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                 validCalculator = new ValidCalculators();
  29
  30                 int i;
  31                 for (i=0; i<globaldata->Estimators.size(); i++) {
  32                         if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) {
  33                                 if (globaldata->Estimators[i] == "sobs") {
  34                                         rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
  35                                 }else if (globaldata->Estimators[i] == "chao") {
  36                                         rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
  37                                 }else if (globaldata->Estimators[i] == "ace") {
  38                                         convert(globaldata->getAbund(), abund);
  39                                         if(abund < 5)
  40                                                 abund = 10;
  41                                         rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
  42                                 }else if (globaldata->Estimators[i] == "jack") {
  43                                         rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
  44                                 }else if (globaldata->Estimators[i] == "shannon") {
  45                                         rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
  46                                 }else if (globaldata->Estimators[i] == "npshannon") {
  47                                         rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
  48                                 }else if (globaldata->Estimators[i] == "simpson") {
  49                                         rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
  50                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  51                                         rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
  52                                 }
  53                         }
  54                 }
  55
  56                 //reset calc for next command
  57                 globaldata->setCalc("");
  58
  59         }
  60         catch(exception& e) {
  61                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64         catch(...) {
  65                 cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68
  69 }
  70
  71 //**********************************************************************************************************************
  72
  73 RareFactCommand::~RareFactCommand(){
  74         delete order;
  75         delete input;
  76         delete rCurve;
  77         delete read;
  78 }
  79
  80 //**********************************************************************************************************************
  81
  82 int RareFactCommand::execute(){
  83         try {
  84                 int count = 1;
  85
  86                 //if the users entered no valid calculators don't execute command
  87                 if (rDisplays.size() == 0) { return 0; }
  88
  89                 read = new ReadPhilFile(globaldata->inputFileName);
  90                 read->read(&*globaldata);
  91
  92                 order = globaldata->gorder;
  93                 input = globaldata->ginput;
  94
  95                 while(order != NULL){
  96
  97                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  98
  99                                 rCurve = new Rarefact(order, rDisplays);
 100                                 convert(globaldata->getFreq(), freq);
 101                                 convert(globaldata->getIters(), nIters);
 102                                 rCurve->getCurve(freq, nIters);
 103
 104                                 delete rCurve;
 105
 106                                 cout << order->getLabel() << '\t' << count << endl;
 107                         }
 108
 109                         order = (input->getOrderVector());
 110                         count++;
 111
 112                 }
 113
 114                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 115                 return 0;
 116         }
 117         catch(exception& e) {
 118                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121         catch(...) {
 122                 cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125 }
 126
 127 //**********************************************************************************************************************