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 (option != "") { mothurOut("There are no valid parameters for the get.label command."); mothurOutEndLine(); abort = true; }
  24
  25                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); mothurOutEndLine(); abort = true; }
  26                 }
  27
  28         }
  29         catch(exception& e) {
  30                 errorOut(e, "GetlabelCommand", "GetlabelCommand");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35
  36 void GetlabelCommand::help(){
  37         try {
  38                 mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
  39                 mothurOut("You may not use any parameters with the get.label command.\n");
  40                 mothurOut("The get.label command should be in the following format: \n");
  41                 mothurOut("get.label()\n");
  42                 mothurOut("Example get.label().\n");
  43         }
  44         catch(exception& e) {
  45                 errorOut(e, "GetlabelCommand", "help");
  46                 exit(1);
  47         }
  48 }
  49
  50 //**********************************************************************************************************************
  51
  52 GetlabelCommand::~GetlabelCommand(){
  53 }
  54
  55 //**********************************************************************************************************************
  56
  57 int GetlabelCommand::execute(){
  58         try {
  59
  60                 if (abort == true) { return 0; }
  61
  62                 filename = globaldata->inputFileName;
  63                 ifstream in;
  64                 openInputFile(filename, in);
  65                 string label;
  66                 int numBins = 0;
  67                 int count = -1;
  68                 while(in.good()) {
  69                         if(count > numBins)
  70                                 count = 0;
  71                         if(count == 0) {
  72                                 mothurOut(label); mothurOutEndLine();
  73                                 in >> numBins;
  74                         }
  75                         in >> label;
  76                         count++;
  77                 }
  78
  79                 in.close();
  80                 return 0;
  81         }
  82
  83         catch(exception& e) {
  84                 errorOut(e, "GetlabelCommand", "execute");
  85                 exit(1);
  86         }
  87 }
  88