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