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                 for (i=0; i<globaldata->singleEstimators.size(); i++) {
  31                         if (globaldata->singleEstimators[i] == "sobs") {
  32                                 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  33                         }else if (globaldata->singleEstimators[i] == "chao") {
  34                                 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  35                         }else if (globaldata->singleEstimators[i] == "ace") {
  36                                 cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
  37                         }else if (globaldata->singleEstimators[i] == "jack") {
  38                                 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  39                         }else if (globaldata->singleEstimators[i] == "shannon") {
  40                                 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  41                         }else if (globaldata->singleEstimators[i] == "npshannon") {
  42                                 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  43                         }else if (globaldata->singleEstimators[i] == "simpson") {
  44                                 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  45                         }else if (globaldata->singleEstimators[i] == "bootstrap") {
  46                                 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  47                         }
  48                 }
  49         }
  50         catch(exception& e) {
  51                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54         catch(...) {
  55                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58
  59 }
  60
  61 //**********************************************************************************************************************
  62
  63 CollectCommand::~CollectCommand(){
  64         delete order;
  65         delete input;
  66         delete cCurve;
  67         delete read;
  68 }
  69
  70 //**********************************************************************************************************************
  71
  72 int CollectCommand::execute(){
  73         try {
  74                 int count = 1;
  75                 read = new ReadPhilFile(globaldata->inputFileName);
  76                 read->read(&*globaldata);
  77
  78                 order = globaldata->gorder;
  79                 input = globaldata->ginput;
  80
  81                 while(order != NULL){
  82
  83                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  84
  85                                 cCurve = new Collect(order, cDisplays);
  86                                 convert(globaldata->getFreq(), freq);
  87                                 cCurve->getCurve(freq);
  88
  89                                 delete cCurve;
  90
  91                                 cout << order->getLabel() << '\t' << count << endl;
  92                         }
  93
  94                         order = (input->getOrderVector());
  95                         count++;
  96
  97                 }
  98
  99                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 100                 return 0;
 101         }
 102         catch(exception& e) {
 103                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 104                 exit(1);
 105         }
 106         catch(...) {
 107                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110 }
 111
 112 //**********************************************************************************************************************