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