collectcommand.cpp

   1 /*
   2  *  collectcommand.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 "collectcommand.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
  23
  24 CollectCommand::CollectCommand(){
  25         try {
  26                 globaldata = GlobalData::getInstance();
  27                 string fileNameRoot;
  28                 fileNameRoot = getRootName(globaldata->inputFileName);
  29                 int i;
  30                 validCalculator = new ValidCalculators();
  31
  32                 for (i=0; i<globaldata->Estimators.size(); i++) {
  33                         if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
  34                                 if (globaldata->Estimators[i] == "sobs") {
  35                                         cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  36                                 }else if (globaldata->Estimators[i] == "chao") {
  37                                         cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  38                                 }else if (globaldata->Estimators[i] == "ace") {
  39                                         cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
  40                                 }else if (globaldata->Estimators[i] == "jack") {
  41                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  42                                 }else if (globaldata->Estimators[i] == "shannon") {
  43                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  44                                 }else if (globaldata->Estimators[i] == "npshannon") {
  45                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  46                                 }else if (globaldata->Estimators[i] == "simpson") {
  47                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  48                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  49                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  50                                 }
  51                         }
  52                 }
  53
  54                 //reset calc for next command
  55                 globaldata->setCalc("");
  56         }
  57         catch(exception& e) {
  58                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. 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 CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65
  66 }
  67
  68 //**********************************************************************************************************************
  69
  70 CollectCommand::~CollectCommand(){
  71         delete order;
  72         delete input;
  73         delete cCurve;
  74         delete read;
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 int CollectCommand::execute(){
  80         try {
  81                 int count = 1;
  82
  83                 //if the users entered no valid calculators don't execute command
  84                 if (cDisplays.size() == 0) { return 0; }
  85
  86                 read = new ReadPhilFile(globaldata->inputFileName);
  87                 read->read(&*globaldata);
  88
  89                 order = globaldata->gorder;
  90                 input = globaldata->ginput;
  91
  92                 while(order != NULL){
  93
  94                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  95
  96                                 cCurve = new Collect(order, cDisplays);
  97                                 convert(globaldata->getFreq(), freq);
  98                                 cCurve->getCurve(freq);
  99
 100                                 delete cCurve;
 101
 102                                 cout << order->getLabel() << '\t' << count << endl;
 103                         }
 104
 105                         order = (input->getOrderVector());
 106                         count++;
 107
 108                 }
 109
 110                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 111                 return 0;
 112         }
 113         catch(exception& e) {
 114                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117         catch(...) {
 118                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121 }
 122
 123 //**********************************************************************************************************************