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 #include "nseqs.h"
  19
  20
  21 //**********************************************************************************************************************
  22 vector<string> VennCommand::getValidParameters(){
  23         try {
  24                 string Array[] =  {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
  25                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "VennCommand", "getValidParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 VennCommand::VennCommand(){
  35         try {
  36                 abort = true;
  37                 //initialize outputTypes
  38                 vector<string> tempOutNames;
  39                 outputTypes["svg"] = tempOutNames;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "VennCommand", "VennCommand");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 vector<string> VennCommand::getRequiredParameters(){
  48         try {
  49                 vector<string> myArray;
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "VennCommand", "getRequiredParameters");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 vector<string> VennCommand::getRequiredFiles(){
  59         try {
  60                 string Array[] =  {"list","shared","or"};
  61                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  62                 return myArray;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "VennCommand", "getRequiredFiles");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 VennCommand::VennCommand(string option)  {
  72         try {
  73                 globaldata = GlobalData::getInstance();
  74                 abort = false;
  75                 allLines = 1;
  76                 labels.clear();
  77
  78                 //allow user to run help
  79                 if(option == "help") { help(); abort = true; }
  80
  81                 else {
  82                         //valid paramters for this command
  83                         string AlignArray[] =  {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
  84                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95
  96                         //make sure the user has already run the read.otu command
  97                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  98                                 m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); abort = true;
  99                         }
 100
 101                         //if the user changes the output directory command factory will send this info to us in the output parameter
 102                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 103                                 outputDir = "";
 104                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 105                         }
 106
 107                         //check for optional parameter and set defaults
 108                         // ...at some point should added some additional type checking...
 109                         label = validParameter.validFile(parameters, "label", false);
 110                         if (label == "not found") { label = ""; }
 111                         else {
 112                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 113                                 else { allLines = 1;  }
 114                         }
 115
 116                         //if the user has not specified any labels use the ones from read.otu
 117                         if (label == "") {
 118                                 allLines = globaldata->allLines;
 119                                 labels = globaldata->labels;
 120                         }
 121
 122                         groups = validParameter.validFile(parameters, "groups", false);
 123                         if (groups == "not found") { groups = ""; }
 124                         else {
 125                                 m->splitAtDash(groups, Groups);
 126                                 globaldata->Groups = Groups;
 127                         }
 128
 129                         format = globaldata->getFormat();
 130                         calc = validParameter.validFile(parameters, "calc", false);
 131                         if (calc == "not found") {
 132                                 if(format == "list") { calc = "sobs"; }
 133                                 else { calc = "sharedsobs"; }
 134                         }
 135                         else {
 136                                  if (calc == "default")  {
 137                                         if(format == "list") { calc = "sobs"; }
 138                                         else { calc = "sharedsobs"; }
 139                                 }
 140                         }
 141                         m->splitAtDash(calc, Estimators);
 142
 143                         string temp;
 144                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 145                         convert(temp, abund);
 146
 147                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 148                         nseqs = m->isTrue(temp);
 149
 150                         temp = validParameter.validFile(parameters, "permute", false);                  if (temp == "not found"){       temp = "f";                             }
 151                         perm = m->isTrue(temp);
 152
 153                         if (abort == false) {
 154                                 validCalculator = new ValidCalculators();
 155
 156                                 int i;
 157
 158                                 if (format == "list") {
 159                                         for (i=0; i<Estimators.size(); i++) {
 160                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 161                                                         if (Estimators[i] == "sobs") {
 162                                                                 vennCalculators.push_back(new Sobs());
 163                                                         }else if (Estimators[i] == "chao") {
 164                                                                 vennCalculators.push_back(new Chao1());
 165                                                         }else if (Estimators[i] == "ace") {
 166                                                                 if(abund < 5)
 167                                                                         abund = 10;
 168                                                                 vennCalculators.push_back(new Ace(abund));
 169                                                         }
 170                                                 }
 171                                         }
 172                                 }else {
 173                                         for (i=0; i<Estimators.size(); i++) {
 174                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 175                                                         if (Estimators[i] == "sharedsobs") {
 176                                                                 vennCalculators.push_back(new SharedSobsCS());
 177                                                         }else if (Estimators[i] == "sharedchao") {
 178                                                                 vennCalculators.push_back(new SharedChao1());
 179                                                         }else if (Estimators[i] == "sharedace") {
 180                                                                 vennCalculators.push_back(new SharedAce());
 181                                                         }
 182                                                 }
 183                                         }
 184                                 }
 185
 186                                 //if the users entered no valid calculators don't execute command
 187                                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true;  }
 188                                 else {  venn = new Venn(outputDir, nseqs);  }
 189                         }
 190
 191                 }
 192
 193
 194
 195         }
 196         catch(exception& e) {
 197                 m->errorOut(e, "VennCommand", "VennCommand");
 198                 exit(1);
 199         }
 200 }
 201
 202 //**********************************************************************************************************************
 203
 204 void VennCommand::help(){
 205         try {
 206                 m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 207                 m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label.  No parameters are required.\n");
 208                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
 209                 m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
 210                 m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
 211                 m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
 212                 m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
 213                 m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
 214                 m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
 215                 m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
 216                 m->mothurOut("If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n");
 217                 m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
 218                 m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 219                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 220         }
 221         catch(exception& e) {
 222                 m->errorOut(e, "VennCommand", "help");
 223                 exit(1);
 224         }
 225 }
 226
 227
 228 //**********************************************************************************************************************
 229
 230 VennCommand::~VennCommand(){
 231         if (abort == false) {
 232                 delete input; globaldata->ginput = NULL;
 233                 delete read;
 234                 delete venn;
 235                 globaldata->sabund = NULL;
 236                 delete validCalculator;
 237         }
 238
 239 }
 240
 241 //**********************************************************************************************************************
 242
 243 int VennCommand::execute(){
 244         try {
 245
 246                 if (abort == true) { return 0; }
 247
 248                 string lastLabel;
 249
 250                 if (format == "sharedfile") {
 251                         //you have groups
 252                         read = new ReadOTUFile(globaldata->inputFileName);
 253                         read->read(&*globaldata);
 254
 255                         input = globaldata->ginput;
 256                         lookup = input->getSharedRAbundVectors();
 257                         lastLabel = lookup[0]->getLabel();
 258
 259                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 260                 }else if (format == "list") {
 261                         //you are using just a list file and have only one group
 262                         read = new ReadOTUFile(globaldata->inputFileName);
 263                         read->read(&*globaldata);
 264
 265                         sabund = globaldata->sabund;
 266                         lastLabel = sabund->getLabel();
 267                         input = globaldata->ginput;
 268                 }
 269
 270                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 271                 set<string> processedLabels;
 272                 set<string> userLabels = labels;
 273
 274                 if (format != "list") {
 275
 276                         //as long as you are not at the end of the file or done wih the lines you want
 277                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 278
 279                                 if (m->control_pressed) {
 280                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 281                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 282                                         globaldata->Groups.clear();
 283                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 284                                         return 0;
 285                                 }
 286
 287                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 288                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 289                                         processedLabels.insert(lookup[0]->getLabel());
 290                                         userLabels.erase(lookup[0]->getLabel());
 291
 292                                         if ((lookup.size() > 4) && (!perm)){
 293                                                 m->mothurOut("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. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 294                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 295
 296                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 297                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 298
 299                                         }else if ((lookup.size() > 4) && (perm)) {
 300                                                 set< set<int> >::iterator it3;
 301                                                 set<int>::iterator it2;
 302                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 303
 304                                                         set<int> poss = *it3;
 305                                                         vector<SharedRAbundVector*> subset;
 306                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 307
 308                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 309                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 310                                                 }
 311                                         }else {
 312                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 313                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 314                                         }
 315                                 }
 316
 317                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 318                                         string saveLabel = lookup[0]->getLabel();
 319
 320                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 321                                         lookup = input->getSharedRAbundVectors(lastLabel);
 322
 323                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 324                                         processedLabels.insert(lookup[0]->getLabel());
 325                                         userLabels.erase(lookup[0]->getLabel());
 326
 327                                         if ((lookup.size() > 4) && (!perm)){
 328                                                 m->mothurOut("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. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 329                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 330
 331                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 332                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 333
 334                                         }else if ((lookup.size() > 4) && (perm)) {
 335                                                 set< set<int> >::iterator it3;
 336                                                 set<int>::iterator it2;
 337                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 338
 339                                                         set<int> poss = *it3;
 340                                                         vector<SharedRAbundVector*> subset;
 341                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 342
 343                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 344                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 345                                                 }
 346                                         }else {
 347                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 348                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 349                                         }
 350
 351                                         //restore real lastlabel to save below
 352                                         lookup[0]->setLabel(saveLabel);
 353                                 }
 354
 355
 356                                 lastLabel = lookup[0]->getLabel();
 357
 358                                 //get next line to process
 359                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 360                                 lookup = input->getSharedRAbundVectors();
 361                         }
 362
 363                         if (m->control_pressed) {
 364                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 365                                         globaldata->Groups.clear();
 366                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 367                                         return 0;
 368                         }
 369
 370
 371                         //output error messages about any remaining user labels
 372                         set<string>::iterator it;
 373                         bool needToRun = false;
 374                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 375                                 m->mothurOut("Your file does not include the label " + *it);
 376                                 if (processedLabels.count(lastLabel) != 1) {
 377                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 378                                         needToRun = true;
 379                                 }else {
 380                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 381                                 }
 382                         }
 383
 384                         //run last label if you need to
 385                         if (needToRun == true)  {
 386                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 387                                         lookup = input->getSharedRAbundVectors(lastLabel);
 388
 389                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 390                                         processedLabels.insert(lookup[0]->getLabel());
 391                                         userLabels.erase(lookup[0]->getLabel());
 392
 393                                         if ((lookup.size() > 4) && (!perm)){
 394                                                 m->mothurOut("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. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 395                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 396
 397                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 398                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 399
 400                                         }else if ((lookup.size() > 4) && (perm)) {
 401                                                 set< set<int> >::iterator it3;
 402                                                 set<int>::iterator it2;
 403                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 404
 405                                                         set<int> poss = *it3;
 406                                                         vector<SharedRAbundVector*> subset;
 407                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 408
 409                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 410                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 411                                                 }
 412                                         }else {
 413                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 414                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 415                                         }
 416
 417                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 418                         }
 419
 420
 421                         //reset groups parameter
 422                         globaldata->Groups.clear();
 423
 424                         if (m->control_pressed) {
 425                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 426                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 427                                         return 0;
 428                         }
 429
 430
 431                 }else{
 432
 433                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 434
 435                                 if (m->control_pressed) {
 436                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 437                                         delete sabund;
 438                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 439                                         return 0;
 440                                 }
 441
 442                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 443
 444                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 445                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 446                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 447
 448
 449                                         processedLabels.insert(sabund->getLabel());
 450                                         userLabels.erase(sabund->getLabel());
 451                                 }
 452
 453                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 454                                         string saveLabel = sabund->getLabel();
 455
 456                                         delete sabund;
 457                                         sabund = input->getSAbundVector(lastLabel);
 458
 459                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 460                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 461                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 462
 463
 464                                         processedLabels.insert(sabund->getLabel());
 465                                         userLabels.erase(sabund->getLabel());
 466
 467                                         //restore real lastlabel to save below
 468                                         sabund->setLabel(saveLabel);
 469                                 }
 470
 471                                 lastLabel = sabund->getLabel();
 472
 473                                 delete sabund;
 474                                 sabund = input->getSAbundVector();
 475                         }
 476
 477                         if (m->control_pressed) {
 478                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 479                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 480                                         return 0;
 481                         }
 482
 483                         //output error messages about any remaining user labels
 484                         set<string>::iterator it;
 485                         bool needToRun = false;
 486                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 487                                 m->mothurOut("Your file does not include the label " + *it);
 488                                 if (processedLabels.count(lastLabel) != 1) {
 489                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 490                                         needToRun = true;
 491                                 }else {
 492                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 493                                 }
 494                         }
 495
 496                         //run last label if you need to
 497                         if (needToRun == true)  {
 498                                 if (sabund != NULL) {   delete sabund;  }
 499                                 sabund = input->getSAbundVector(lastLabel);
 500
 501                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 502                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 503                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 504
 505                                 delete sabund;
 506
 507                         }
 508
 509                         if (m->control_pressed) {
 510                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 511                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 512                                         return 0;
 513                         }
 514                 }
 515
 516                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 517
 518                 m->mothurOutEndLine();
 519                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 520                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 521                 m->mothurOutEndLine();
 522
 523
 524                 return 0;
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "VennCommand", "execute");
 528                 exit(1);
 529         }
 530 }
 531 //**********************************************************************************************************************
 532 //returns a vector of sets containing the 4 group combinations
 533 set< set<int> > VennCommand::findCombinations(int lookupSize){
 534         try {
 535                 set< set<int> > combos;
 536
 537                 set<int> possibles;
 538                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 539
 540                 getCombos(possibles, combos);
 541
 542                 return combos;
 543
 544         }
 545         catch(exception& e) {
 546                 m->errorOut(e, "VennCommand", "findCombinations");
 547                 exit(1);
 548         }
 549 }
 550 //**********************************************************************************************************************
 551 //recusively finds combos of 4
 552 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 553         try {
 554
 555                 if (possibles.size() == 4) { //done
 556                         if (combos.count(possibles) == 0) { //no dups
 557                                 combos.insert(possibles);
 558                         }
 559                 }else { //we still have work to do
 560                         set<int>::iterator it;
 561                         set<int>::iterator it2;
 562                         for (it = possibles.begin(); it != possibles.end(); it++) {
 563
 564                                 set<int> newPossibles;
 565                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 566                                         if (*it != *it2) {
 567                                                 newPossibles.insert(*it2);
 568                                         }
 569                                 }
 570                                 getCombos(newPossibles, combos);
 571                         }
 572                 }
 573
 574                 return 0;
 575         }
 576         catch(exception& e) {
 577                 m->errorOut(e, "VennCommand", "getCombos");
 578                 exit(1);
 579         }
 580 }
 581
 582 //**********************************************************************************************************************