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","svg",false,false,true); parameters.push_back(plist);
  24                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); 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 psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
  31                 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
  32                 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
  33                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  34                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  35
  36                 vector<string> myArray;
  37                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "VennCommand", "setParameters");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string VennCommand::getHelpString(){
  47         try {
  48                 string helpString = "";
  49                 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, fontsize and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  50                 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";
  51                 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";
  52                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  53                 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
  54                 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
  55                 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";
  56                 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";
  57                 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";
  58                 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
  59                 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";
  60                 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
  61         helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n";
  62                 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
  63                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  64                 return helpString;
  65         }
  66         catch(exception& e) {
  67                 m->errorOut(e, "VennCommand", "getHelpString");
  68                 exit(1);
  69         }
  70 }
  71 //**********************************************************************************************************************
  72 string VennCommand::getOutputPattern(string type) {
  73     try {
  74         string pattern = "";
  75
  76         if (type == "svg") {  pattern = "[filename],svg"; }
  77         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  78
  79         return pattern;
  80     }
  81     catch(exception& e) {
  82         m->errorOut(e, "VennCommand", "getOutputPattern");
  83         exit(1);
  84     }
  85 }
  86
  87 //**********************************************************************************************************************
  88 VennCommand::VennCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  92                 vector<string> tempOutNames;
  93                 outputTypes["svg"] = tempOutNames;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "VennCommand", "VennCommand");
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************
 101
 102 VennCommand::VennCommand(string option)  {
 103         try {
 104                 abort = false; calledHelp = false;
 105                 allLines = 1;
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; calledHelp = true; }
 109                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 110
 111                 else {
 112                         vector<string> myArray = setParameters();
 113
 114                         OptionParser parser(option);
 115                         map<string,string> parameters = parser.getParameters();
 116                         map<string,string>::iterator it;
 117
 118                         ValidParameters validParameter;
 119
 120                         //check to make sure all parameters are valid for command
 121                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 122                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 123                         }
 124
 125                         //if the user changes the input directory command factory will send this info to us in the output parameter
 126                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 127                         if (inputDir == "not found"){   inputDir = "";          }
 128                         else {
 129                                 string path;
 130                                 it = parameters.find("shared");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 136                                 }
 137
 138                                 it = parameters.find("list");
 139                                 //user has given a template file
 140                                 if(it != parameters.end()){
 141                                         path = m->hasPath(it->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 144                                 }
 145                         }
 146
 147                         //check for required parameters
 148                         listfile = validParameter.validFile(parameters, "list", true);
 149                         if (listfile == "not open") { listfile = ""; abort = true; }
 150                         else if (listfile == "not found") { listfile = ""; }
 151                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 152
 153                         sharedfile = validParameter.validFile(parameters, "shared", true);
 154                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 155                         else if (sharedfile == "not found") { sharedfile = ""; }
 156                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 157
 158                         if ((sharedfile == "") && (listfile == "")) {
 159                                 //is there are current file available for any of these?
 160                                 //give priority to shared, then list, then rabund, then sabund
 161                                 //if there is a current shared file, use it
 162                                 sharedfile = m->getSharedFile();
 163                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 164                                 else {
 165                                         listfile = m->getListFile();
 166                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 167                                         else {
 168                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 169                                                 abort = true;
 170                                         }
 171                                 }
 172                         }
 173
 174                         //if the user changes the output directory command factory will send this info to us in the output parameter
 175                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 176
 177                         //check for optional parameter and set defaults
 178                         // ...at some point should added some additional type checking...
 179                         label = validParameter.validFile(parameters, "label", false);
 180                         if (label == "not found") { label = ""; }
 181                         else {
 182                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 183                                 else { allLines = 1;  }
 184                         }
 185
 186                         groups = validParameter.validFile(parameters, "groups", false);
 187                         if (groups == "not found") { groups = ""; }
 188                         else {
 189                                 m->splitAtDash(groups, Groups);
 190                                 m->setGroups(Groups);
 191                         }
 192
 193                         calc = validParameter.validFile(parameters, "calc", false);
 194                         if (calc == "not found") {
 195                                 if(format == "list") { calc = "sobs"; }
 196                                 else { calc = "sharedsobs"; }
 197                         }
 198                         else {
 199                                  if (calc == "default")  {
 200                                         if(format == "list") { calc = "sobs"; }
 201                                         else { calc = "sharedsobs"; }
 202                                 }
 203                         }
 204                         m->splitAtDash(calc, Estimators);
 205                         if (m->inUsersGroups("citation", Estimators)) {
 206                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 207                                 //remove citation from list of calcs
 208                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 209                         }
 210
 211                         string temp;
 212                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 213                         m->mothurConvert(temp, abund);
 214
 215                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 216                         nseqs = m->isTrue(temp);
 217
 218                         temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "f";                             }
 219                         perm = m->isTrue(temp);
 220
 221             temp = validParameter.validFile(parameters, "sharedotus", false);           if (temp == "not found"){       temp = "t";                             }
 222                         sharedOtus = m->isTrue(temp);
 223
 224                         temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
 225                         m->mothurConvert(temp, fontsize);
 226
 227                 }
 228
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "VennCommand", "VennCommand");
 232                 exit(1);
 233         }
 234 }
 235 //**********************************************************************************************************************
 236
 237 int VennCommand::execute(){
 238         try {
 239
 240                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 241
 242                 ValidCalculators validCalculator;
 243
 244                 if (format == "list") {
 245                         for (int i=0; i<Estimators.size(); i++) {
 246                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 247                                         if (Estimators[i] == "sobs") {
 248                                                 vennCalculators.push_back(new Sobs());
 249                                         }else if (Estimators[i] == "chao") {
 250                                                 vennCalculators.push_back(new Chao1());
 251                                         }else if (Estimators[i] == "ace") {
 252                                                 if(abund < 5) { abund = 10; }
 253                                                 vennCalculators.push_back(new Ace(abund));
 254                                         }
 255                                 }
 256                         }
 257                 }else {
 258                         for (int i=0; i<Estimators.size(); i++) {
 259                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 260                                         if (Estimators[i] == "sharedsobs") {
 261                                                 vennCalculators.push_back(new SharedSobsCS());
 262                                         }else if (Estimators[i] == "sharedchao") {
 263                                                 vennCalculators.push_back(new SharedChao1());
 264                                         }else if (Estimators[i] == "sharedace") {
 265                                                 vennCalculators.push_back(new SharedAce());
 266                                         }
 267                                 }
 268                         }
 269                 }
 270
 271                 //if the users entered no valid calculators don't execute command
 272                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 273
 274                 venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
 275                 input = new InputData(inputfile, format);
 276
 277                 string lastLabel;
 278
 279                 if (format == "sharedfile") {
 280                         lookup = input->getSharedRAbundVectors();
 281                         lastLabel = lookup[0]->getLabel();
 282
 283                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 284                 }else if (format == "list") {
 285                         sabund = input->getSAbundVector();
 286                         lastLabel = sabund->getLabel();
 287                 }
 288
 289                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 290                 set<string> processedLabels;
 291                 set<string> userLabels = labels;
 292
 293                 if (format != "list") {
 294
 295                         //as long as you are not at the end of the file or done wih the lines you want
 296                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 297
 298                                 if (m->control_pressed) {
 299                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 300                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 301                                         m->clearGroups(); delete venn; delete input;
 302                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 303                                         return 0;
 304                                 }
 305
 306                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 307                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 308                                         processedLabels.insert(lookup[0]->getLabel());
 309                                         userLabels.erase(lookup[0]->getLabel());
 310
 311                                         if ((lookup.size() > 4) && (!perm)){
 312                                                 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();
 313                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 314
 315                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 316                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 317
 318                                         }else if ((lookup.size() > 4) && (perm)) {
 319                                                 set< set<int> >::iterator it3;
 320                                                 set<int>::iterator it2;
 321                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 322
 323                                                         set<int> poss = *it3;
 324                                                         vector<SharedRAbundVector*> subset;
 325                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 326
 327                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 328                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 329                                                 }
 330                                         }else {
 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                                 }
 335
 336                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 337                                         string saveLabel = lookup[0]->getLabel();
 338
 339                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 340                                         lookup = input->getSharedRAbundVectors(lastLabel);
 341
 342                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 343                                         processedLabels.insert(lookup[0]->getLabel());
 344                                         userLabels.erase(lookup[0]->getLabel());
 345
 346                                         if ((lookup.size() > 4) && (!perm)){
 347                                                 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();
 348                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 349
 350                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 351                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 352
 353                                         }else if ((lookup.size() > 4) && (perm)) {
 354                                                 set< set<int> >::iterator it3;
 355                                                 set<int>::iterator it2;
 356                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 357
 358                                                         set<int> poss = *it3;
 359                                                         vector<SharedRAbundVector*> subset;
 360                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 361
 362                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 363                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 364                                                 }
 365                                         }else {
 366                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 367                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 368                                         }
 369
 370                                         //restore real lastlabel to save below
 371                                         lookup[0]->setLabel(saveLabel);
 372                                 }
 373
 374
 375                                 lastLabel = lookup[0]->getLabel();
 376
 377                                 //get next line to process
 378                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 379                                 lookup = input->getSharedRAbundVectors();
 380                         }
 381
 382                         if (m->control_pressed) {
 383                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 384                                         m->clearGroups(); delete venn; delete input;
 385                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 386                                         return 0;
 387                         }
 388
 389
 390                         //output error messages about any remaining user labels
 391                         set<string>::iterator it;
 392                         bool needToRun = false;
 393                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 394                                 m->mothurOut("Your file does not include the label " + *it);
 395                                 if (processedLabels.count(lastLabel) != 1) {
 396                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 397                                         needToRun = true;
 398                                 }else {
 399                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 400                                 }
 401                         }
 402
 403                         //run last label if you need to
 404                         if (needToRun == true)  {
 405                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 406                                         lookup = input->getSharedRAbundVectors(lastLabel);
 407
 408                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 409                                         processedLabels.insert(lookup[0]->getLabel());
 410                                         userLabels.erase(lookup[0]->getLabel());
 411
 412                                         if ((lookup.size() > 4) && (!perm)){
 413                                                 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();
 414                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 415
 416                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 417                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 418
 419                                         }else if ((lookup.size() > 4) && (perm)) {
 420                                                 set< set<int> >::iterator it3;
 421                                                 set<int>::iterator it2;
 422                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 423
 424                                                         set<int> poss = *it3;
 425                                                         vector<SharedRAbundVector*> subset;
 426                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 427
 428                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 429                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 430                                                 }
 431                                         }else {
 432                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 433                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 434                                         }
 435
 436                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 437                         }
 438
 439
 440                         //reset groups parameter
 441                         m->clearGroups();
 442
 443                         if (m->control_pressed) {
 444                                         m->clearGroups(); delete venn; delete input;
 445                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 446                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 447                                         return 0;
 448                         }
 449
 450
 451                 }else{
 452
 453                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 454
 455                                 if (m->control_pressed) {
 456                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 457                                         delete sabund; delete venn; delete input;
 458                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 459                                         return 0;
 460                                 }
 461
 462                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 463
 464                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 465                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 466                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 467
 468
 469                                         processedLabels.insert(sabund->getLabel());
 470                                         userLabels.erase(sabund->getLabel());
 471                                 }
 472
 473                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 474                                         string saveLabel = sabund->getLabel();
 475
 476                                         delete sabund;
 477                                         sabund = input->getSAbundVector(lastLabel);
 478
 479                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 480                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 481                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 482
 483
 484                                         processedLabels.insert(sabund->getLabel());
 485                                         userLabels.erase(sabund->getLabel());
 486
 487                                         //restore real lastlabel to save below
 488                                         sabund->setLabel(saveLabel);
 489                                 }
 490
 491                                 lastLabel = sabund->getLabel();
 492
 493                                 delete sabund;
 494                                 sabund = input->getSAbundVector();
 495                         }
 496
 497                         if (m->control_pressed) {
 498                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 499                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 500                                         delete venn; delete input;
 501                                         return 0;
 502                         }
 503
 504                         //output error messages about any remaining user labels
 505                         set<string>::iterator it;
 506                         bool needToRun = false;
 507                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 508                                 m->mothurOut("Your file does not include the label " + *it);
 509                                 if (processedLabels.count(lastLabel) != 1) {
 510                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 511                                         needToRun = true;
 512                                 }else {
 513                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 514                                 }
 515                         }
 516
 517                         //run last label if you need to
 518                         if (needToRun == true)  {
 519                                 if (sabund != NULL) {   delete sabund;  }
 520                                 sabund = input->getSAbundVector(lastLabel);
 521
 522                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 523                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 524                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 525
 526                                 delete sabund;
 527
 528                         }
 529
 530                         if (m->control_pressed) {
 531                                         delete venn; delete input;
 532                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 533                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 534                                         return 0;
 535                         }
 536                 }
 537
 538                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 539                 delete venn; delete input;
 540
 541                 m->mothurOutEndLine();
 542                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 543                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 544                 m->mothurOutEndLine();
 545
 546
 547                 return 0;
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "VennCommand", "execute");
 551                 exit(1);
 552         }
 553 }
 554 //**********************************************************************************************************************
 555 //returns a vector of sets containing the 4 group combinations
 556 set< set<int> > VennCommand::findCombinations(int lookupSize){
 557         try {
 558                 set< set<int> > combos;
 559
 560                 set<int> possibles;
 561                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 562
 563                 getCombos(possibles, combos);
 564
 565                 return combos;
 566
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "VennCommand", "findCombinations");
 570                 exit(1);
 571         }
 572 }
 573 //**********************************************************************************************************************
 574 //recusively finds combos of 4
 575 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 576         try {
 577
 578                 if (possibles.size() == 4) { //done
 579                         if (combos.count(possibles) == 0) { //no dups
 580                                 combos.insert(possibles);
 581                         }
 582                 }else { //we still have work to do
 583                         set<int>::iterator it;
 584                         set<int>::iterator it2;
 585                         for (it = possibles.begin(); it != possibles.end(); it++) {
 586
 587                                 set<int> newPossibles;
 588                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 589                                         if (*it != *it2) {
 590                                                 newPossibles.insert(*it2);
 591                                         }
 592                                 }
 593                                 getCombos(newPossibles, combos);
 594                         }
 595                 }
 596
 597                 return 0;
 598         }
 599         catch(exception& e) {
 600                 m->errorOut(e, "VennCommand", "getCombos");
 601                 exit(1);
 602         }
 603 }
 604
 605 //**********************************************************************************************************************