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