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                 int count = 1;
 119
 120                 //if the users entered no valid calculators don't execute command
 121                 if (sumCalculators.size() == 0) { return 0; }
 122
 123                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
 124                 openOutputFile(outputFileName, outputFileHandle);
 125                 outputFileHandle << "label";
 126
 127                 read = new ReadOTUFile(globaldata->inputFileName);
 128                 read->read(&*globaldata);
 129
 130                 sabund = globaldata->sabund;
 131                 SAbundVector* lastSAbund = sabund;
 132                 input = globaldata->ginput;
 133
 134                 for(int i=0;i<sumCalculators.size();i++){
 135                         if(sumCalculators[i]->getCols() == 1){
 136                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
 137                         }
 138                         else{
 139                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
 140                         }
 141                 }
 142                 outputFileHandle << endl;
 143
 144                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 145                 set<string> processedLabels;
 146                 set<string> userLabels = globaldata->labels;
 147                 set<int> userLines = globaldata->lines;
 148
 149                 while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 150
 151                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 152
 153                                 cout << sabund->getLabel() << '\t' << count << endl;
 154                                 processedLabels.insert(sabund->getLabel());
 155                                 userLabels.erase(sabund->getLabel());
 156                                 userLines.erase(count);
 157
 158
 159                                 outputFileHandle << sabund->getLabel();
 160                                 for(int i=0;i<sumCalculators.size();i++){
 161                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 162                                         outputFileHandle << '\t';
 163                                         sumCalculators[i]->print(outputFileHandle);
 164                                 }
 165                                 outputFileHandle << endl;
 166                         }
 167
 168                         if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
 169
 170                                 cout << lastSAbund->getLabel() << '\t' << count << endl;
 171                                 processedLabels.insert(lastSAbund->getLabel());
 172                                 userLabels.erase(lastSAbund->getLabel());
 173
 174                                 outputFileHandle << lastSAbund->getLabel();
 175                                 for(int i=0;i<sumCalculators.size();i++){
 176                                         vector<double> data = sumCalculators[i]->getValues(lastSAbund);
 177                                         outputFileHandle << '\t';
 178                                         sumCalculators[i]->print(outputFileHandle);
 179                                 }
 180                                 outputFileHandle << endl;
 181                         }
 182
 183                         if (count != 1) { delete lastSAbund; }
 184                         lastSAbund = sabund;
 185
 186                         sabund = input->getSAbundVector();
 187                         count++;
 188                 }
 189
 190                 //output error messages about any remaining user labels
 191                 set<string>::iterator it;
 192                 bool needToRun = false;
 193                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 194                         cout << "Your file does not include the label "<< *it;
 195                         if (processedLabels.count(lastSAbund->getLabel()) != 1) {
 196                                 cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
 197                                 needToRun = true;
 198                         }else {
 199                                 cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
 200                         }
 201                 }
 202
 203                 //run last line if you need to
 204                 if (needToRun == true)  {
 205                         cout << lastSAbund->getLabel() << '\t' << count << endl;
 206                         outputFileHandle << lastSAbund->getLabel();
 207                         for(int i=0;i<sumCalculators.size();i++){
 208                                 vector<double> data = sumCalculators[i]->getValues(lastSAbund);
 209                                 outputFileHandle << '\t';
 210                                 sumCalculators[i]->print(outputFileHandle);
 211                         }
 212                         outputFileHandle << endl;
 213                 }
 214
 215                 delete lastSAbund;
 216                 return 0;
 217         }
 218         catch(exception& e) {
 219                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 220                 exit(1);
 221         }
 222         catch(...) {
 223                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 224                 exit(1);
 225         }
 226 }
 227
 228 //**********************************************************************************************************************