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