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
  21 //**********************************************************************************************************************
  22
  23 SummaryCommand::SummaryCommand(){
  24         try {
  25                 globaldata = GlobalData::getInstance();
  26                 validCalculator = new ValidCalculators();
  27                 int i;
  28
  29                 for (i=0; i<globaldata->Estimators.size(); i++) {
  30                         if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
  31                                 if(globaldata->Estimators[i] == "sobs"){
  32                                         sumCalculators.push_back(new Sobs());
  33                                 }else if(globaldata->Estimators[i] == "chao"){
  34                                         sumCalculators.push_back(new Chao1());
  35                                 }else if(globaldata->Estimators[i] == "ace"){
  36                                         convert(globaldata->getAbund(), abund);
  37                                         if(abund < 5)
  38                                                 abund = 10;
  39                                         sumCalculators.push_back(new Ace(abund));
  40                                 }else if(globaldata->Estimators[i] == "jack"){
  41                                         sumCalculators.push_back(new Jackknife());
  42                                 }else if(globaldata->Estimators[i] == "shannon"){
  43                                         sumCalculators.push_back(new Shannon());
  44                                 }else if(globaldata->Estimators[i] == "npshannon"){
  45                                         sumCalculators.push_back(new NPShannon());
  46                                 }else if(globaldata->Estimators[i] == "simpson"){
  47                                         sumCalculators.push_back(new Simpson());
  48                                 }else if(globaldata->Estimators[i] == "bootstrap"){
  49                                         sumCalculators.push_back(new Bootstrap());
  50                                 }else if (globaldata->Estimators[i] == "nseqs") {
  51                                         sumCalculators.push_back(new NSeqs());
  52                                 }
  53                         }
  54                 }
  55
  56                 //reset calc for next command
  57                 globaldata->setCalc("");
  58
  59         }
  60         catch(exception& e) {
  61                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64         catch(...) {
  65                 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 SummaryCommand::~SummaryCommand(){
  72         delete sabund;
  73         delete input;
  74         delete read;
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 int SummaryCommand::execute(){
  80         try {
  81
  82                 //if the users entered no valid calculators don't execute command
  83                 if (sumCalculators.size() == 0) { return 0; }
  84
  85                 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
  86                 openOutputFile(outputFileName, outputFileHandle);
  87                 outputFileHandle << "label";
  88
  89                 read = new ReadPhilFile(globaldata->inputFileName);
  90                 read->read(&*globaldata);
  91
  92                 for(int i=0;i<sumCalculators.size();i++){
  93                         if(sumCalculators[i]->getCols() == 1){
  94                                 outputFileHandle << '\t' << sumCalculators[i]->getName();
  95                         }
  96                         else{
  97                                 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
  98                         }
  99                 }
 100                 outputFileHandle << endl;
 101
 102                 sabund = globaldata->sabund;
 103                 input = globaldata->ginput;
 104                 int count = 1;
 105                 while(sabund != NULL){
 106
 107                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 108
 109                                 cout << sabund->getLabel() << '\t' << count << endl;
 110
 111                                 outputFileHandle << sabund->getLabel();
 112                                 for(int i=0;i<sumCalculators.size();i++){
 113                                         vector<double> data = sumCalculators[i]->getValues(sabund);
 114                                         outputFileHandle << '\t';
 115                                         sumCalculators[i]->print(outputFileHandle);
 116                                 }
 117                                 outputFileHandle << endl;
 118                         }
 119
 120                         sabund = input->getSAbundVector();
 121                         count++;
 122                 }
 123
 124                 return 0;
 125         }
 126         catch(exception& e) {
 127                 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 128                 exit(1);
 129         }
 130         catch(...) {
 131                 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 132                 exit(1);
 133         }
 134 }
 135
 136 //**********************************************************************************************************************