rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12
  13 //**********************************************************************************************************************
  14
  15 RareFactSharedCommand::RareFactSharedCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 string fileNameRoot, groups;
  19                 fileNameRoot = getRootName(globaldata->inputFileName);
  20                 groupmap = globaldata->gGroupmap;
  21
  22                 //initialize groups for label
  23                 groups = "";
  24                 for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
  25                         groups = groups + groupmap->namesOfGroups[i];
  26                 }
  27
  28                 int i;
  29                 for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
  30                         if (globaldata->sharedRareEstimators[i] == "sharedobserved") {
  31                                 rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"sharedObserved", groups)));
  32                         }
  33                 }
  34         }
  35         catch(exception& e) {
  36                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  37                 exit(1);
  38         }
  39         catch(...) {
  40                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  41                 exit(1);
  42         }
  43
  44 }
  45
  46 //**********************************************************************************************************************
  47
  48 RareFactSharedCommand::~RareFactSharedCommand(){
  49         delete order;
  50         delete input;
  51         delete rCurve;
  52         delete read;
  53 }
  54
  55 //**********************************************************************************************************************
  56
  57 int RareFactSharedCommand::execute(){
  58         try {
  59                 int count = 1;
  60                 read = new ReadPhilFile(globaldata->inputFileName);
  61                 read->read(&*globaldata);
  62
  63                 input = globaldata->ginput;
  64                 list = globaldata->glist;
  65                 order = list->getSharedOrderVector();
  66
  67                 while(order != NULL){
  68
  69                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  70                                 //create collectors curve
  71                                 rCurve = new Rarefact(order, rDisplays);
  72                                 convert(globaldata->getFreq(), freq);
  73                                 convert(globaldata->getIters(), nIters);
  74                                 rCurve->getSharedCurve(freq, nIters);
  75
  76                                 delete rCurve;
  77
  78                                 cout << order->getLabel() << '\t' << count << endl;
  79                         }
  80
  81                         list = input->getListVector(); //get new list vector to process
  82                         if (list != NULL) {
  83                                 order = list->getSharedOrderVector(); //gets new order vector with group info.
  84                                 count++;
  85                         }else {
  86                                 break;
  87                         }
  88
  89                 }
  90
  91                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
  92                 return 0;
  93         }
  94         catch(exception& e) {
  95                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98         catch(...) {
  99                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102 }
 103
 104
 105 //**********************************************************************************************************************