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 "coverage.h"
  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] == "coverage") {
  44                                         cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
  45                                 }else if (globaldata->Estimators[i] == "ace") {
  46                                         convert(globaldata->getAbund(), abund);
  47                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  48                                 }else if (globaldata->Estimators[i] == "jack") {
  49                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  50                                 }else if (globaldata->Estimators[i] == "shannon") {
  51                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  52                                 }else if (globaldata->Estimators[i] == "npshannon") {
  53                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  54                                 }else if (globaldata->Estimators[i] == "simpson") {
  55                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  56                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  57                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  58                                 }else if (globaldata->Estimators[i] == "geometric") {
  59                                         cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
  60                                 }else if (globaldata->Estimators[i] == "qstat") {
  61                                         cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
  62                                 }else if (globaldata->Estimators[i] == "logseries") {
  63                                         cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
  64                                 }else if (globaldata->Estimators[i] == "bergerparker") {
  65                                         cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
  66                                 }else if (globaldata->Estimators[i] == "bstick") {
  67                                         cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick")));
  68                                 }
  69                         }
  70                 }
  71
  72                 //reset calc for next command
  73                 globaldata->setCalc("");
  74         }
  75         catch(exception& e) {
  76                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  77                 exit(1);
  78         }
  79         catch(...) {
  80                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  81                 exit(1);
  82         }
  83
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 CollectCommand::~CollectCommand(){
  89         delete order;
  90         delete input;
  91         delete cCurve;
  92         delete read;
  93 }
  94
  95 //**********************************************************************************************************************
  96
  97 int CollectCommand::execute(){
  98         try {
  99                 int count = 1;
 100
 101                 //if the users entered no valid calculators don't execute command
 102                 if (cDisplays.size() == 0) { return 0; }
 103
 104                 read = new ReadOTUFile(globaldata->inputFileName);
 105                 read->read(&*globaldata);
 106
 107                 order = globaldata->gorder;
 108                 input = globaldata->ginput;
 109                 set<string> orderList;
 110
 111                 while(order != NULL){
 112
 113                         orderList.insert(order->getLabel());
 114                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 115                                 cCurve = new Collect(order, cDisplays);
 116                                 convert(globaldata->getFreq(), freq);
 117                                 cCurve->getCurve(freq);
 118
 119                                 delete cCurve;
 120
 121                                 cout << order->getLabel() << '\t' << count << endl;
 122                         }
 123                         order = (input->getOrderVector());
 124                         count++;
 125                 }
 126                 set<string>::iterator i;
 127                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 128                         if(orderList.count(*i) == 0)
 129                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 130                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 131                 return 0;
 132         }
 133         catch(exception& e) {
 134                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 135                 exit(1);
 136         }
 137         catch(...) {
 138                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 139                 exit(1);
 140         }
 141 }
 142
 143 //**********************************************************************************************************************