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         m = MothurOut::getInstance();
  16         //m->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
  24                 if (globaldata->getOrderFile() == "") {
  25                         //you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.
  26                         //So when you run the collect or summary commands you miss a line.
  27                         input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
  28                         inputList = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
  29                         inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
  30                         inputRabund = new InputData(philFile, globaldata->getFormat());
  31                 }else {//there is an orderfile
  32                         input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
  33                 }
  34
  35                 //memory leak prevention
  36                 //if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
  37                 globaldata->ginput = input;     //saving to be used by collector and rarefact commands.
  38
  39                 if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
  40
  41 //cout << input << '\t' << globaldata << endl;
  42                         order = input->getOrderVector();
  43                         //memory leak prevention
  44
  45                         //if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
  46                         globaldata->gorder = order;     //saving to be used by collect and rarefact commands.
  47                         sabund = inputSabund->getSAbundVector();
  48                         //if (globaldata->sabund != NULL) { delete globaldata->sabund;  }
  49                         globaldata->sabund = sabund; //saving to be used by summary command.
  50                         delete inputSabund;
  51
  52                         rabund = inputRabund->getRAbundVector();
  53                         //if (globaldata->rabund != NULL) { delete globaldata->rabund;  }
  54                         globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
  55                         delete inputRabund;
  56
  57                         list = inputList->getListVector();
  58                         //if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
  59                         globaldata->gListVector = list;
  60                         delete inputList;
  61
  62                 }else if (globaldata->getFormat() == "shared") {
  63                         SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
  64                         //memory leak prevention
  65                         //if (globaldata->gSharedList != NULL) { delete globaldata->gSharedList;  }
  66                         globaldata->gSharedList = SharedList;
  67                         delete inputSabund;
  68                         delete inputRabund;
  69                         delete inputList;
  70                 }
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "ReadOTUFile", "read");
  74                 exit(1);
  75         }
  76 }
  77
  78 /***********************************************************************/
  79
  80 ReadOTUFile::~ReadOTUFile(){
  81 //      delete input;
  82 //      delete order;
  83 }
  84
  85 /***********************************************************************/
  86