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