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                                 convert(globaldata->getAbund(), abund);
  40                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  41                                 }else if (globaldata->Estimators[i] == "jack") {
  42                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  43                                 }else if (globaldata->Estimators[i] == "shannon") {
  44                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  45                                 }else if (globaldata->Estimators[i] == "npshannon") {
  46                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  47                                 }else if (globaldata->Estimators[i] == "simpson") {
  48                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  49                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  50                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  51                                 }
  52                         }
  53                 }
  54
  55                 //reset calc for next command
  56                 globaldata->setCalc("");
  57         }
  58         catch(exception& e) {
  59                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  60                 exit(1);
  61         }
  62         catch(...) {
  63                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  64                 exit(1);
  65         }
  66
  67 }
  68
  69 //**********************************************************************************************************************
  70
  71 CollectCommand::~CollectCommand(){
  72         delete order;
  73         delete input;
  74         delete cCurve;
  75         delete read;
  76 }
  77
  78 //**********************************************************************************************************************
  79
  80 int CollectCommand::execute(){
  81         try {
  82                 int count = 1;
  83
  84                 //if the users entered no valid calculators don't execute command
  85                 if (cDisplays.size() == 0) { return 0; }
  86
  87                 read = new ReadPhilFile(globaldata->inputFileName);
  88                 read->read(&*globaldata);
  89
  90                 order = globaldata->gorder;
  91                 input = globaldata->ginput;
  92                 set<string> orderList;
  93
  94                 while(order != NULL){
  95
  96                         orderList.insert(order->getLabel());
  97                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  98                                 cCurve = new Collect(order, cDisplays);
  99                                 convert(globaldata->getFreq(), freq);
 100                                 cCurve->getCurve(freq);
 101
 102                                 delete cCurve;
 103
 104                                 cout << order->getLabel() << '\t' << count << endl;
 105                         }
 106                         order = (input->getOrderVector());
 107                         count++;
 108                 }
 109                 set<string>::iterator i;
 110                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 111                         if(orderList.count(*i) == 0)
 112                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 113                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 114                 return 0;
 115         }
 116         catch(exception& e) {
 117                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120         catch(...) {
 121                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124 }
 125
 126 //**********************************************************************************************************************