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                 int i;
  26                 for (i=0; i<globaldata->summaryEstimators.size(); i++) {
  27                         if(globaldata->summaryEstimators[i] == "sobs"){
  28                                 sumCalculators.push_back(new Sobs());
  29                         }else if(globaldata->summaryEstimators[i] == "chao"){
  30                                 sumCalculators.push_back(new Chao1());
  31                         }else if(globaldata->summaryEstimators[i] == "ace"){
  32                                 sumCalculators.push_back(new Ace());
  33                         }else if(globaldata->summaryEstimators[i] == "jack"){
  34                                 sumCalculators.push_back(new Jackknife());
  35                         }else if(globaldata->summaryEstimators[i] == "shannon"){
  36                                 sumCalculators.push_back(new Shannon());
  37                         }else if(globaldata->summaryEstimators[i] == "npshannon"){
  38                                 sumCalculators.push_back(new NPShannon());
  39                         }else if(globaldata->summaryEstimators[i] == "simpson"){
  40                                 sumCalculators.push_back(new Simpson());
  41                         }else if(globaldata->summaryEstimators[i] == "bootstrap"){
  42                                 sumCalculators.push_back(new Bootstrap());
  43                         }
  44                 }
  45         }
  46         catch(exception& e) {
  47                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  48                 exit(1);
  49         }
  50         catch(...) {
  51                 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56
  57 SummaryCommand::~SummaryCommand(){
  58         delete sabund;
  59         delete input;
  60         delete read;
  61 }
  62
  63 //**********************************************************************************************************************
  64
  65 int SummaryCommand::execute(){
  66         try {
  67                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
  68                 openOutputFile(outputFileName, outputFileHandle);
  69                 outputFileHandle << "label";
  70
  71                 read = new ReadPhilFile(globaldata->inputFileName);
  72                 read->read(&*globaldata);
  73
  74                 for(int i=0;i<sumCalculators.size();i++){
  75                         if(sumCalculators[i]->getCols() == 1){
  76                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
  77                         }
  78                         else{
  79                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
  80                         }
  81                 }
  82                 outputFileHandle << endl;
  83
  84                 sabund = globaldata->sabund;
  85                 input = globaldata->ginput;
  86                 int count = 1;
  87                 while(sabund != NULL){
  88
  89                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
  90
  91                                 cout << sabund->getLabel() << '\t' << count << endl;
  92
  93                                 outputFileHandle << sabund->getLabel();
  94                                 for(int i=0;i<sumCalculators.size();i++){
  95                                         vector<double> data = sumCalculators[i]->getValues(sabund);
  96                                         outputFileHandle << '\t';
  97                                         sumCalculators[i]->print(outputFileHandle);
  98                                 }
  99                                 outputFileHandle << endl;
 100                         }
 101
 102                         sabund = input->getSAbundVector();
 103                         count++;
 104                 }
 105
 106                 return 0;
 107         }
 108         catch(exception& e) {
 109                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112         catch(...) {
 113                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 114                 exit(1);
 115         }
 116 }
 117
 118 //**********************************************************************************************************************