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 #include "efron.h"
  28 #include "boneh.h"
  29 #include "solow.h"
  30 #include "shen.h"
  31
  32 //**********************************************************************************************************************
  33
  34 SummaryCommand::SummaryCommand(){
  35         try {
  36                 globaldata = GlobalData::getInstance();
  37                 validCalculator = new ValidCalculators();
  38                 int i;
  39
  40                 for (i=0; i<globaldata->Estimators.size(); i++) {
  41                         if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
  42                                 if(globaldata->Estimators[i] == "sobs"){
  43                                         sumCalculators.push_back(new Sobs());
  44                                 }else if(globaldata->Estimators[i] == "chao"){
  45                                         sumCalculators.push_back(new Chao1());
  46                                 }else if(globaldata->Estimators[i] == "coverage"){
  47                                         sumCalculators.push_back(new Coverage());
  48                                 }else if(globaldata->Estimators[i] == "geometric"){
  49                                         sumCalculators.push_back(new Geom());
  50                                 }else if(globaldata->Estimators[i] == "logseries"){
  51                                         sumCalculators.push_back(new LogSD());
  52                                 }else if(globaldata->Estimators[i] == "qstat"){
  53                                         sumCalculators.push_back(new QStat());
  54                                 }else if(globaldata->Estimators[i] == "bergerparker"){
  55                                         sumCalculators.push_back(new BergerParker());
  56                                 }else if(globaldata->Estimators[i] == "bstick"){
  57                                         sumCalculators.push_back(new BStick());
  58                                 }else if(globaldata->Estimators[i] == "ace"){
  59                                         convert(globaldata->getAbund(), abund);
  60                                         if(abund < 5)
  61                                                 abund = 10;
  62                                         sumCalculators.push_back(new Ace(abund));
  63                                 }else if(globaldata->Estimators[i] == "jack"){
  64                                         sumCalculators.push_back(new Jackknife());
  65                                 }else if(globaldata->Estimators[i] == "shannon"){
  66                                         sumCalculators.push_back(new Shannon());
  67                                 }else if(globaldata->Estimators[i] == "npshannon"){
  68                                         sumCalculators.push_back(new NPShannon());
  69                                 }else if(globaldata->Estimators[i] == "simpson"){
  70                                         sumCalculators.push_back(new Simpson());
  71                                 }else if(globaldata->Estimators[i] == "bootstrap"){
  72                                         sumCalculators.push_back(new Bootstrap());
  73                                 }else if (globaldata->Estimators[i] == "nseqs") {
  74                                         sumCalculators.push_back(new NSeqs());
  75                                 }else if (globaldata->Estimators[i] == "goodscoverage") {
  76                                         sumCalculators.push_back(new GoodsCoverage());
  77                                 }else if (globaldata->Estimators[i] == "efron") {
  78                                         convert(globaldata->getSize(), size);
  79                                         sumCalculators.push_back(new Efron(size));
  80                                 }else if (globaldata->Estimators[i] == "boneh") {
  81                                         convert(globaldata->getSize(), size);
  82                                         sumCalculators.push_back(new Boneh(size));
  83                                 }else if (globaldata->Estimators[i] == "solow") {
  84                                         convert(globaldata->getSize(), size);
  85                                         sumCalculators.push_back(new Solow(size));
  86                                 }else if (globaldata->Estimators[i] == "shen") {
  87                                         convert(globaldata->getSize(), size);
  88                                         sumCalculators.push_back(new Shen(size));
  89                                 }
  90                         }
  91                 }
  92
  93                 //reset calc for next command
  94                 globaldata->setCalc("");
  95
  96         }
  97         catch(exception& e) {
  98                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  99                 exit(1);
 100         }
 101         catch(...) {
 102                 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108 SummaryCommand::~SummaryCommand(){
 109         delete sabund;
 110         delete input;
 111         delete read;
 112 }
 113
 114 //**********************************************************************************************************************
 115
 116 int SummaryCommand::execute(){
 117         try {
 118
 119                 //if the users entered no valid calculators don't execute command
 120                 if (sumCalculators.size() == 0) { return 0; }
 121
 122                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
 123                 openOutputFile(outputFileName, outputFileHandle);
 124                 outputFileHandle << "label";
 125
 126                 read = new ReadOTUFile(globaldata->inputFileName);
 127                 read->read(&*globaldata);
 128
 129                 for(int i=0;i<sumCalculators.size();i++){
 130                         if(sumCalculators[i]->getCols() == 1){
 131                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
 132                         }
 133                         else{
 134                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 135                         }
 136                 }
 137                 outputFileHandle << endl;
 138
 139                 sabund = globaldata->sabund;
 140                 input = globaldata->ginput;
 141                 int count = 1;
 142                 while(sabund != NULL){
 143
 144                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 145
 146                                 cout << sabund->getLabel() << '\t' << count << endl;
 147
 148                                 outputFileHandle << sabund->getLabel();
 149                                 for(int i=0;i<sumCalculators.size();i++){
 150                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 151                                         outputFileHandle << '\t';
 152                                         sumCalculators[i]->print(outputFileHandle);
 153                                 }
 154
 155                                 outputFileHandle << endl;
 156                         }
 157                         sabund = input->getSAbundVector();
 158                         count++;
 159                 }
 160
 161                 return 0;
 162         }
 163         catch(exception& e) {
 164                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167         catch(...) {
 168                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171 }
 172
 173 //**********************************************************************************************************************