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;
  19                 fileNameRoot = getRootName(globaldata->inputFileName);
  20
  21                 int i;
  22                 for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
  23                         if (globaldata->sharedRareEstimators[i] == "sharedobserved") {
  24                                 rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  25                         }
  26                 }
  27         }
  28         catch(exception& e) {
  29                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32         catch(...) {
  33                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36
  37 }
  38
  39 //**********************************************************************************************************************
  40
  41 RareFactSharedCommand::~RareFactSharedCommand(){
  42         delete order;
  43         delete input;
  44         delete rCurve;
  45         delete read;
  46 }
  47
  48 //**********************************************************************************************************************
  49
  50 int RareFactSharedCommand::execute(){
  51         try {
  52                 int count = 1;
  53                 read = new ReadPhilFile(globaldata->inputFileName);
  54                 read->read(&*globaldata);
  55
  56                 input = globaldata->ginput;
  57                 SharedList = globaldata->gSharedList;
  58                 order = SharedList->getSharedOrderVector();
  59
  60                 while(order != NULL){
  61
  62                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  63                                 //create collectors curve
  64                                 rCurve = new Rarefact(order, rDisplays);
  65                                 convert(globaldata->getFreq(), freq);
  66                                 convert(globaldata->getIters(), nIters);
  67                                 rCurve->getSharedCurve(freq, nIters);
  68
  69                                 delete rCurve;
  70
  71                                 cout << order->getLabel() << '\t' << count << endl;
  72                         }
  73
  74                         SharedList = input->getSharedListVector(); //get new list vector to process
  75                         if (SharedList != NULL) {
  76                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
  77                                 count++;
  78                         }else {
  79                                 break;
  80                         }
  81
  82                 }
  83
  84                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
  85                 return 0;
  86         }
  87         catch(exception& e) {
  88                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91         catch(...) {
  92                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95 }
  96
  97
  98 //**********************************************************************************************************************