in.eof() != true) { in >> nextLabel; }
 177                 }
 178
 179                 in.close();
 180                 out.close();
 181
 182                 if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
 183
 184                 m->mothurOutEndLine();
 185                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 186                 m->mothurOut(outputFile); m->mothurOutEndLine();        outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
 187                 m->mothurOutEndLine();
 188
 189                 return 0;
 190         }
 191
 192         catch(exception& e) {
 193                 m->errorOut(e, "GetgroupCommand", "execute");
 194                 exit(1);
 195         }
 196 }
 197
 198