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 vector<string> VennCommand::setParameters(){
  22         try {
  23                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  24                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  25                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  27                 CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
  28                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  29                 CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
  30                 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "VennCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string VennCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  48                 helpString += "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";
  49                 helpString += "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";
  50                 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
  51                 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
  52                 helpString += "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";
  53                 helpString += "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";
  54                 helpString += "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 shared file.\n";
  55                 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
  56                 helpString += "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";
  57                 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
  58                 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
  59                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "VennCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67
  68 //**********************************************************************************************************************
  69 VennCommand::VennCommand(){
  70         try {
  71                 abort = true; calledHelp = true;
  72                 setParameters();
  73                 vector<string> tempOutNames;
  74                 outputTypes["svg"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "VennCommand", "VennCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82
  83 VennCommand::VennCommand(string option)  {
  84         try {
  85                 abort = false; calledHelp = false;
  86                 allLines = 1;
  87
  88                 //allow user to run help
  89                 if(option == "help") { help(); abort = true; calledHelp = true; }
  90
  91                 else {
  92                         vector<string> myArray = setParameters();
  93
  94                         OptionParser parser(option);
  95                         map<string,string> parameters = parser.getParameters();
  96                         map<string,string>::iterator it;
  97
  98                         ValidParameters validParameter;
  99
 100                         //check to make sure all parameters are valid for command
 101                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 102                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 103                         }
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("shared");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 116                                 }
 117
 118                                 it = parameters.find("list");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 124                                 }
 125                         }
 126
 127                         //check for required parameters
 128                         listfile = validParameter.validFile(parameters, "list", true);
 129                         if (listfile == "not open") { listfile = ""; abort = true; }
 130                         else if (listfile == "not found") { listfile = ""; }
 131                         else {  format = "list"; inputfile = listfile; }
 132
 133                         sharedfile = validParameter.validFile(parameters, "shared", true);
 134                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 135                         else if (sharedfile == "not found") { sharedfile = ""; }
 136                         else {  format = "sharedfile"; inputfile = sharedfile; }
 137
 138                         if ((sharedfile == "") && (listfile == "")) {
 139                                 //is there are current file available for any of these?
 140                                 //give priority to shared, then list, then rabund, then sabund
 141                                 //if there is a current shared file, use it
 142                                 sharedfile = m->getSharedFile();
 143                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 144                                 else {
 145                                         listfile = m->getListFile();
 146                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 147                                         else {
 148                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 149                                                 abort = true;
 150                                         }
 151                                 }
 152                         }
 153
 154                         //if the user changes the output directory command factory will send this info to us in the output parameter
 155                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 156
 157                         //check for optional parameter and set defaults
 158                         // ...at some point should added some additional type checking...
 159                         label = validParameter.validFile(parameters, "label", false);
 160                         if (label == "not found") { label = ""; }
 161                         else {
 162                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 163                                 else { allLines = 1;  }
 164                         }
 165
 166                         groups = validParameter.validFile(parameters, "groups", false);
 167                         if (groups == "not found") { groups = ""; }
 168                         else {
 169                                 m->splitAtDash(groups, Groups);
 170                                 m->Groups = Groups;
 171                         }
 172
 173                         calc = validParameter.validFile(parameters, "calc", false);
 174                         if (calc == "not found") {
 175                                 if(format == "list") { calc = "sobs"; }
 176                                 else { calc = "sharedsobs"; }
 177                         }
 178                         else {
 179                                  if (calc == "default")  {
 180                                         if(format == "list") { calc = "sobs"; }
 181                                         else { calc = "sharedsobs"; }
 182                                 }
 183                         }
 184                         m->splitAtDash(calc, Estimators);
 185
 186                         string temp;
 187                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 188                         convert(temp, abund);
 189
 190                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 191                         nseqs = m->isTrue(temp);
 192
 193                         temp = validParameter.validFile(parameters, "permute", false);                  if (temp == "not found"){       temp = "f";                             }
 194                         perm = m->isTrue(temp);
 195
 196                 }
 197
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "VennCommand", "VennCommand");
 201                 exit(1);
 202         }
 203 }
 204 //**********************************************************************************************************************
 205
 206 int VennCommand::execute(){
 207         try {
 208
 209                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 210
 211                 ValidCalculators validCalculator;
 212
 213                 if (format == "list") {
 214                         for (int i=0; i<Estimators.size(); i++) {
 215                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 216                                         if (Estimators[i] == "sobs") {
 217                                                 vennCalculators.push_back(new Sobs());
 218                                         }else if (Estimators[i] == "chao") {
 219                                                 vennCalculators.push_back(new Chao1());
 220                                         }else if (Estimators[i] == "ace") {
 221                                                 if(abund < 5)
 222                                                         abund = 10;
 223                                                 vennCalculators.push_back(new Ace(abund));
 224                                         }
 225                                 }
 226                         }
 227                 }else {
 228                         for (int i=0; i<Estimators.size(); i++) {
 229                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 230                                         if (Estimators[i] == "sharedsobs") {
 231                                                 vennCalculators.push_back(new SharedSobsCS());
 232                                         }else if (Estimators[i] == "sharedchao") {
 233                                                 vennCalculators.push_back(new SharedChao1());
 234                                         }else if (Estimators[i] == "sharedace") {
 235                                                 vennCalculators.push_back(new SharedAce());
 236                                         }
 237                                 }
 238                         }
 239                 }
 240
 241                 //if the users entered no valid calculators don't execute command
 242                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 243
 244                 venn = new Venn(outputDir, nseqs, inputfile);
 245                 input = new InputData(inputfile, format);
 246
 247                 string lastLabel;
 248
 249                 if (format == "sharedfile") {
 250                         lookup = input->getSharedRAbundVectors();
 251                         lastLabel = lookup[0]->getLabel();
 252
 253                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 254                 }else if (format == "list") {
 255                         sabund = input->getSAbundVector();
 256                         lastLabel = sabund->getLabel();
 257                 }
 258
 259                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 260                 set<string> processedLabels;
 261                 set<string> userLabels = labels;
 262
 263                 if (format != "list") {
 264
 265                         //as long as you are not at the end of the file or done wih the lines you want
 266                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 267
 268                                 if (m->control_pressed) {
 269                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 270                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 271                                         m->Groups.clear(); delete venn; delete input;
 272                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 273                                         return 0;
 274                                 }
 275
 276                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 277                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 278                                         processedLabels.insert(lookup[0]->getLabel());
 279                                         userLabels.erase(lookup[0]->getLabel());
 280
 281                                         if ((lookup.size() > 4) && (!perm)){
 282                                                 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();
 283                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 284
 285                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 286                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 287
 288                                         }else if ((lookup.size() > 4) && (perm)) {
 289                                                 set< set<int> >::iterator it3;
 290                                                 set<int>::iterator it2;
 291                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 292
 293                                                         set<int> poss = *it3;
 294                                                         vector<SharedRAbundVector*> subset;
 295                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 296
 297                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 298                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 299                                                 }
 300                                         }else {
 301                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 302                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 303                                         }
 304                                 }
 305
 306                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 307                                         string saveLabel = lookup[0]->getLabel();
 308
 309                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 310                                         lookup = input->getSharedRAbundVectors(lastLabel);
 311
 312                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 313                                         processedLabels.insert(lookup[0]->getLabel());
 314                                         userLabels.erase(lookup[0]->getLabel());
 315
 316                                         if ((lookup.size() > 4) && (!perm)){
 317                                                 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();
 318                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 319
 320                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 321                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 322
 323                                         }else if ((lookup.size() > 4) && (perm)) {
 324                                                 set< set<int> >::iterator it3;
 325                                                 set<int>::iterator it2;
 326                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 327
 328                                                         set<int> poss = *it3;
 329                                                         vector<SharedRAbundVector*> subset;
 330                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 331
 332                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 333                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 334                                                 }
 335                                         }else {
 336                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 337                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 338                                         }
 339
 340                                         //restore real lastlabel to save below
 341                                         lookup[0]->setLabel(saveLabel);
 342                                 }
 343
 344
 345                                 lastLabel = lookup[0]->getLabel();
 346
 347                                 //get next line to process
 348                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 349                                 lookup = input->getSharedRAbundVectors();
 350                         }
 351
 352                         if (m->control_pressed) {
 353                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 354                                         m->Groups.clear(); delete venn; delete input;
 355                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 356                                         return 0;
 357                         }
 358
 359
 360                         //output error messages about any remaining user labels
 361                         set<string>::iterator it;
 362                         bool needToRun = false;
 363                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 364                                 m->mothurOut("Your file does not include the label " + *it);
 365                                 if (processedLabels.count(lastLabel) != 1) {
 366                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 367                                         needToRun = true;
 368                                 }else {
 369                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 370                                 }
 371                         }
 372
 373                         //run last label if you need to
 374                         if (needToRun == true)  {
 375                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 376                                         lookup = input->getSharedRAbundVectors(lastLabel);
 377
 378                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 379                                         processedLabels.insert(lookup[0]->getLabel());
 380                                         userLabels.erase(lookup[0]->getLabel());
 381
 382                                         if ((lookup.size() > 4) && (!perm)){
 383                                                 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();
 384                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 385
 386                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 387                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 388
 389                                         }else if ((lookup.size() > 4) && (perm)) {
 390                                                 set< set<int> >::iterator it3;
 391                                                 set<int>::iterator it2;
 392                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 393
 394                                                         set<int> poss = *it3;
 395                                                         vector<SharedRAbundVector*> subset;
 396                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 397
 398                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 399                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 400                                                 }
 401                                         }else {
 402                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 403                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 404                                         }
 405
 406                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 407                         }
 408
 409
 410                         //reset groups parameter
 411                         m->Groups.clear();
 412
 413                         if (m->control_pressed) {
 414                                         m->Groups.clear(); delete venn; delete input;
 415                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 416                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 417                                         return 0;
 418                         }
 419
 420
 421                 }else{
 422
 423                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 424
 425                                 if (m->control_pressed) {
 426                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 427                                         delete sabund; delete venn; delete input;
 428                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 429                                         return 0;
 430                                 }
 431
 432                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 433
 434                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 435                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 436                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 437
 438
 439                                         processedLabels.insert(sabund->getLabel());
 440                                         userLabels.erase(sabund->getLabel());
 441                                 }
 442
 443                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 444                                         string saveLabel = sabund->getLabel();
 445
 446                                         delete sabund;
 447                                         sabund = input->getSAbundVector(lastLabel);
 448
 449                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 450                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 451                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 452
 453
 454                                         processedLabels.insert(sabund->getLabel());
 455                                         userLabels.erase(sabund->getLabel());
 456
 457                                         //restore real lastlabel to save below
 458                                         sabund->setLabel(saveLabel);
 459                                 }
 460
 461                                 lastLabel = sabund->getLabel();
 462
 463                                 delete sabund;
 464                                 sabund = input->getSAbundVector();
 465                         }
 466
 467                         if (m->control_pressed) {
 468                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 469                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 470                                         delete venn; delete input;
 471                                         return 0;
 472                         }
 473
 474                         //output error messages about any remaining user labels
 475                         set<string>::iterator it;
 476                         bool needToRun = false;
 477                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 478                                 m->mothurOut("Your file does not include the label " + *it);
 479                                 if (processedLabels.count(lastLabel) != 1) {
 480                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 481                                         needToRun = true;
 482                                 }else {
 483                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 484                                 }
 485                         }
 486
 487                         //run last label if you need to
 488                         if (needToRun == true)  {
 489                                 if (sabund != NULL) {   delete sabund;  }
 490                                 sabund = input->getSAbundVector(lastLabel);
 491
 492                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 493                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 494                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 495
 496                                 delete sabund;
 497
 498                         }
 499
 500                         if (m->control_pressed) {
 501                                         delete venn; delete input;
 502                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 503                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 504                                         return 0;
 505                         }
 506                 }
 507
 508                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 509                 delete venn; delete input;
 510
 511                 m->mothurOutEndLine();
 512                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 513                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 514                 m->mothurOutEndLine();
 515
 516
 517                 return 0;
 518         }
 519         catch(exception& e) {
 520                 m->errorOut(e, "VennCommand", "execute");
 521                 exit(1);
 522         }
 523 }
 524 //**********************************************************************************************************************
 525 //returns a vector of sets containing the 4 group combinations
 526 set< set<int> > VennCommand::findCombinations(int lookupSize){
 527         try {
 528                 set< set<int> > combos;
 529
 530                 set<int> possibles;
 531                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 532
 533                 getCombos(possibles, combos);
 534
 535                 return combos;
 536
 537         }
 538         catch(exception& e) {
 539                 m->errorOut(e, "VennCommand", "findCombinations");
 540                 exit(1);
 541         }
 542 }
 543 //**********************************************************************************************************************
 544 //recusively finds combos of 4
 545 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 546         try {
 547
 548                 if (possibles.size() == 4) { //done
 549                         if (combos.count(possibles) == 0) { //no dups
 550                                 combos.insert(possibles);
 551                         }
 552                 }else { //we still have work to do
 553                         set<int>::iterator it;
 554                         set<int>::iterator it2;
 555                         for (it = possibles.begin(); it != possibles.end(); it++) {
 556
 557                                 set<int> newPossibles;
 558                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 559                                         if (*it != *it2) {
 560                                                 newPossibles.insert(*it2);
 561                                         }
 562                                 }
 563                                 getCombos(newPossibles, combos);
 564                         }
 565                 }
 566
 567                 return 0;
 568         }
 569         catch(exception& e) {
 570                 m->errorOut(e, "VennCommand", "getCombos");
 571                 exit(1);
 572         }
 573 }
 574
 575 //**********************************************************************************************************************