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; calledHelp = true;
  37                 vector<string> tempOutNames;
  38                 outputTypes["svg"] = tempOutNames;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "VennCommand", "VennCommand");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 vector<string> VennCommand::getRequiredParameters(){
  47         try {
  48                 vector<string> myArray;
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "VennCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> VennCommand::getRequiredFiles(){
  58         try {
  59                 string Array[] =  {"list","shared","or"};
  60                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  61                 return myArray;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "VennCommand", "getRequiredFiles");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69
  70 VennCommand::VennCommand(string option)  {
  71         try {
  72                 globaldata = GlobalData::getInstance();
  73                 abort = false; calledHelp = false;
  74                 allLines = 1;
  75                 labels.clear();
  76
  77                 //allow user to run help
  78                 if(option == "help") { help(); abort = true; calledHelp = true; }
  79
  80                 else {
  81                         //valid paramters for this command
  82                         string AlignArray[] =  {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
  83                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  84
  85                         OptionParser parser(option);
  86                         map<string,string> parameters = parser.getParameters();
  87
  88                         ValidParameters validParameter;
  89
  90                         //check to make sure all parameters are valid for command
  91                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  92                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  93                         }
  94
  95                         //make sure the user has already run the read.otu command
  96                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  97                                 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;
  98                         }
  99
 100                         //if the user changes the output directory command factory will send this info to us in the output parameter
 101                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 102                                 outputDir = "";
 103                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 104                         }
 105
 106                         //check for optional parameter and set defaults
 107                         // ...at some point should added some additional type checking...
 108                         label = validParameter.validFile(parameters, "label", false);
 109                         if (label == "not found") { label = ""; }
 110                         else {
 111                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 112                                 else { allLines = 1;  }
 113                         }
 114
 115                         //if the user has not specified any labels use the ones from read.otu
 116                         if (label == "") {
 117                                 allLines = globaldata->allLines;
 118                                 labels = globaldata->labels;
 119                         }
 120
 121                         groups = validParameter.validFile(parameters, "groups", false);
 122                         if (groups == "not found") { groups = ""; }
 123                         else {
 124                                 m->splitAtDash(groups, Groups);
 125                                 globaldata->Groups = Groups;
 126                         }
 127
 128                         format = globaldata->getFormat();
 129                         calc = validParameter.validFile(parameters, "calc", false);
 130                         if (calc == "not found") {
 131                                 if(format == "list") { calc = "sobs"; }
 132                                 else { calc = "sharedsobs"; }
 133                         }
 134                         else {
 135                                  if (calc == "default")  {
 136                                         if(format == "list") { calc = "sobs"; }
 137                                         else { calc = "sharedsobs"; }
 138                                 }
 139                         }
 140                         m->splitAtDash(calc, Estimators);
 141
 142                         string temp;
 143                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 144                         convert(temp, abund);
 145
 146                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 147                         nseqs = m->isTrue(temp);
 148
 149                         temp = validParameter.validFile(parameters, "permute", false);                  if (temp == "not found"){       temp = "f";                             }
 150                         perm = m->isTrue(temp);
 151
 152                         if (abort == false) {
 153                                 validCalculator = new ValidCalculators();
 154
 155                                 int i;
 156
 157                                 if (format == "list") {
 158                                         for (i=0; i<Estimators.size(); i++) {
 159                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 160                                                         if (Estimators[i] == "sobs") {
 161                                                                 vennCalculators.push_back(new Sobs());
 162                                                         }else if (Estimators[i] == "chao") {
 163                                                                 vennCalculators.push_back(new Chao1());
 164                                                         }else if (Estimators[i] == "ace") {
 165                                                                 if(abund < 5)
 166                                                                         abund = 10;
 167                                                                 vennCalculators.push_back(new Ace(abund));
 168                                                         }
 169                                                 }
 170                                         }
 171                                 }else {
 172                                         for (i=0; i<Estimators.size(); i++) {
 173                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 174                                                         if (Estimators[i] == "sharedsobs") {
 175                                                                 vennCalculators.push_back(new SharedSobsCS());
 176                                                         }else if (Estimators[i] == "sharedchao") {
 177                                                                 vennCalculators.push_back(new SharedChao1());
 178                                                         }else if (Estimators[i] == "sharedace") {
 179                                                                 vennCalculators.push_back(new SharedAce());
 180                                                         }
 181                                                 }
 182                                         }
 183                                 }
 184
 185                                 //if the users entered no valid calculators don't execute command
 186                                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true;  }
 187                                 else {  venn = new Venn(outputDir, nseqs);  }
 188                         }
 189
 190                 }
 191
 192
 193
 194         }
 195         catch(exception& e) {
 196                 m->errorOut(e, "VennCommand", "VennCommand");
 197                 exit(1);
 198         }
 199 }
 200
 201 //**********************************************************************************************************************
 202
 203 void VennCommand::help(){
 204         try {
 205                 m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 206                 m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label.  No parameters are required.\n");
 207                 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");
 208                 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");
 209                 m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
 210                 m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
 211                 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");
 212                 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");
 213                 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");
 214                 m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
 215                 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");
 216                 m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
 217                 m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 218                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "VennCommand", "help");
 222                 exit(1);
 223         }
 224 }
 225
 226
 227 //**********************************************************************************************************************
 228
 229 VennCommand::~VennCommand(){
 230         if (abort == false) {
 231                 delete input; globaldata->ginput = NULL;
 232                 delete read;
 233                 delete venn;
 234                 globaldata->sabund = NULL;
 235                 delete validCalculator;
 236         }
 237
 238 }
 239
 240 //**********************************************************************************************************************
 241
 242 int VennCommand::execute(){
 243         try {
 244
 245                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 246
 247                 string lastLabel;
 248
 249                 if (format == "sharedfile") {
 250                         //you have groups
 251                         read = new ReadOTUFile(globaldata->inputFileName);
 252                         read->read(&*globaldata);
 253
 254                         input = globaldata->ginput;
 255                         lookup = input->getSharedRAbundVectors();
 256                         lastLabel = lookup[0]->getLabel();
 257
 258                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 259                 }else if (format == "list") {
 260                         //you are using just a list file and have only one group
 261                         read = new ReadOTUFile(globaldata->inputFileName);
 262                         read->read(&*globaldata);
 263
 264                         sabund = globaldata->sabund;
 265                         lastLabel = sabund->getLabel();
 266                         input = globaldata->ginput;
 267                 }
 268
 269                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 270                 set<string> processedLabels;
 271                 set<string> userLabels = labels;
 272
 273                 if (format != "list") {
 274
 275                         //as long as you are not at the end of the file or done wih the lines you want
 276                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 277
 278                                 if (m->control_pressed) {
 279                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 280                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 281                                         globaldata->Groups.clear();
 282                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 283                                         return 0;
 284                                 }
 285
 286                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 287                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 288                                         processedLabels.insert(lookup[0]->getLabel());
 289                                         userLabels.erase(lookup[0]->getLabel());
 290
 291                                         if ((lookup.size() > 4) && (!perm)){
 292                                                 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();
 293                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 294
 295                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 296                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 297
 298                                         }else if ((lookup.size() > 4) && (perm)) {
 299                                                 set< set<int> >::iterator it3;
 300                                                 set<int>::iterator it2;
 301                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 302
 303                                                         set<int> poss = *it3;
 304                                                         vector<SharedRAbundVector*> subset;
 305                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 306
 307                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 308                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 309                                                 }
 310                                         }else {
 311                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 312                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 313                                         }
 314                                 }
 315
 316                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 317                                         string saveLabel = lookup[0]->getLabel();
 318
 319                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 320                                         lookup = input->getSharedRAbundVectors(lastLabel);
 321
 322                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 323                                         processedLabels.insert(lookup[0]->getLabel());
 324                                         userLabels.erase(lookup[0]->getLabel());
 325
 326                                         if ((lookup.size() > 4) && (!perm)){
 327                                                 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();
 328                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 329
 330                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 331                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 332
 333                                         }else if ((lookup.size() > 4) && (perm)) {
 334                                                 set< set<int> >::iterator it3;
 335                                                 set<int>::iterator it2;
 336                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 337
 338                                                         set<int> poss = *it3;
 339                                                         vector<SharedRAbundVector*> subset;
 340                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 341
 342                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 343                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 344                                                 }
 345                                         }else {
 346                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 347                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 348                                         }
 349
 350                                         //restore real lastlabel to save below
 351                                         lookup[0]->setLabel(saveLabel);
 352                                 }
 353
 354
 355                                 lastLabel = lookup[0]->getLabel();
 356
 357                                 //get next line to process
 358                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 359                                 lookup = input->getSharedRAbundVectors();
 360                         }
 361
 362                         if (m->control_pressed) {
 363                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 364                                         globaldata->Groups.clear();
 365                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 366                                         return 0;
 367                         }
 368
 369
 370                         //output error messages about any remaining user labels
 371                         set<string>::iterator it;
 372                         bool needToRun = false;
 373                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 374                                 m->mothurOut("Your file does not include the label " + *it);
 375                                 if (processedLabels.count(lastLabel) != 1) {
 376                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 377                                         needToRun = true;
 378                                 }else {
 379                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 380                                 }
 381                         }
 382
 383                         //run last label if you need to
 384                         if (needToRun == true)  {
 385                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 386                                         lookup = input->getSharedRAbundVectors(lastLabel);
 387
 388                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 389                                         processedLabels.insert(lookup[0]->getLabel());
 390                                         userLabels.erase(lookup[0]->getLabel());
 391
 392                                         if ((lookup.size() > 4) && (!perm)){
 393                                                 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();
 394                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 395
 396                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 397                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 398
 399                                         }else if ((lookup.size() > 4) && (perm)) {
 400                                                 set< set<int> >::iterator it3;
 401                                                 set<int>::iterator it2;
 402                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 403
 404                                                         set<int> poss = *it3;
 405                                                         vector<SharedRAbundVector*> subset;
 406                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 407
 408                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 409                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 410                                                 }
 411                                         }else {
 412                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 413                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 414                                         }
 415
 416                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 417                         }
 418
 419
 420                         //reset groups parameter
 421                         globaldata->Groups.clear();
 422
 423                         if (m->control_pressed) {
 424                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 425                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 426                                         return 0;
 427                         }
 428
 429
 430                 }else{
 431
 432                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 433
 434                                 if (m->control_pressed) {
 435                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 436                                         delete sabund;
 437                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 438                                         return 0;
 439                                 }
 440
 441                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 442
 443                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 444                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 445                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 446
 447
 448                                         processedLabels.insert(sabund->getLabel());
 449                                         userLabels.erase(sabund->getLabel());
 450                                 }
 451
 452                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 453                                         string saveLabel = sabund->getLabel();
 454
 455                                         delete sabund;
 456                                         sabund = input->getSAbundVector(lastLabel);
 457
 458                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 459                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 460                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 461
 462
 463                                         processedLabels.insert(sabund->getLabel());
 464                                         userLabels.erase(sabund->getLabel());
 465
 466                                         //restore real lastlabel to save below
 467                                         sabund->setLabel(saveLabel);
 468                                 }
 469
 470                                 lastLabel = sabund->getLabel();
 471
 472                                 delete sabund;
 473                                 sabund = input->getSAbundVector();
 474                         }
 475
 476                         if (m->control_pressed) {
 477                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 478                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 479                                         return 0;
 480                         }
 481
 482                         //output error messages about any remaining user labels
 483                         set<string>::iterator it;
 484                         bool needToRun = false;
 485                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 486                                 m->mothurOut("Your file does not include the label " + *it);
 487                                 if (processedLabels.count(lastLabel) != 1) {
 488                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 489                                         needToRun = true;
 490                                 }else {
 491                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 492                                 }
 493                         }
 494
 495                         //run last label if you need to
 496                         if (needToRun == true)  {
 497                                 if (sabund != NULL) {   delete sabund;  }
 498                                 sabund = input->getSAbundVector(lastLabel);
 499
 500                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 501                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 502                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 503
 504                                 delete sabund;
 505
 506                         }
 507
 508                         if (m->control_pressed) {
 509                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 510                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 511                                         return 0;
 512                         }
 513                 }
 514
 515                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 516
 517                 m->mothurOutEndLine();
 518                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 519                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 520                 m->mothurOutEndLine();
 521
 522
 523                 return 0;
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "VennCommand", "execute");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531 //returns a vector of sets containing the 4 group combinations
 532 set< set<int> > VennCommand::findCombinations(int lookupSize){
 533         try {
 534                 set< set<int> > combos;
 535
 536                 set<int> possibles;
 537                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 538
 539                 getCombos(possibles, combos);
 540
 541                 return combos;
 542
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "VennCommand", "findCombinations");
 546                 exit(1);
 547         }
 548 }
 549 //**********************************************************************************************************************
 550 //recusively finds combos of 4
 551 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 552         try {
 553
 554                 if (possibles.size() == 4) { //done
 555                         if (combos.count(possibles) == 0) { //no dups
 556                                 combos.insert(possibles);
 557                         }
 558                 }else { //we still have work to do
 559                         set<int>::iterator it;
 560                         set<int>::iterator it2;
 561                         for (it = possibles.begin(); it != possibles.end(); it++) {
 562
 563                                 set<int> newPossibles;
 564                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 565                                         if (*it != *it2) {
 566                                                 newPossibles.insert(*it2);
 567                                         }
 568                                 }
 569                                 getCombos(newPossibles, combos);
 570                         }
 571                 }
 572
 573                 return 0;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "VennCommand", "getCombos");
 577                 exit(1);
 578         }
 579 }
 580
 581 //**********************************************************************************************************************