readotu.cpp

   1 /*
   2  *  readotu.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readotu.h"
  11
  12 /***********************************************************************/
  13
  14 ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
  15
  16         openInputFile(philFile, fileHandle);
  17 }
  18
  19 /***********************************************************************/
  20 //This function reads the list, rabund or sabund files to be used by collect and rarefact command.
  21 void ReadOTUFile::read(GlobalData* globaldata){
  22         try {
  23                 if (globaldata->getOrderFile() == "") {
  24                         //you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.
  25                         //So when you run the collect or summary commands you miss a line.
  26                         input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
  27                         inputList = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
  28                         inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
  29                 }else {//there is an orderfile
  30                         input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
  31                 }
  32
  33                 //memory leak prevention
  34                 //if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
  35                 globaldata->ginput = input;     //saving to be used by collector and rarefact commands.
  36
  37                 if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
  38                         order = input->getOrderVector();
  39                         //memory leak prevention
  40                         //if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
  41                         globaldata->gorder = order;     //saving to be used by collect and rarefact commands.
  42                         sabund = inputSabund->getSAbundVector();
  43                         globaldata->sabund = sabund; //saving to be used by summary command.
  44                         list = inputList->getListVector();
  45                         globaldata->gListVector = list;
  46                 }else if (globaldata->getFormat() == "shared") {
  47                         SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
  48                         //memory leak prevention
  49                         //if (globaldata->gSharedList != NULL) { delete globaldata->gSharedList;  }
  50                         globaldata->gSharedList = SharedList;
  51                 }
  52         }
  53         catch(exception& e) {
  54                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOTUFile class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57         catch(...) {
  58                 cout << "An unknown error has occurred in the ReadOTUFile class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61 }
  62
  63 /***********************************************************************/
  64
  65 ReadOTUFile::~ReadOTUFile(){
  66 //      delete input;
  67 //      delete order;
  68 }
  69
  70 /***********************************************************************/
  71