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 #include "goodscoverage.h"
  26 #include "efron.h"
  27 #include "boneh.h"
  28 #include "solow.h"
  29 #include "shen.h"
  30 #include "coverage.h"
  31
  32
  33 //**********************************************************************************************************************
  34 CollectCommand::CollectCommand(){
  35         try {
  36                 globaldata = GlobalData::getInstance();
  37                 string fileNameRoot;
  38                 fileNameRoot = getRootName(globaldata->inputFileName);
  39                 int i;
  40                 validCalculator = new ValidCalculators();
  41                 for (i=0; i<globaldata->Estimators.size(); i++) {
  42                         if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
  43                                 if (globaldata->Estimators[i] == "sobs") {
  44                                         cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  45                                 }else if (globaldata->Estimators[i] == "chao") {
  46                                         cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  47                                 }else if (globaldata->Estimators[i] == "nseqs") {
  48                                         cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
  49                                 }else if (globaldata->Estimators[i] == "coverage") {
  50                                         cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
  51                                 }else if (globaldata->Estimators[i] == "ace") {
  52                                         convert(globaldata->getAbund(), abund);
  53                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  54                                 }else if (globaldata->Estimators[i] == "jack") {
  55                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  56                                 }else if (globaldata->Estimators[i] == "shannon") {
  57                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  58                                 }else if (globaldata->Estimators[i] == "npshannon") {
  59                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  60                                 }else if (globaldata->Estimators[i] == "simpson") {
  61                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  62                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  63                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  64                                 }else if (globaldata->Estimators[i] == "geometric") {
  65                                         cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
  66                                 }else if (globaldata->Estimators[i] == "qstat") {
  67                                         cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
  68                                 }else if (globaldata->Estimators[i] == "logseries") {
  69                                         cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
  70                                 }else if (globaldata->Estimators[i] == "bergerparker") {
  71                                         cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
  72                                 }else if (globaldata->Estimators[i] == "bstick") {
  73                                         cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
  74                                 }else if (globaldata->Estimators[i] == "goodscoverage") {
  75                                         cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
  76                                 }else if (globaldata->Estimators[i] == "efron") {
  77                                         convert(globaldata->getSize(), size);
  78                                         cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
  79                                 }else if (globaldata->Estimators[i] == "boneh") {
  80                                         convert(globaldata->getSize(), size);
  81                                         cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
  82                                 }else if (globaldata->Estimators[i] == "solow") {
  83                                         convert(globaldata->getSize(), size);
  84                                         cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
  85                                 }else if (globaldata->Estimators[i] == "shen") {
  86                                         convert(globaldata->getSize(), size);
  87                                         cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen")));
  88                                 }
  89                         }
  90                 }
  91
  92                 //reset calc for next command
  93                 globaldata->setCalc("");
  94         }
  95         catch(exception& e) {
  96                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99         catch(...) {
 100                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 101                 exit(1);
 102         }
 103
 104 }
 105
 106 //**********************************************************************************************************************
 107
 108 CollectCommand::~CollectCommand(){
 109         delete order;
 110         delete input;
 111         delete cCurve;
 112         delete read;
 113 }
 114
 115 //**********************************************************************************************************************
 116
 117 int CollectCommand::execute(){
 118         try {
 119                 int count = 1;
 120
 121                 //if the users entered no valid calculators don't execute command
 122                 if (cDisplays.size() == 0) { return 0; }
 123
 124                 read = new ReadOTUFile(globaldata->inputFileName);
 125                 read->read(&*globaldata);
 126
 127                 order = globaldata->gorder;
 128                 input = globaldata->ginput;
 129                 set<string> orderList;
 130
 131                 while(order != NULL){
 132
 133                         orderList.insert(order->getLabel());
 134                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 135                                 cCurve = new Collect(order, cDisplays);
 136                                 convert(globaldata->getFreq(), freq);
 137                                 cCurve->getCurve(freq);
 138
 139                                 delete cCurve;
 140
 141                                 cout << order->getLabel() << '\t' << count << endl;
 142                         }
 143
 144                         delete order;
 145                         order = (input->getOrderVector());
 146                         count++;
 147                 }
 148                 set<string>::iterator i;
 149                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 150                         if(orderList.count(*i) == 0)
 151                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 152                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 153                 return 0;
 154         }
 155         catch(exception& e) {
 156                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159         catch(...) {
 160                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163 }
 164
 165 //**********************************************************************************************************************