getlinecommand.cpp

   1 /*
   2  *  GetlineCommand.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 "getlinecommand.h"
  11
  12 //**********************************************************************************************************************
  13 GetlineCommand::GetlineCommand(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.line command."); mothurOutEndLine(); abort = true; }
  23
  24                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.line command."); mothurOutEndLine(); abort = true; }
  25                 }
  26
  27         }
  28         catch(exception& e) {
  29                 errorOut(e, "GetlineCommand", "GetlineCommand");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34
  35 void GetlineCommand::help(){
  36         try {
  37                 mothurOut("The get.line command can only be executed after a successful read.otu command.\n");
  38                 mothurOut("You may not use any parameters with the get.line command.\n");
  39                 mothurOut("The get.line command should be in the following format: \n");
  40                 mothurOut("get.line()\n");
  41                 mothurOut("Example get.line().\n");
  42         }
  43         catch(exception& e) {
  44                 errorOut(e, "GetlineCommand", "help");
  45                 exit(1);
  46         }
  47 }
  48
  49 //**********************************************************************************************************************
  50
  51 GetlineCommand::~GetlineCommand(){
  52 }
  53
  54 //**********************************************************************************************************************
  55
  56 int GetlineCommand::execute(){
  57         try {
  58
  59                 if (abort == true) { return 0; }
  60
  61                 ifstream in;
  62                 openInputFile(globaldata->inputFileName, in);
  63                 string label;
  64                 int numBins = 0;
  65                 int count = -1;
  66                 int line = 1;
  67                 while(in.good()) {
  68                         if(count > numBins)
  69                                 count = 0;
  70                         if(count == 0) {
  71                                 mothurOut(toString(line)); mothurOutEndLine();
  72                                 in >> numBins;
  73                                 line++;
  74                         }
  75                         in >> label;
  76                         count++;
  77                 }
  78
  79                 in.close();
  80                 return 0;
  81         }
  82
  83         catch(exception& e) {
  84                 errorOut(e, "GetlineCommand", "execute");
  85                 exit(1);
  86         }
  87 }
  88
  89
  90