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