venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18
  19
  20 //**********************************************************************************************************************
  21
  22 VennCommand::VennCommand(){
  23         try {
  24                 globaldata = GlobalData::getInstance();
  25                 format = globaldata->getFormat();
  26                 validCalculator = new ValidCalculators();
  27
  28                 int i;
  29
  30                 if (format == "list") {
  31                         for (i=0; i<globaldata->Estimators.size(); i++) {
  32                                 if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) {
  33                                         if (globaldata->Estimators[i] == "sobs") {
  34                                                 vennCalculators.push_back(new Sobs());
  35                                         }else if (globaldata->Estimators[i] == "chao") {
  36                                                 vennCalculators.push_back(new Chao1());
  37                                         }else if (globaldata->Estimators[i] == "ace") {
  38                                                 convert(globaldata->getAbund(), abund);
  39                                                 if(abund < 5)
  40                                                         abund = 10;
  41                                                 vennCalculators.push_back(new Ace(abund));
  42                                         //}else if (globaldata->Estimators[i] == "jack") {
  43                                                 //vennCalculators.push_back(new Jackknife());
  44                                         }
  45                                 }
  46                         }
  47                 }else {
  48                         for (i=0; i<globaldata->Estimators.size(); i++) {
  49                                 if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) {
  50                                         if (globaldata->Estimators[i] == "sharedsobs") {
  51                                                 vennCalculators.push_back(new SharedSobsCS());
  52                                         }else if (globaldata->Estimators[i] == "sharedchao") {
  53                                                 vennCalculators.push_back(new SharedChao1());
  54                                         }else if (globaldata->Estimators[i] == "sharedace") {
  55                                                 vennCalculators.push_back(new SharedAce());
  56                                         }
  57                                 }
  58                         }
  59                 }
  60
  61                 venn = new Venn();
  62
  63                 //reset calc for next command
  64                 globaldata->setCalc("");
  65
  66
  67         }
  68         catch(exception& e) {
  69                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72         catch(...) {
  73                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 VennCommand::~VennCommand(){
  80         delete input;
  81         delete read;
  82         delete venn;
  83         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 int VennCommand::execute(){
  89         try {
  90                 int count = 1;
  91                 SAbundVector* lastSAbund;
  92                 vector<SharedRAbundVector*> lastLookup;
  93
  94                 //if the users entered no valid calculators don't execute command
  95                 if (vennCalculators.size() == 0) { return 0; }
  96
  97                 if (format == "sharedfile") {
  98                         //you have groups
  99                         read = new ReadOTUFile(globaldata->inputFileName);
 100                         read->read(&*globaldata);
 101
 102                         input = globaldata->ginput;
 103                         lookup = input->getSharedRAbundVectors();
 104                         lastLookup = lookup;
 105                 }else if (format == "list") {
 106                         //you are using just a list file and have only one group
 107                         read = new ReadOTUFile(globaldata->inputFileName);
 108                         read->read(&*globaldata);
 109
 110                         sabund = globaldata->sabund;
 111                         lastSAbund = globaldata->sabund;
 112                         input = globaldata->ginput;
 113                 }
 114
 115                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 116                 set<string> processedLabels;
 117                 set<string> userLabels = globaldata->labels;
 118
 119                 if (format != "list") {
 120
 121                         //as long as you are not at the end of the file or done wih the lines you want
 122                         while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 123
 124                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 125                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
 126                                         processedLabels.insert(lookup[0]->getLabel());
 127                                         userLabels.erase(lookup[0]->getLabel());
 128
 129                                         if (lookup.size() > 4) {
 130                                                 cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
 131                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 132                                         }
 133                                         venn->getPic(lookup, vennCalculators);
 134                                 }
 135
 136                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 137                                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 138                                         processedLabels.insert(lastLookup[0]->getLabel());
 139                                         userLabels.erase(lastLookup[0]->getLabel());
 140
 141                                         if (lastLookup.size() > 4) {
 142                                                 cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
 143                                                 for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
 144                                         }
 145                                         venn->getPic(lastLookup, vennCalculators);
 146                                 }
 147
 148                                 //prevent memory leak
 149                                 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 150                                 lastLookup = lookup;
 151
 152                                 //get next line to process
 153                                 lookup = input->getSharedRAbundVectors();
 154                                 count++;
 155                         }
 156
 157                         //output error messages about any remaining user labels
 158                         set<string>::iterator it;
 159                         bool needToRun = false;
 160                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 161                                 cout << "Your file does not include the label "<< *it;
 162                                 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 163                                         cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 164                                         needToRun = true;
 165                                 }else {
 166                                         cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 167                                 }
 168                         }
 169
 170                         //run last line if you need to
 171                         if (needToRun == true)  {
 172                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 173                                 if (lastLookup.size() > 4) {
 174                                         cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
 175                                         for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
 176                                 }
 177                                 venn->getPic(lastLookup, vennCalculators);
 178                         }
 179
 180                         for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 181
 182                         //reset groups parameter
 183                         globaldata->Groups.clear();
 184
 185                 }else{
 186
 187                         while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 188
 189                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 190
 191                                         cout << sabund->getLabel() << '\t' << count << endl;
 192                                         venn->getPic(sabund, vennCalculators);
 193
 194                                         processedLabels.insert(sabund->getLabel());
 195                                         userLabels.erase(sabund->getLabel());
 196                                 }
 197
 198                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
 199
 200                                         cout << lastSAbund->getLabel() << '\t' << count << endl;
 201                                         venn->getPic(lastSAbund, vennCalculators);
 202
 203                                         processedLabels.insert(lastSAbund->getLabel());
 204                                         userLabels.erase(lastSAbund->getLabel());
 205                                 }
 206
 207                                 if (count != 1) { delete lastSAbund; }
 208                                 lastSAbund = sabund;
 209
 210                                 sabund = input->getSAbundVector();
 211                                 count++;
 212                         }
 213
 214                         //output error messages about any remaining user labels
 215                         set<string>::iterator it;
 216                         bool needToRun = false;
 217                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 218                                 cout << "Your file does not include the label "<< *it;
 219                                 if (processedLabels.count(lastSAbund->getLabel()) != 1) {
 220                                         cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
 221                                         needToRun = true;
 222                                 }else {
 223                                         cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
 224                                 }
 225                         }
 226
 227                         //run last line if you need to
 228                         if (needToRun == true)  {
 229                                 cout << lastSAbund->getLabel() << '\t' << count << endl;
 230                                 venn->getPic(lastSAbund, vennCalculators);
 231                         }
 232                         delete lastSAbund;
 233                 }
 234
 235
 236                 globaldata->setGroups("");
 237                 return 0;
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247 }
 248
 249 //**********************************************************************************************************************