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                         if (option != "") { mothurOut("There are no valid parameters for the get.group command."); mothurOutEndLine(); abort = true; }
  23
  24                         if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
  25
  26                         if (abort == false) {
  27                                 //open shared file
  28                                 sharedfile = globaldata->getSharedFile();
  29                                 openInputFile(sharedfile, in);
  30
  31                                 //open output file
  32                                 outputFile = getRootName(sharedfile) + "bootGroups";
  33                                 openOutputFile(outputFile, out);
  34
  35                         }
  36                 }
  37         }
  38         catch(exception& e) {
  39                 errorOut(e, "GetgroupCommand", "GetgroupCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44
  45 void GetgroupCommand::help(){
  46         try {
  47                 mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
  48                 //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 concensus command.\n");
  49                 mothurOut("You may not use any parameters with the get.group command.\n");
  50                 mothurOut("The get.group command should be in the following format: \n");
  51                 mothurOut("get.group()\n");
  52                 mothurOut("Example get.group().\n");
  53
  54         }
  55         catch(exception& e) {
  56                 errorOut(e, "GetgroupCommand", "help");
  57                 exit(1);
  58         }
  59 }
  60
  61 //**********************************************************************************************************************
  62
  63 GetgroupCommand::~GetgroupCommand(){
  64 }
  65
  66 //**********************************************************************************************************************
  67
  68 int GetgroupCommand::execute(){
  69         try {
  70
  71                 if (abort == true) { return 0; }
  72
  73                 int num, inputData, count;
  74                 count = 0;
  75                 string holdLabel, nextLabel, groupN, label;
  76
  77                 //read in first row since you know there is at least 1 group.
  78                 in >> label >> groupN >> num;
  79                 holdLabel = label;
  80
  81                 //output first group
  82                 mothurOut(groupN); mothurOutEndLine();
  83                 out << groupN << '\t' << groupN << endl;
  84
  85                 //get rest of line
  86                 for(int i=0;i<num;i++){
  87                         in >> inputData;
  88                 }
  89
  90                 if (in.eof() != true) { in >> nextLabel; }
  91
  92                 //read the rest of the groups info in
  93                 while ((nextLabel == holdLabel) && (in.eof() != true)) {
  94                         in >> groupN >> num;
  95                         count++;
  96
  97                         //output next group
  98                         mothurOut(groupN); mothurOutEndLine();
  99                         out << groupN << '\t' << groupN << endl;
 100
 101                         //fill vector.
 102                         for(int i=0;i<num;i++){
 103                                 in >> inputData;
 104                         }
 105
 106                         if (in.eof() != true) { in >> nextLabel; }
 107                 }
 108
 109                 in.close();
 110                 out.close();
 111                 return 0;
 112         }
 113
 114         catch(exception& e) {
 115                 errorOut(e, "GetgroupCommand", "execute");
 116                 exit(1);
 117         }
 118 }
 119
 120