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                         inputRabund = new InputData(philFile, globaldata->getFormat());
  30                 }else {//there is an orderfile
  31                         input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
  32                 }
  33
  34                 //memory leak prevention
  35                 //if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
  36                 globaldata->ginput = input;     //saving to be used by collector and rarefact commands.
  37
  38                 if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
  39                         order = input->getOrderVector();
  40                         //memory leak prevention
  41                         //if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
  42                         globaldata->gorder = order;     //saving to be used by collect and rarefact commands.
  43                         sabund = inputSabund->getSAbundVector();
  44                         globaldata->sabund = sabund; //saving to be used by summary command.
  45                         rabund = inputRabund->getRAbundVector();
  46                         globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
  47                         list = inputList->getListVector();
  48                         globaldata->gListVector = list;
  49                 }else if (globaldata->getFormat() == "shared") {
  50                         SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
  51                         //memory leak prevention
  52                         //if (globaldata->gSharedList != NULL) { delete globaldata->gSharedList;  }
  53                         globaldata->gSharedList = SharedList;
  54                 }
  55         }
  56         catch(exception& e) {
  57                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOTUFile class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60         catch(...) {
  61                 cout << "An unknown error has occurred in the ReadOTUFile class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64 }
  65
  66 /***********************************************************************/
  67
  68 ReadOTUFile::~ReadOTUFile(){
  69 //      delete input;
  70 //      delete order;
  71 }
  72
  73 /***********************************************************************/
  74