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                 convert(globaldata->getFreq(), freq);
  40                 int i;
  41                 validCalculator = new ValidCalculators();
  42
  43                 for (i=0; i<globaldata->Estimators.size(); i++) {
  44                         if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
  45                                 if (globaldata->Estimators[i] == "sobs") {
  46                                         cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  47                                 }else if (globaldata->Estimators[i] == "chao") {
  48                                         cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  49                                 }else if (globaldata->Estimators[i] == "nseqs") {
  50                                         cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
  51                                 }else if (globaldata->Estimators[i] == "coverage") {
  52                                         cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
  53                                 }else if (globaldata->Estimators[i] == "ace") {
  54                                         convert(globaldata->getAbund(), abund);
  55                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  56                                 }else if (globaldata->Estimators[i] == "jack") {
  57                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  58                                 }else if (globaldata->Estimators[i] == "shannon") {
  59                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  60                                 }else if (globaldata->Estimators[i] == "npshannon") {
  61                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  62                                 }else if (globaldata->Estimators[i] == "simpson") {
  63                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  64                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  65                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  66                                 }else if (globaldata->Estimators[i] == "geometric") {
  67                                         cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
  68                                 }else if (globaldata->Estimators[i] == "qstat") {
  69                                         cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
  70                                 }else if (globaldata->Estimators[i] == "logseries") {
  71                                         cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
  72                                 }else if (globaldata->Estimators[i] == "bergerparker") {
  73                                         cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
  74                                 }else if (globaldata->Estimators[i] == "bstick") {
  75                                         cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
  76                                 }else if (globaldata->Estimators[i] == "goodscoverage") {
  77                                         cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
  78                                 }else if (globaldata->Estimators[i] == "efron") {
  79                                         convert(globaldata->getSize(), size);
  80                                         cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
  81                                 }else if (globaldata->Estimators[i] == "boneh") {
  82                                         convert(globaldata->getSize(), size);
  83                                         cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
  84                                 }else if (globaldata->Estimators[i] == "solow") {
  85                                         convert(globaldata->getSize(), size);
  86                                         cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
  87                                 }else if (globaldata->Estimators[i] == "shen") {
  88                                         convert(globaldata->getSize(), size);
  89                                         cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen")));
  90                                 }
  91                         }
  92                 }
  93
  94                 //reset calc for next command
  95                 globaldata->setCalc("");
  96         }
  97         catch(exception& e) {
  98                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  99                 exit(1);
 100         }
 101         catch(...) {
 102                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105
 106 }
 107
 108 //**********************************************************************************************************************
 109
 110 CollectCommand::~CollectCommand(){
 111         delete order;
 112         delete input;
 113         delete cCurve;
 114         delete read;
 115 }
 116
 117 //**********************************************************************************************************************
 118
 119 int CollectCommand::execute(){
 120         try {
 121                 int count = 1;
 122
 123                 //if the users entered no valid calculators don't execute command
 124                 if (cDisplays.size() == 0) { return 0; }
 125
 126                 read = new ReadOTUFile(globaldata->inputFileName);
 127                 read->read(&*globaldata);
 128
 129                 order = globaldata->gorder;
 130                 lastOrder = order;
 131                 input = globaldata->ginput;
 132
 133                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 134                 set<string> processedLabels;
 135                 set<string> userLabels = globaldata->labels;
 136
 137                 while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 138
 139                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 140
 141                                 cCurve = new Collect(order, cDisplays);
 142                                 cCurve->getCurve(freq);
 143                                 delete cCurve;
 144
 145                                 cout << order->getLabel() << '\t' << count << endl;
 146                                 processedLabels.insert(order->getLabel());
 147                                 userLabels.erase(order->getLabel());
 148
 149                         //you have a label the user want that is smaller than this line and the last line has not already been processed
 150                         }
 151
 152                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
 153                                 cCurve = new Collect(lastOrder, cDisplays);
 154                                 cCurve->getCurve(freq);
 155                                 delete cCurve;
 156
 157                                 cout << lastOrder->getLabel() << '\t' << count << endl;
 158                                 processedLabels.insert(lastOrder->getLabel());
 159                                 userLabels.erase(lastOrder->getLabel());
 160                         }
 161
 162                         if (count != 1) { delete lastOrder; }
 163                         lastOrder = order;
 164                         order = (input->getOrderVector());
 165                         count++;
 166                 }
 167
 168                 //output error messages about any remaining user labels
 169                 set<string>::iterator it;
 170                 bool needToRun = false;
 171                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 172                         cout << "Your file does not include the label "<< *it;
 173                         if (processedLabels.count(lastOrder->getLabel()) != 1) {
 174                                 cout << ". I will use " << lastOrder->getLabel() << "." << endl;
 175                                 needToRun = true;
 176                         }else {
 177                                 cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
 178                         }
 179                 }
 180
 181                 //run last line if you need to
 182                 if (needToRun == true)  {
 183                         cCurve = new Collect(lastOrder, cDisplays);
 184                         cCurve->getCurve(freq);
 185                         delete cCurve;
 186
 187                         cout << lastOrder->getLabel() << '\t' << count << endl;
 188                 }
 189
 190                 delete lastOrder;
 191                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 192                 return 0;
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203
 204 //**********************************************************************************************************************