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