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;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["bootgroup"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> GetgroupCommand::getRequiredParameters(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "GetgroupCommand", "getRequiredParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> GetgroupCommand::getRequiredFiles(){
  50         try {
  51                 string Array[] =  {"shared"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetgroupCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 GetgroupCommand::GetgroupCommand(string option)  {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"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                         //check to make sure all parameters are valid for command
  79                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  80                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  81                         }
  82
  83                         //initialize outputTypes
  84                         vector<string> tempOutNames;
  85                         outputTypes["bootgroup"] = tempOutNames;
  86
  87                         //if the user changes the output directory command factory will send this info to us in the output parameter
  88                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = "";         }
  89
  90                         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; }
  91
  92                         if (abort == false) {
  93                                 //open shared file
  94                                 sharedfile = globaldata->getSharedFile();
  95                                 m->openInputFile(sharedfile, in);
  96
  97                                 //open output file
  98                                 if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
  99                                 outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
 100                                 m->openOutputFile(outputFile, out);
 101
 102                         }
 103                 }
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111
 112 void GetgroupCommand::help(){
 113         try {
 114                 m->mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
 115                 //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");
 116                 m->mothurOut("You may not use any parameters with the get.group command.\n");
 117                 m->mothurOut("The get.group command should be in the following format: \n");
 118                 m->mothurOut("get.group()\n");
 119                 m->mothurOut("Example get.group().\n");
 120
 121         }
 122         catch(exception& e) {
 123                 m->errorOut(e, "GetgroupCommand", "help");
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************
 129
 130 GetgroupCommand::~GetgroupCommand(){
 131 }
 132
 133 //**********************************************************************************************************************
 134
 135 int GetgroupCommand::execute(){
 136         try {
 137
 138                 if (abort == true) { return 0; }
 139
 140                 int num, inputData, count;
 141                 count = 0;
 142                 string holdLabel, nextLabel, groupN, label;
 143
 144                 //read in first row since you know there is at least 1 group.
 145                 in >> label >> groupN >> num;
 146                 holdLabel = label;
 147
 148                 //output first group
 149                 m->mothurOut(groupN); m->mothurOutEndLine();
 150                 out << groupN << '\t' << groupN << endl;
 151
 152                 //get rest of line
 153                 for(int i=0;i<num;i++){
 154                         in >> inputData;
 155                 }
 156
 157                 if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 158
 159                 if (in.eof() != true) { in >> nextLabel; }
 160
 161                 //read the rest of the groups info in
 162                 while ((nextLabel == holdLabel) && (in.eof() != true)) {
 163                         if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
 164
 165                         in >> groupN >> num;
 166                         count++;
 167
 168                         //output next group
 169                         m->mothurOut(groupN); m->mothurOutEndLine();
 170                         out << groupN << '\t' << groupN << endl;
 171
 172                         //fill vector.
 173                         for(int i=0;i<num;i++){
 174                                 in >> inputData;
 175                         }
 176
 177                         if (in.eof() != true) { in >> nextLabel; }
 178                 }
 179
 180                 in.close();
 181                 out.close();
 182
 183                 if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
 184
 185                 m->mothurOutEndLine();
 186                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 187                 m->mothurOut(outputFile); m->mothurOutEndLine();        outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
 188                 m->mothurOutEndLine();
 189
 190                 return 0;
 191         }
 192
 193         catch(exception& e) {
 194                 m->errorOut(e, "GetgroupCommand", "execute");
 195                 exit(1);
 196         }
 197 }
 198
 199