getsabundcommand.cpp

   1 /*
   2  *  getsabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getsabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetSAbundCommand::GetSAbundCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 filename = getRootName(globaldata->inputFileName) + "sabund";
  18
  19                 openOutputFile(filename, out);
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29
  30 }
  31
  32 //**********************************************************************************************************************
  33
  34 GetSAbundCommand::~GetSAbundCommand(){
  35 }
  36
  37 //**********************************************************************************************************************
  38
  39 int GetSAbundCommand::execute(){
  40         try {
  41                 int count = 1;
  42
  43                 //using order vector so you don't have to distinguish between the list and rabund files
  44                 read = new ReadOTUFile(globaldata->inputFileName);
  45                 read->read(&*globaldata);
  46
  47                 order = globaldata->gorder;
  48                 lastOrder = order;
  49                 input = globaldata->ginput;
  50
  51                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  52                 set<string> processedLabels;
  53                 set<string> userLabels = globaldata->labels;
  54                 set<int> userLines = globaldata->lines;
  55
  56
  57                 while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  58
  59                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  60                                         cout << order->getLabel() << '\t' << count << endl;
  61                                         sabund = new SAbundVector();
  62                                         *sabund = (order->getSAbundVector());
  63                                         sabund->print(out);
  64                                         delete sabund;
  65
  66                                         processedLabels.insert(order->getLabel());
  67                                         userLabels.erase(order->getLabel());
  68                                         userLines.erase(count);
  69                         }
  70
  71                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
  72                                         cout << lastOrder->getLabel() << '\t' << count << endl;
  73                                         sabund = new SAbundVector();
  74                                         *sabund = (lastOrder->getSAbundVector());
  75                                         sabund->print(out);
  76                                         delete sabund;
  77
  78                                         processedLabels.insert(lastOrder->getLabel());
  79                                         userLabels.erase(lastOrder->getLabel());
  80                         }
  81
  82                         if (count != 1) { delete lastOrder; }
  83                         lastOrder = order;
  84
  85                         order = (input->getOrderVector());
  86                         count++;
  87                 }
  88
  89                 //output error messages about any remaining user labels
  90                 set<string>::iterator it;
  91                 bool needToRun = false;
  92                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
  93                         cout << "Your file does not include the label "<< *it;
  94                         if (processedLabels.count(lastOrder->getLabel()) != 1) {
  95                                 cout << ". I will use " << lastOrder->getLabel() << "." << endl;
  96                                 needToRun = true;
  97                         }else {
  98                                 cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
  99                         }
 100                 }
 101
 102                 //run last line if you need to
 103                 if (needToRun == true)  {
 104                         cout << lastOrder->getLabel() << '\t' << count << endl;
 105                         sabund = new SAbundVector();
 106                         *sabund = (lastOrder->getSAbundVector());
 107                         sabund->print(out);
 108                         delete sabund;
 109                 }
 110                 delete lastOrder;
 111
 112                 out.close();
 113                 return 0;
 114         }
 115
 116         catch(exception& e) {
 117                 cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120         catch(...) {
 121                 cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124 }
 125
 126 //**********************************************************************************************************************
 127
 128