getlabelcommand.cpp

   1 /*
   2  *  GetlabelCommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 1/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlabelcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetlabelCommand::GetlabelCommand(string option)  {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }
  24                 }
  25
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33
  34 void GetlabelCommand::help(){
  35         try {
  36                 m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
  37                 m->mothurOut("You may not use any parameters with the get.label command.\n");
  38                 m->mothurOut("The get.label command should be in the following format: \n");
  39                 m->mothurOut("get.label()\n");
  40                 m->mothurOut("Example get.label().\n");
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "GetlabelCommand", "help");
  44                 exit(1);
  45         }
  46 }
  47
  48 //**********************************************************************************************************************
  49
  50 GetlabelCommand::~GetlabelCommand(){
  51 }
  52
  53 //**********************************************************************************************************************
  54
  55 int GetlabelCommand::execute(){
  56         try {
  57
  58                 if (abort == true) { return 0; }
  59
  60                 filename = globaldata->inputFileName;
  61                 ifstream in;
  62                 openInputFile(filename, in);
  63                 string label;
  64                 int numBins = 0;
  65                 int count = -1;
  66                 while(in.good()) {
  67
  68                         if (m->control_pressed) { in.close();  return 0; }
  69
  70                         if(count > numBins)
  71                                 count = 0;
  72                         if(count == 0) {
  73                                 m->mothurOut(label); m->mothurOutEndLine();
  74                                 in >> numBins;
  75                         }
  76                         in >> label;
  77                         count++;
  78                 }
  79
  80                 in.close();
  81                 return 0;
  82         }
  83
  84         catch(exception& e) {
  85                 m->errorOut(e, "GetlabelCommand", "execute");
  86                 exit(1);
  87         }
  88 }
  89