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 pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
  31                 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "VennCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string VennCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  49                 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";
  50                 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";
  51                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  52                 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
  53                 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
  54                 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";
  55                 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";
  56                 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";
  57                 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
  58                 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";
  59                 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
  60                 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
  61                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  62                 return helpString;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "VennCommand", "getHelpString");
  66                 exit(1);
  67         }
  68 }
  69
  70 //**********************************************************************************************************************
  71 VennCommand::VennCommand(){
  72         try {
  73                 abort = true; calledHelp = true;
  74                 setParameters();
  75                 vector<string> tempOutNames;
  76                 outputTypes["svg"] = tempOutNames;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "VennCommand", "VennCommand");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84
  85 VennCommand::VennCommand(string option)  {
  86         try {
  87                 abort = false; calledHelp = false;
  88                 allLines = 1;
  89
  90                 //allow user to run help
  91                 if(option == "help") { help(); abort = true; calledHelp = true; }
  92                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  93
  94                 else {
  95                         vector<string> myArray = setParameters();
  96
  97                         OptionParser parser(option);
  98                         map<string,string> parameters = parser.getParameters();
  99                         map<string,string>::iterator it;
 100
 101                         ValidParameters validParameter;
 102
 103                         //check to make sure all parameters are valid for command
 104                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 105                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 106                         }
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("shared");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 119                                 }
 120
 121                                 it = parameters.find("list");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 127                                 }
 128                         }
 129
 130                         //check for required parameters
 131                         listfile = validParameter.validFile(parameters, "list", true);
 132                         if (listfile == "not open") { listfile = ""; abort = true; }
 133                         else if (listfile == "not found") { listfile = ""; }
 134                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 135
 136                         sharedfile = validParameter.validFile(parameters, "shared", true);
 137                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 138                         else if (sharedfile == "not found") { sharedfile = ""; }
 139                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 140
 141                         if ((sharedfile == "") && (listfile == "")) {
 142                                 //is there are current file available for any of these?
 143                                 //give priority to shared, then list, then rabund, then sabund
 144                                 //if there is a current shared file, use it
 145                                 sharedfile = m->getSharedFile();
 146                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 147                                 else {
 148                                         listfile = m->getListFile();
 149                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 150                                         else {
 151                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 152                                                 abort = true;
 153                                         }
 154                                 }
 155                         }
 156
 157                         //if the user changes the output directory command factory will send this info to us in the output parameter
 158                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 159
 160                         //check for optional parameter and set defaults
 161                         // ...at some point should added some additional type checking...
 162                         label = validParameter.validFile(parameters, "label", false);
 163                         if (label == "not found") { label = ""; }
 164                         else {
 165                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 166                                 else { allLines = 1;  }
 167                         }
 168
 169                         groups = validParameter.validFile(parameters, "groups", false);
 170                         if (groups == "not found") { groups = ""; }
 171                         else {
 172                                 m->splitAtDash(groups, Groups);
 173                                 m->setGroups(Groups);
 174                         }
 175
 176                         calc = validParameter.validFile(parameters, "calc", false);
 177                         if (calc == "not found") {
 178                                 if(format == "list") { calc = "sobs"; }
 179                                 else { calc = "sharedsobs"; }
 180                         }
 181                         else {
 182                                  if (calc == "default")  {
 183                                         if(format == "list") { calc = "sobs"; }
 184                                         else { calc = "sharedsobs"; }
 185                                 }
 186                         }
 187                         m->splitAtDash(calc, Estimators);
 188                         if (m->inUsersGroups("citation", Estimators)) {
 189                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 190                                 //remove citation from list of calcs
 191                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 192                         }
 193
 194                         string temp;
 195                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 196                         m->mothurConvert(temp, abund);
 197
 198                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 199                         nseqs = m->isTrue(temp);
 200
 201                         temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "f";                             }
 202                         perm = m->isTrue(temp);
 203
 204                         temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
 205                         m->mothurConvert(temp, fontsize);
 206
 207                 }
 208
 209         }
 210         catch(exception& e) {
 211                 m->errorOut(e, "VennCommand", "VennCommand");
 212                 exit(1);
 213         }
 214 }
 215 //**********************************************************************************************************************
 216
 217 int VennCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 221
 222                 ValidCalculators validCalculator;
 223
 224                 if (format == "list") {
 225                         for (int i=0; i<Estimators.size(); i++) {
 226                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 227                                         if (Estimators[i] == "sobs") {
 228                                                 vennCalculators.push_back(new Sobs());
 229                                         }else if (Estimators[i] == "chao") {
 230                                                 vennCalculators.push_back(new Chao1());
 231                                         }else if (Estimators[i] == "ace") {
 232                                                 if(abund < 5)
 233                                                         abund = 10;
 234                                                 vennCalculators.push_back(new Ace(abund));
 235                                         }
 236                                 }
 237                         }
 238                 }else {
 239                         for (int i=0; i<Estimators.size(); i++) {
 240                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 241                                         if (Estimators[i] == "sharedsobs") {
 242                                                 vennCalculators.push_back(new SharedSobsCS());
 243                                         }else if (Estimators[i] == "sharedchao") {
 244                                                 vennCalculators.push_back(new SharedChao1());
 245                                         }else if (Estimators[i] == "sharedace") {
 246                                                 vennCalculators.push_back(new SharedAce());
 247                                         }
 248                                 }
 249                         }
 250                 }
 251
 252                 //if the users entered no valid calculators don't execute command
 253                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 254
 255                 venn = new Venn(outputDir, nseqs, inputfile, fontsize);
 256                 input = new InputData(inputfile, format);
 257
 258                 string lastLabel;
 259
 260                 if (format == "sharedfile") {
 261                         lookup = input->getSharedRAbundVectors();
 262                         lastLabel = lookup[0]->getLabel();
 263
 264                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 265                 }else if (format == "list") {
 266                         sabund = input->getSAbundVector();
 267                         lastLabel = sabund->getLabel();
 268                 }
 269
 270                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 271                 set<string> processedLabels;
 272                 set<string> userLabels = labels;
 273
 274                 if (format != "list") {
 275
 276                         //as long as you are not at the end of the file or done wih the lines you want
 277                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 278
 279                                 if (m->control_pressed) {
 280                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 281                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 282                                         m->clearGroups(); delete venn; delete input;
 283                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 284                                         return 0;
 285                                 }
 286
 287                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 288                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 289                                         processedLabels.insert(lookup[0]->getLabel());
 290                                         userLabels.erase(lookup[0]->getLabel());
 291
 292                                         if ((lookup.size() > 4) && (!perm)){
 293                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 294                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 295
 296                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 297                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 298
 299                                         }else if ((lookup.size() > 4) && (perm)) {
 300                                                 set< set<int> >::iterator it3;
 301                                                 set<int>::iterator it2;
 302                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 303
 304                                                         set<int> poss = *it3;
 305                                                         vector<SharedRAbundVector*> subset;
 306                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 307
 308                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 309                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 310                                                 }
 311                                         }else {
 312                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 313                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 314                                         }
 315                                 }
 316
 317                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 318                                         string saveLabel = lookup[0]->getLabel();
 319
 320                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 321                                         lookup = input->getSharedRAbundVectors(lastLabel);
 322
 323                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 324                                         processedLabels.insert(lookup[0]->getLabel());
 325                                         userLabels.erase(lookup[0]->getLabel());
 326
 327                                         if ((lookup.size() > 4) && (!perm)){
 328                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 329                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 330
 331                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 332                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 333
 334                                         }else if ((lookup.size() > 4) && (perm)) {
 335                                                 set< set<int> >::iterator it3;
 336                                                 set<int>::iterator it2;
 337                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 338
 339                                                         set<int> poss = *it3;
 340                                                         vector<SharedRAbundVector*> subset;
 341                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 342
 343                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 344                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 345                                                 }
 346                                         }else {
 347                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 348                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 349                                         }
 350
 351                                         //restore real lastlabel to save below
 352                                         lookup[0]->setLabel(saveLabel);
 353                                 }
 354
 355
 356                                 lastLabel = lookup[0]->getLabel();
 357
 358                                 //get next line to process
 359                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 360                                 lookup = input->getSharedRAbundVectors();
 361                         }
 362
 363                         if (m->control_pressed) {
 364                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 365                                         m->clearGroups(); delete venn; delete input;
 366                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 367                                         return 0;
 368                         }
 369
 370
 371                         //output error messages about any remaining user labels
 372                         set<string>::iterator it;
 373                         bool needToRun = false;
 374                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 375                                 m->mothurOut("Your file does not include the label " + *it);
 376                                 if (processedLabels.count(lastLabel) != 1) {
 377                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 378                                         needToRun = true;
 379                                 }else {
 380                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 381                                 }
 382                         }
 383
 384                         //run last label if you need to
 385                         if (needToRun == true)  {
 386                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 387                                         lookup = input->getSharedRAbundVectors(lastLabel);
 388
 389                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 390                                         processedLabels.insert(lookup[0]->getLabel());
 391                                         userLabels.erase(lookup[0]->getLabel());
 392
 393                                         if ((lookup.size() > 4) && (!perm)){
 394                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 395                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 396
 397                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 398                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 399
 400                                         }else if ((lookup.size() > 4) && (perm)) {
 401                                                 set< set<int> >::iterator it3;
 402                                                 set<int>::iterator it2;
 403                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 404
 405                                                         set<int> poss = *it3;
 406                                                         vector<SharedRAbundVector*> subset;
 407                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 408
 409                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 410                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 411                                                 }
 412                                         }else {
 413                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 414                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 415                                         }
 416
 417                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 418                         }
 419
 420
 421                         //reset groups parameter
 422                         m->clearGroups();
 423
 424                         if (m->control_pressed) {
 425                                         m->clearGroups(); delete venn; delete input;
 426                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 427                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 428                                         return 0;
 429                         }
 430
 431
 432                 }else{
 433
 434                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 435
 436                                 if (m->control_pressed) {
 437                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 438                                         delete sabund; delete venn; delete input;
 439                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 440                                         return 0;
 441                                 }
 442
 443                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 444
 445                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 446                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 447                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 448
 449
 450                                         processedLabels.insert(sabund->getLabel());
 451                                         userLabels.erase(sabund->getLabel());
 452                                 }
 453
 454                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 455                                         string saveLabel = sabund->getLabel();
 456
 457                                         delete sabund;
 458                                         sabund = input->getSAbundVector(lastLabel);
 459
 460                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 461                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 462                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 463
 464
 465                                         processedLabels.insert(sabund->getLabel());
 466                                         userLabels.erase(sabund->getLabel());
 467
 468                                         //restore real lastlabel to save below
 469                                         sabund->setLabel(saveLabel);
 470                                 }
 471
 472                                 lastLabel = sabund->getLabel();
 473
 474                                 delete sabund;
 475                                 sabund = input->getSAbundVector();
 476                         }
 477
 478                         if (m->control_pressed) {
 479                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 480                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 481                                         delete venn; delete input;
 482                                         return 0;
 483                         }
 484
 485                         //output error messages about any remaining user labels
 486                         set<string>::iterator it;
 487                         bool needToRun = false;
 488                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 489                                 m->mothurOut("Your file does not include the label " + *it);
 490                                 if (processedLabels.count(lastLabel) != 1) {
 491                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 492                                         needToRun = true;
 493                                 }else {
 494                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 495                                 }
 496                         }
 497
 498                         //run last label if you need to
 499                         if (needToRun == true)  {
 500                                 if (sabund != NULL) {   delete sabund;  }
 501                                 sabund = input->getSAbundVector(lastLabel);
 502
 503                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 504                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 505                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 506
 507                                 delete sabund;
 508
 509                         }
 510
 511                         if (m->control_pressed) {
 512                                         delete venn; delete input;
 513                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 514                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 515                                         return 0;
 516                         }
 517                 }
 518
 519                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 520                 delete venn; delete input;
 521
 522                 m->mothurOutEndLine();
 523                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 524                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 525                 m->mothurOutEndLine();
 526
 527
 528                 return 0;
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "VennCommand", "execute");
 532                 exit(1);
 533         }
 534 }
 535 //**********************************************************************************************************************
 536 //returns a vector of sets containing the 4 group combinations
 537 set< set<int> > VennCommand::findCombinations(int lookupSize){
 538         try {
 539                 set< set<int> > combos;
 540
 541                 set<int> possibles;
 542                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 543
 544                 getCombos(possibles, combos);
 545
 546                 return combos;
 547
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "VennCommand", "findCombinations");
 551                 exit(1);
 552         }
 553 }
 554 //**********************************************************************************************************************
 555 //recusively finds combos of 4
 556 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 557         try {
 558
 559                 if (possibles.size() == 4) { //done
 560                         if (combos.count(possibles) == 0) { //no dups
 561                                 combos.insert(possibles);
 562                         }
 563                 }else { //we still have work to do
 564                         set<int>::iterator it;
 565                         set<int>::iterator it2;
 566                         for (it = possibles.begin(); it != possibles.end(); it++) {
 567
 568                                 set<int> newPossibles;
 569                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 570                                         if (*it != *it2) {
 571                                                 newPossibles.insert(*it2);
 572                                         }
 573                                 }
 574                                 getCombos(newPossibles, combos);
 575                         }
 576                 }
 577
 578                 return 0;
 579         }
 580         catch(exception& e) {
 581                 m->errorOut(e, "VennCommand", "getCombos");
 582                 exit(1);
 583         }
 584 }
 585
 586 //**********************************************************************************************************************