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 #include "coverage.h"
  21
  22 //**********************************************************************************************************************
  23
  24
  25 RareFactCommand::RareFactCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 string fileNameRoot;
  29                 fileNameRoot = getRootName(globaldata->inputFileName);
  30                 validCalculator = new ValidCalculators();
  31
  32                 int i;
  33                 for (i=0; i<globaldata->Estimators.size(); i++) {
  34                         if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) {
  35                                 if (globaldata->Estimators[i] == "sobs") {
  36                                         rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
  37                                 }else if (globaldata->Estimators[i] == "chao") {
  38                                         rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
  39                                 }else if (globaldata->Estimators[i] == "ace") {
  40                                         convert(globaldata->getAbund(), abund);
  41                                         if(abund < 5)
  42                                                 abund = 10;
  43                                         rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
  44                                 }else if (globaldata->Estimators[i] == "jack") {
  45                                         rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
  46                                 }else if (globaldata->Estimators[i] == "shannon") {
  47                                         rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
  48                                 }else if (globaldata->Estimators[i] == "npshannon") {
  49                                         rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
  50                                 }else if (globaldata->Estimators[i] == "simpson") {
  51                                         rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
  52                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  53                                         rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
  54                                 }else if (globaldata->Estimators[i] == "coverage") {
  55                                         rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
  56                                 }else if (globaldata->Estimators[i] == "nseqs") {
  57                                         rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
  58                                 }
  59                         }
  60                 }
  61
  62                 //reset calc for next command
  63                 globaldata->setCalc("");
  64
  65         }
  66         catch(exception& e) {
  67                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  68                 exit(1);
  69         }
  70         catch(...) {
  71                 cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  72                 exit(1);
  73         }
  74
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 RareFactCommand::~RareFactCommand(){
  80         delete order;
  81         delete input;
  82         delete rCurve;
  83         delete read;
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 int RareFactCommand::execute(){
  89         try {
  90                 int count = 1;
  91
  92                 //if the users entered no valid calculators don't execute command
  93                 if (rDisplays.size() == 0) { return 0; }
  94
  95                 read = new ReadOTUFile(globaldata->inputFileName);
  96                 read->read(&*globaldata);
  97
  98                 order = globaldata->gorder;
  99                 input = globaldata->ginput;
 100
 101                 while(order != NULL){
 102
 103                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 104
 105                                 rCurve = new Rarefact(order, rDisplays);
 106                                 convert(globaldata->getFreq(), freq);
 107                                 convert(globaldata->getIters(), nIters);
 108                                 rCurve->getCurve(freq, nIters);
 109
 110                                 delete rCurve;
 111
 112                                 cout << order->getLabel() << '\t' << count << endl;
 113                         }
 114
 115                         order = (input->getOrderVector());
 116                         count++;
 117
 118                 }
 119
 120                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 121                 return 0;
 122         }
 123         catch(exception& e) {
 124                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 125                 exit(1);
 126         }
 127         catch(...) {
 128                 cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 129                 exit(1);
 130         }
 131 }
 132
 133 //**********************************************************************************************************************