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 "chao1.h"
  14 #include "bootstrap.h"
  15 #include "simpson.h"
  16 #include "npshannon.h"
  17 #include "shannon.h"
  18 #include "jackknife.h"
  19
  20 //**********************************************************************************************************************
  21
  22 SummaryCommand::SummaryCommand(){
  23         try {
  24                 globaldata = GlobalData::getInstance();
  25                 validCalculator = new ValidCalculators();
  26                 int i;
  27
  28                 for (i=0; i<globaldata->Estimators.size(); i++) {
  29                         if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
  30                                 if(globaldata->Estimators[i] == "sobs"){
  31                                         sumCalculators.push_back(new Sobs());
  32                                 }else if(globaldata->Estimators[i] == "chao"){
  33                                         sumCalculators.push_back(new Chao1());
  34                                 }else if(globaldata->Estimators[i] == "ace"){
  35                                         convert(globaldata->getAbund(), abund);
  36                                         if(abund < 5)
  37                                                 abund = 10;
  38                                         sumCalculators.push_back(new Ace());
  39                                 }else if(globaldata->Estimators[i] == "jack"){
  40                                         sumCalculators.push_back(new Jackknife());
  41                                 }else if(globaldata->Estimators[i] == "shannon"){
  42                                         sumCalculators.push_back(new Shannon());
  43                                 }else if(globaldata->Estimators[i] == "npshannon"){
  44                                         sumCalculators.push_back(new NPShannon());
  45                                 }else if(globaldata->Estimators[i] == "simpson"){
  46                                         sumCalculators.push_back(new Simpson());
  47                                 }else if(globaldata->Estimators[i] == "bootstrap"){
  48                                         sumCalculators.push_back(new Bootstrap());
  49                                 }
  50                         }
  51                 }
  52
  53                 //reset calc for next command
  54                 globaldata->setCalc("");
  55
  56         }
  57         catch(exception& e) {
  58                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61         catch(...) {
  62                 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67
  68 SummaryCommand::~SummaryCommand(){
  69         delete sabund;
  70         delete input;
  71         delete read;
  72 }
  73
  74 //**********************************************************************************************************************
  75
  76 int SummaryCommand::execute(){
  77         try {
  78
  79                 //if the users entered no valid calculators don't execute command
  80                 if (sumCalculators.size() == 0) { return 0; }
  81
  82                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
  83                 openOutputFile(outputFileName, outputFileHandle);
  84                 outputFileHandle << "label";
  85
  86                 read = new ReadPhilFile(globaldata->inputFileName);
  87                 read->read(&*globaldata);
  88
  89                 for(int i=0;i<sumCalculators.size();i++){
  90                         if(sumCalculators[i]->getCols() == 1){
  91                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
  92                         }
  93                         else{
  94                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
  95                         }
  96                 }
  97                 outputFileHandle << endl;
  98
  99                 sabund = globaldata->sabund;
 100                 input = globaldata->ginput;
 101                 int count = 1;
 102                 while(sabund != NULL){
 103
 104                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 105
 106                                 cout << sabund->getLabel() << '\t' << count << endl;
 107
 108                                 outputFileHandle << sabund->getLabel();
 109                                 for(int i=0;i<sumCalculators.size();i++){
 110                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 111                                         outputFileHandle << '\t';
 112                                         sumCalculators[i]->print(outputFileHandle);
 113                                 }
 114                                 outputFileHandle << endl;
 115                         }
 116
 117                         sabund = input->getSAbundVector();
 118                         count++;
 119                 }
 120
 121                 return 0;
 122         }
 123         catch(exception& e) {
 124                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 125                 exit(1);
 126         }
 127         catch(...) {
 128                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 129                 exit(1);
 130         }
 131 }
 132
 133 //**********************************************************************************************************************