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 vector<string> GetlabelCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetlabelCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 vector<string> GetlabelCommand::getRequiredParameters(){
  26         try {
  27                 vector<string> myArray;
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "GetlabelCommand", "getRequiredParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 vector<string> GetlabelCommand::getRequiredFiles(){
  37         try {
  38                 string Array[] =  {"list","rabund","sabund", "or"};
  39                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "GetlabelCommand", "getRequiredFiles");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48
  49 GetlabelCommand::GetlabelCommand(string option)  {
  50         try {
  51                 globaldata = GlobalData::getInstance();
  52                 abort = false; calledHelp = false;
  53
  54                 //allow user to run help
  55                 if(option == "help") { help(); abort = true; calledHelp = true; }
  56
  57                 else {
  58                         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; }
  59                 }
  60
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68
  69 void GetlabelCommand::help(){
  70         try {
  71                 m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
  72                 m->mothurOut("You may not use any parameters with the get.label command.\n");
  73                 m->mothurOut("The get.label command should be in the following format: \n");
  74                 m->mothurOut("get.label()\n");
  75                 m->mothurOut("Example get.label().\n");
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "GetlabelCommand", "help");
  79                 exit(1);
  80         }
  81 }
  82
  83 //**********************************************************************************************************************
  84
  85 GetlabelCommand::~GetlabelCommand(){
  86 }
  87
  88 //**********************************************************************************************************************
  89
  90 int GetlabelCommand::execute(){
  91         try {
  92
  93                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  94
  95                 filename = globaldata->inputFileName;
  96                 ifstream in;
  97                 m->openInputFile(filename, in);
  98                 string label;
  99                 int numBins = 0;
 100                 int count = -1;
 101                 while(in.good()) {
 102
 103                         if (m->control_pressed) { in.close();  return 0; }
 104
 105                         if(count > numBins)
 106                                 count = 0;
 107                         if(count == 0) {
 108                                 m->mothurOut(label); m->mothurOutEndLine();
 109                                 in >> numBins;
 110                         }
 111                         in >> label;
 112                         count++;
 113                 }
 114
 115                 in.close();
 116                 return 0;
 117         }
 118
 119         catch(exception& e) {
 120                 m->errorOut(e, "GetlabelCommand", "execute");
 121                 exit(1);
 122         }
 123 }
 124