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