rarefactcommand.cpp

   1 /*
   2  *  rarefactcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 #include "bootstrap.h"
  15 #include "simpson.h"
  16 #include "npshannon.h"
  17 #include "shannon.h"
  18 #include "jackknife.h"
  19
  20 //**********************************************************************************************************************
  21
  22
  23 RareFactCommand::RareFactCommand(){
  24         try {
  25                 globaldata = GlobalData::getInstance();
  26                 string fileNameRoot;
  27                 fileNameRoot = getRootName(globaldata->inputFileName);
  28                 int i;
  29                 for (i=0; i<globaldata->rareEstimators.size(); i++) {
  30                         if (globaldata->rareEstimators[i] == "sobs") {
  31                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
  32                         }else if (globaldata->rareEstimators[i] == "chao") {
  33                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
  34                         }else if (globaldata->rareEstimators[i] == "ace") {
  35                                 rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
  36                         }else if (globaldata->rareEstimators[i] == "jack") {
  37                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
  38                         }else if (globaldata->rareEstimators[i] == "shannon") {
  39                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
  40                         }else if (globaldata->rareEstimators[i] == "npshannon") {
  41                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
  42                         }else if (globaldata->rareEstimators[i] == "simpson") {
  43                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
  44                         }else if (globaldata->rareEstimators[i] == "bootstrap") {
  45                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
  46                         }
  47                 }
  48
  49
  50         }
  51         catch(exception& e) {
  52                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55         catch(...) {
  56                 cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59
  60 }
  61
  62 //**********************************************************************************************************************
  63
  64 RareFactCommand::~RareFactCommand(){
  65         delete order;
  66         delete input;
  67         delete rCurve;
  68         delete read;
  69 }
  70
  71 //**********************************************************************************************************************
  72
  73 int RareFactCommand::execute(){
  74         try {
  75                 int count = 1;
  76                 read = new ReadPhilFile(globaldata->inputFileName);
  77                 read->read(&*globaldata);
  78
  79                 order = globaldata->gorder;
  80                 input = globaldata->ginput;
  81
  82                 while(order != NULL){
  83
  84                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  85
  86                                 rCurve = new Rarefact(order, rDisplays);
  87                                 convert(globaldata->getFreq(), freq);
  88                                 convert(globaldata->getIters(), nIters);
  89                                 rCurve->getCurve(freq, nIters);
  90
  91                                 delete rCurve;
  92
  93                                 cout << order->getLabel() << '\t' << count << endl;
  94                         }
  95
  96                         order = (input->getOrderVector());
  97                         count++;
  98
  99                 }
 100
 101                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 102                 return 0;
 103         }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108         catch(...) {
 109                 cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112 }
 113
 114 //**********************************************************************************************************************