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 "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 #include "geom.h"
  21 #include "qstat.h"
  22 #include "logsd.h"
  23 #include "bergerparker.h"
  24 #include "bstick.h"
  25
  26
  27 //**********************************************************************************************************************
  28 CollectCommand::CollectCommand(){
  29         try {
  30                 globaldata = GlobalData::getInstance();
  31                 string fileNameRoot;
  32                 fileNameRoot = getRootName(globaldata->inputFileName);
  33                 int i;
  34                 validCalculator = new ValidCalculators();
  35                 for (i=0; i<globaldata->Estimators.size(); i++) {
  36                         if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
  37                                 if (globaldata->Estimators[i] == "sobs") {
  38                                         cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  39                                 }else if (globaldata->Estimators[i] == "chao") {
  40                                         cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  41                                 }else if (globaldata->Estimators[i] == "nseqs") {
  42                                         cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
  43                                 }else if (globaldata->Estimators[i] == "ace") {
  44                                         convert(globaldata->getAbund(), abund);
  45                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  46                                 }else if (globaldata->Estimators[i] == "jack") {
  47                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  48                                 }else if (globaldata->Estimators[i] == "shannon") {
  49                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  50                                 }else if (globaldata->Estimators[i] == "npshannon") {
  51                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  52                                 }else if (globaldata->Estimators[i] == "simpson") {
  53                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  54                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  55                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  56                                 }else if (globaldata->Estimators[i] == "geom") {
  57                                         cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom")));
  58                                 }else if (globaldata->Estimators[i] == "qstat") {
  59                                         cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
  60                                 }else if (globaldata->Estimators[i] == "logsd") {
  61                                         cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd")));
  62                                 }else if (globaldata->Estimators[i] == "bergerparker") {
  63                                         cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
  64                                 }else if (globaldata->Estimators[i] == "bstick") {
  65                                         cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick")));
  66                                 }
  67                         }
  68                 }
  69
  70                 //reset calc for next command
  71                 globaldata->setCalc("");
  72         }
  73         catch(exception& e) {
  74                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77         catch(...) {
  78                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81
  82 }
  83
  84 //**********************************************************************************************************************
  85
  86 CollectCommand::~CollectCommand(){
  87         delete order;
  88         delete input;
  89         delete cCurve;
  90         delete read;
  91 }
  92
  93 //**********************************************************************************************************************
  94
  95 int CollectCommand::execute(){
  96         try {
  97                 int count = 1;
  98
  99                 //if the users entered no valid calculators don't execute command
 100                 if (cDisplays.size() == 0) { return 0; }
 101
 102                 read = new ReadOTUFile(globaldata->inputFileName);
 103                 read->read(&*globaldata);
 104
 105                 order = globaldata->gorder;
 106                 input = globaldata->ginput;
 107                 set<string> orderList;
 108
 109                 while(order != NULL){
 110
 111                         orderList.insert(order->getLabel());
 112                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 113                                 cCurve = new Collect(order, cDisplays);
 114                                 convert(globaldata->getFreq(), freq);
 115                                 cCurve->getCurve(freq);
 116
 117                                 delete cCurve;
 118
 119                                 cout << order->getLabel() << '\t' << count << endl;
 120                         }
 121                         order = (input->getOrderVector());
 122                         count++;
 123                 }
 124                 set<string>::iterator i;
 125                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 126                         if(orderList.count(*i) == 0)
 127                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 128                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 129                 return 0;
 130         }
 131         catch(exception& e) {
 132                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 133                 exit(1);
 134         }
 135         catch(...) {
 136                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 137                 exit(1);
 138         }
 139 }
 140
 141 //**********************************************************************************************************************