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 "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "npshannon.h"
  18 #include "shannon.h"
  19 #include "jackknife.h"
  20
  21 //**********************************************************************************************************************
  22
  23
  24 RareFactCommand::RareFactCommand(){
  25         try {
  26                 globaldata = GlobalData::getInstance();
  27                 string fileNameRoot;
  28                 fileNameRoot = getRootName(globaldata->inputFileName);
  29                 validCalculator = new ValidCalculators();
  30
  31                 int i;
  32                 for (i=0; i<globaldata->Estimators.size(); i++) {
  33                         if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) {
  34                                 if (globaldata->Estimators[i] == "sobs") {
  35                                         rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
  36                                 }else if (globaldata->Estimators[i] == "chao") {
  37                                         rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
  38                                 }else if (globaldata->Estimators[i] == "ace") {
  39                                         convert(globaldata->getAbund(), abund);
  40                                         if(abund < 5)
  41                                                 abund = 10;
  42                                         rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
  43                                 }else if (globaldata->Estimators[i] == "jack") {
  44                                         rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
  45                                 }else if (globaldata->Estimators[i] == "shannon") {
  46                                         rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
  47                                 }else if (globaldata->Estimators[i] == "npshannon") {
  48                                         rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
  49                                 }else if (globaldata->Estimators[i] == "simpson") {
  50                                         rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
  51                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  52                                         rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
  53                                 }else if (globaldata->Estimators[i] == "nseqs") {
  54                                         rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
  55                                 }
  56                         }
  57                 }
  58
  59                 //reset calc for next command
  60                 globaldata->setCalc("");
  61
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71
  72 }
  73
  74 //**********************************************************************************************************************
  75
  76 RareFactCommand::~RareFactCommand(){
  77         delete order;
  78         delete input;
  79         delete rCurve;
  80         delete read;
  81 }
  82
  83 //**********************************************************************************************************************
  84
  85 int RareFactCommand::execute(){
  86         try {
  87                 int count = 1;
  88
  89                 //if the users entered no valid calculators don't execute command
  90                 if (rDisplays.size() == 0) { return 0; }
  91
  92                 read = new ReadOTUFile(globaldata->inputFileName);
  93                 read->read(&*globaldata);
  94
  95                 order = globaldata->gorder;
  96                 input = globaldata->ginput;
  97
  98                 while(order != NULL){
  99
 100                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 101
 102                                 rCurve = new Rarefact(order, rDisplays);
 103                                 convert(globaldata->getFreq(), freq);
 104                                 convert(globaldata->getIters(), nIters);
 105                                 rCurve->getCurve(freq, nIters);
 106
 107                                 delete rCurve;
 108
 109                                 cout << order->getLabel() << '\t' << count << endl;
 110                         }
 111
 112                         order = (input->getOrderVector());
 113                         count++;
 114
 115                 }
 116
 117                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 118                 return 0;
 119         }
 120         catch(exception& e) {
 121                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124         catch(...) {
 125                 cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 126                 exit(1);
 127         }
 128 }
 129
 130 //**********************************************************************************************************************