summarycommand.cpp

   1 /*
   2  *  summarycommand.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 "summarycommand.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 "geom.h"
  21 #include "logsd.h"
  22 #include "qstat.h"
  23 #include "bergerparker.h"
  24 #include "bstick.h"
  25 #include "goodscoverage.h"
  26 #include "coverage.h"
  27
  28 //**********************************************************************************************************************
  29
  30 SummaryCommand::SummaryCommand(){
  31         try {
  32                 globaldata = GlobalData::getInstance();
  33                 validCalculator = new ValidCalculators();
  34                 int i;
  35
  36                 for (i=0; i<globaldata->Estimators.size(); i++) {
  37                         if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
  38                                 if(globaldata->Estimators[i] == "sobs"){
  39                                         sumCalculators.push_back(new Sobs());
  40                                 }else if(globaldata->Estimators[i] == "chao"){
  41                                         sumCalculators.push_back(new Chao1());
  42                                 }else if(globaldata->Estimators[i] == "coverage"){
  43                                         sumCalculators.push_back(new Coverage());
  44                                 }else if(globaldata->Estimators[i] == "geometric"){
  45                                         sumCalculators.push_back(new Geom());
  46                                 }else if(globaldata->Estimators[i] == "logseries"){
  47                                         sumCalculators.push_back(new LogSD());
  48                                 }else if(globaldata->Estimators[i] == "qstat"){
  49                                         sumCalculators.push_back(new QStat());
  50                                 }else if(globaldata->Estimators[i] == "bergerparker"){
  51                                         sumCalculators.push_back(new BergerParker());
  52                                 }else if(globaldata->Estimators[i] == "bstick"){
  53                                         sumCalculators.push_back(new BStick());
  54                                 }else if(globaldata->Estimators[i] == "ace"){
  55                                         convert(globaldata->getAbund(), abund);
  56                                         if(abund < 5)
  57                                                 abund = 10;
  58                                         sumCalculators.push_back(new Ace(abund));
  59                                 }else if(globaldata->Estimators[i] == "jack"){
  60                                         sumCalculators.push_back(new Jackknife());
  61                                 }else if(globaldata->Estimators[i] == "shannon"){
  62                                         sumCalculators.push_back(new Shannon());
  63                                 }else if(globaldata->Estimators[i] == "npshannon"){
  64                                         sumCalculators.push_back(new NPShannon());
  65                                 }else if(globaldata->Estimators[i] == "simpson"){
  66                                         sumCalculators.push_back(new Simpson());
  67                                 }else if(globaldata->Estimators[i] == "bootstrap"){
  68                                         sumCalculators.push_back(new Bootstrap());
  69                                 }else if (globaldata->Estimators[i] == "nseqs") {
  70                                         sumCalculators.push_back(new NSeqs());
  71                                 }else if (globaldata->Estimators[i] == "goodscoverage") {
  72                                         sumCalculators.push_back(new GoodsCoverage());
  73                                 }
  74                         }
  75                 }
  76
  77                 //reset calc for next command
  78                 globaldata->setCalc("");
  79
  80         }
  81         catch(exception& e) {
  82                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85         catch(...) {
  86                 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 SummaryCommand::~SummaryCommand(){
  93         delete sabund;
  94         delete input;
  95         delete read;
  96 }
  97
  98 //**********************************************************************************************************************
  99
 100 int SummaryCommand::execute(){
 101         try {
 102
 103                 //if the users entered no valid calculators don't execute command
 104                 if (sumCalculators.size() == 0) { return 0; }
 105
 106                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
 107                 openOutputFile(outputFileName, outputFileHandle);
 108                 outputFileHandle << "label";
 109
 110                 read = new ReadOTUFile(globaldata->inputFileName);
 111                 read->read(&*globaldata);
 112
 113                 for(int i=0;i<sumCalculators.size();i++){
 114                         if(sumCalculators[i]->getCols() == 1){
 115                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
 116                         }
 117                         else{
 118                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 119                         }
 120                 }
 121                 outputFileHandle << endl;
 122
 123                 sabund = globaldata->sabund;
 124                 input = globaldata->ginput;
 125                 int count = 1;
 126                 while(sabund != NULL){
 127
 128                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 129
 130                                 cout << sabund->getLabel() << '\t' << count << endl;
 131
 132                                 outputFileHandle << sabund->getLabel();
 133                                 for(int i=0;i<sumCalculators.size();i++){
 134                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 135                                         outputFileHandle << '\t';
 136                                         sumCalculators[i]->print(outputFileHandle);
 137                                 }
 138
 139                                 outputFileHandle << endl;
 140                         }
 141                         sabund = input->getSAbundVector();
 142                         count++;
 143                 }
 144
 145                 return 0;
 146         }
 147         catch(exception& e) {
 148                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 149                 exit(1);
 150         }
 151         catch(...) {
 152                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 153                 exit(1);
 154         }
 155 }
 156
 157 //**********************************************************************************************************************