rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15
  16 RareFactSharedCommand::RareFactSharedCommand(){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19                 string fileNameRoot;
  20                 fileNameRoot = getRootName(globaldata->inputFileName);
  21                 format = globaldata->getFormat();
  22                 validCalculator = new ValidCalculators();
  23
  24                 int i;
  25                 for (i=0; i<globaldata->Estimators.size(); i++) {
  26                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  27                                 if (globaldata->Estimators[i] == "sharedobserved") {
  28                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  29                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  30                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
  31                                 }
  32
  33                         }
  34                 }
  35
  36                 //reset calc for next command
  37                 globaldata->setCalc("");
  38
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48
  49 }
  50
  51 //**********************************************************************************************************************
  52
  53 RareFactSharedCommand::~RareFactSharedCommand(){
  54         delete input;
  55         delete rCurve;
  56         delete read;
  57 }
  58
  59 //**********************************************************************************************************************
  60
  61 int RareFactSharedCommand::execute(){
  62         try {
  63                 int count = 1;
  64
  65                 //if the users entered no valid calculators don't execute command
  66                 if (rDisplays.size() == 0) { return 0; }
  67
  68                 read = new ReadOTUFile(globaldata->inputFileName);
  69                 read->read(&*globaldata);
  70
  71                 input = globaldata->ginput;
  72                 lookup = input->getSharedRAbundVectors();
  73
  74                 if (lookup.size() < 2) {
  75                         cout << "I cannot run the command without at least 2 valid groups.";
  76                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
  77                         return 0;
  78                 }
  79
  80
  81                 while(lookup[0] != NULL){
  82
  83                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
  84                                 //create collectors curve
  85                                 rCurve = new Rarefact(lookup, rDisplays);
  86                                 convert(globaldata->getFreq(), freq);
  87                                 convert(globaldata->getIters(), nIters);
  88                                 rCurve->getSharedCurve(freq, nIters);
  89
  90                                 delete rCurve;
  91
  92                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
  93                         }
  94
  95                         //prevent memory leak
  96                         for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
  97
  98                         //get next line to process
  99                         lookup = input->getSharedRAbundVectors();
 100                         count++;
 101                 }
 102
 103                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 104
 105                 //reset groups parameter
 106                 globaldata->Groups.clear();  globaldata->setGroups("");
 107
 108                 return 0;
 109         }
 110         catch(exception& e) {
 111                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114         catch(...) {
 115                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 116                 exit(1);
 117         }
 118 }
 119
 120
 121 //**********************************************************************************************************************