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 string VennCommand::getOutputFileNameTag(string type, string inputName=""){
  72         try {
  73         string outputFileName = "";
  74                 map<string, vector<string> >::iterator it;
  75
  76         //is this a type this command creates
  77         it = outputTypes.find(type);
  78         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  79         else {
  80             if (type == "svg")            {   outputFileName =  "svg";   }
  81             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  82         }
  83         return outputFileName;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "VennCommand", "getOutputFileNameTag");
  87                 exit(1);
  88         }
  89 }
  90
  91 //**********************************************************************************************************************
  92 VennCommand::VennCommand(){
  93         try {
  94                 abort = true; calledHelp = true;
  95                 setParameters();
  96                 vector<string> tempOutNames;
  97                 outputTypes["svg"] = tempOutNames;
  98         }
  99         catch(exception& e) {
 100                 m->errorOut(e, "VennCommand", "VennCommand");
 101                 exit(1);
 102         }
 103 }
 104 //**********************************************************************************************************************
 105
 106 VennCommand::VennCommand(string option)  {
 107         try {
 108                 abort = false; calledHelp = false;
 109                 allLines = 1;
 110
 111                 //allow user to run help
 112                 if(option == "help") { help(); abort = true; calledHelp = true; }
 113                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 114
 115                 else {
 116                         vector<string> myArray = setParameters();
 117
 118                         OptionParser parser(option);
 119                         map<string,string> parameters = parser.getParameters();
 120                         map<string,string>::iterator it;
 121
 122                         ValidParameters validParameter;
 123
 124                         //check to make sure all parameters are valid for command
 125                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 126                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 127                         }
 128
 129                         //if the user changes the input directory command factory will send this info to us in the output parameter
 130                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 131                         if (inputDir == "not found"){   inputDir = "";          }
 132                         else {
 133                                 string path;
 134                                 it = parameters.find("shared");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 140                                 }
 141
 142                                 it = parameters.find("list");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 148                                 }
 149                         }
 150
 151                         //check for required parameters
 152                         listfile = validParameter.validFile(parameters, "list", true);
 153                         if (listfile == "not open") { listfile = ""; abort = true; }
 154                         else if (listfile == "not found") { listfile = ""; }
 155                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 156
 157                         sharedfile = validParameter.validFile(parameters, "shared", true);
 158                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 159                         else if (sharedfile == "not found") { sharedfile = ""; }
 160                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 161
 162                         if ((sharedfile == "") && (listfile == "")) {
 163                                 //is there are current file available for any of these?
 164                                 //give priority to shared, then list, then rabund, then sabund
 165                                 //if there is a current shared file, use it
 166                                 sharedfile = m->getSharedFile();
 167                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 168                                 else {
 169                                         listfile = m->getListFile();
 170                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 171                                         else {
 172                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 173                                                 abort = true;
 174                                         }
 175                                 }
 176                         }
 177
 178                         //if the user changes the output directory command factory will send this info to us in the output parameter
 179                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 180
 181                         //check for optional parameter and set defaults
 182                         // ...at some point should added some additional type checking...
 183                         label = validParameter.validFile(parameters, "label", false);
 184                         if (label == "not found") { label = ""; }
 185                         else {
 186                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 187                                 else { allLines = 1;  }
 188                         }
 189
 190                         groups = validParameter.validFile(parameters, "groups", false);
 191                         if (groups == "not found") { groups = ""; }
 192                         else {
 193                                 m->splitAtDash(groups, Groups);
 194                                 m->setGroups(Groups);
 195                         }
 196
 197                         calc = validParameter.validFile(parameters, "calc", false);
 198                         if (calc == "not found") {
 199                                 if(format == "list") { calc = "sobs"; }
 200                                 else { calc = "sharedsobs"; }
 201                         }
 202                         else {
 203                                  if (calc == "default")  {
 204                                         if(format == "list") { calc = "sobs"; }
 205                                         else { calc = "sharedsobs"; }
 206                                 }
 207                         }
 208                         m->splitAtDash(calc, Estimators);
 209                         if (m->inUsersGroups("citation", Estimators)) {
 210                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 211                                 //remove citation from list of calcs
 212                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 213                         }
 214
 215                         string temp;
 216                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 217                         m->mothurConvert(temp, abund);
 218
 219                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 220                         nseqs = m->isTrue(temp);
 221
 222                         temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "f";                             }
 223                         perm = m->isTrue(temp);
 224
 225                         temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
 226                         m->mothurConvert(temp, fontsize);
 227
 228                 }
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "VennCommand", "VennCommand");
 233                 exit(1);
 234         }
 235 }
 236 //**********************************************************************************************************************
 237
 238 int VennCommand::execute(){
 239         try {
 240
 241                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 242
 243                 ValidCalculators validCalculator;
 244
 245                 if (format == "list") {
 246                         for (int i=0; i<Estimators.size(); i++) {
 247                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 248                                         if (Estimators[i] == "sobs") {
 249                                                 vennCalculators.push_back(new Sobs());
 250                                         }else if (Estimators[i] == "chao") {
 251                                                 vennCalculators.push_back(new Chao1());
 252                                         }else if (Estimators[i] == "ace") {
 253                                                 if(abund < 5)
 254                                                         abund = 10;
 255                                                 vennCalculators.push_back(new Ace(abund));
 256                                         }
 257                                 }
 258                         }
 259                 }else {
 260                         for (int i=0; i<Estimators.size(); i++) {
 261                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 262                                         if (Estimators[i] == "sharedsobs") {
 263                                                 vennCalculators.push_back(new SharedSobsCS());
 264                                         }else if (Estimators[i] == "sharedchao") {
 265                                                 vennCalculators.push_back(new SharedChao1());
 266                                         }else if (Estimators[i] == "sharedace") {
 267                                                 vennCalculators.push_back(new SharedAce());
 268                                         }
 269                                 }
 270                         }
 271                 }
 272
 273                 //if the users entered no valid calculators don't execute command
 274                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 275
 276                 venn = new Venn(outputDir, nseqs, inputfile, fontsize);
 277                 input = new InputData(inputfile, format);
 278
 279                 string lastLabel;
 280
 281                 if (format == "sharedfile") {
 282                         lookup = input->getSharedRAbundVectors();
 283                         lastLabel = lookup[0]->getLabel();
 284
 285                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 286                 }else if (format == "list") {
 287                         sabund = input->getSAbundVector();
 288                         lastLabel = sabund->getLabel();
 289                 }
 290
 291                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 292                 set<string> processedLabels;
 293                 set<string> userLabels = labels;
 294
 295                 if (format != "list") {
 296
 297                         //as long as you are not at the end of the file or done wih the lines you want
 298                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 299
 300                                 if (m->control_pressed) {
 301                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 302                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 303                                         m->clearGroups(); delete venn; delete input;
 304                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 305                                         return 0;
 306                                 }
 307
 308                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 309                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 310                                         processedLabels.insert(lookup[0]->getLabel());
 311                                         userLabels.erase(lookup[0]->getLabel());
 312
 313                                         if ((lookup.size() > 4) && (!perm)){
 314                                                 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();
 315                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 316
 317                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 318                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 319
 320                                         }else if ((lookup.size() > 4) && (perm)) {
 321                                                 set< set<int> >::iterator it3;
 322                                                 set<int>::iterator it2;
 323                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 324
 325                                                         set<int> poss = *it3;
 326                                                         vector<SharedRAbundVector*> subset;
 327                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 328
 329                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 330                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 331                                                 }
 332                                         }else {
 333                                                 vector<string> outfilenames = venn->getPic(lookup, 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                                 }
 337
 338                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 339                                         string saveLabel = lookup[0]->getLabel();
 340
 341                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 342                                         lookup = input->getSharedRAbundVectors(lastLabel);
 343
 344                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 345                                         processedLabels.insert(lookup[0]->getLabel());
 346                                         userLabels.erase(lookup[0]->getLabel());
 347
 348                                         if ((lookup.size() > 4) && (!perm)){
 349                                                 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();
 350                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 351
 352                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 353                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 354
 355                                         }else if ((lookup.size() > 4) && (perm)) {
 356                                                 set< set<int> >::iterator it3;
 357                                                 set<int>::iterator it2;
 358                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 359
 360                                                         set<int> poss = *it3;
 361                                                         vector<SharedRAbundVector*> subset;
 362                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 363
 364                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 365                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 366                                                 }
 367                                         }else {
 368                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 369                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 370                                         }
 371
 372                                         //restore real lastlabel to save below
 373                                         lookup[0]->setLabel(saveLabel);
 374                                 }
 375
 376
 377                                 lastLabel = lookup[0]->getLabel();
 378
 379                                 //get next line to process
 380                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 381                                 lookup = input->getSharedRAbundVectors();
 382                         }
 383
 384                         if (m->control_pressed) {
 385                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 386                                         m->clearGroups(); delete venn; delete input;
 387                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 388                                         return 0;
 389                         }
 390
 391
 392                         //output error messages about any remaining user labels
 393                         set<string>::iterator it;
 394                         bool needToRun = false;
 395                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 396                                 m->mothurOut("Your file does not include the label " + *it);
 397                                 if (processedLabels.count(lastLabel) != 1) {
 398                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 399                                         needToRun = true;
 400                                 }else {
 401                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 402                                 }
 403                         }
 404
 405                         //run last label if you need to
 406                         if (needToRun == true)  {
 407                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 408                                         lookup = input->getSharedRAbundVectors(lastLabel);
 409
 410                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 411                                         processedLabels.insert(lookup[0]->getLabel());
 412                                         userLabels.erase(lookup[0]->getLabel());
 413
 414                                         if ((lookup.size() > 4) && (!perm)){
 415                                                 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();
 416                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 417
 418                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 419                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 420
 421                                         }else if ((lookup.size() > 4) && (perm)) {
 422                                                 set< set<int> >::iterator it3;
 423                                                 set<int>::iterator it2;
 424                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 425
 426                                                         set<int> poss = *it3;
 427                                                         vector<SharedRAbundVector*> subset;
 428                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 429
 430                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 431                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 432                                                 }
 433                                         }else {
 434                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 435                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 436                                         }
 437
 438                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 439                         }
 440
 441
 442                         //reset groups parameter
 443                         m->clearGroups();
 444
 445                         if (m->control_pressed) {
 446                                         m->clearGroups(); delete venn; delete input;
 447                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 448                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 449                                         return 0;
 450                         }
 451
 452
 453                 }else{
 454
 455                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 456
 457                                 if (m->control_pressed) {
 458                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 459                                         delete sabund; delete venn; delete input;
 460                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 461                                         return 0;
 462                                 }
 463
 464                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 465
 466                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 467                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 468                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 469
 470
 471                                         processedLabels.insert(sabund->getLabel());
 472                                         userLabels.erase(sabund->getLabel());
 473                                 }
 474
 475                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 476                                         string saveLabel = sabund->getLabel();
 477
 478                                         delete sabund;
 479                                         sabund = input->getSAbundVector(lastLabel);
 480
 481                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 482                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 483                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 484
 485
 486                                         processedLabels.insert(sabund->getLabel());
 487                                         userLabels.erase(sabund->getLabel());
 488
 489                                         //restore real lastlabel to save below
 490                                         sabund->setLabel(saveLabel);
 491                                 }
 492
 493                                 lastLabel = sabund->getLabel();
 494
 495                                 delete sabund;
 496                                 sabund = input->getSAbundVector();
 497                         }
 498
 499                         if (m->control_pressed) {
 500                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 501                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 502                                         delete venn; delete input;
 503                                         return 0;
 504                         }
 505
 506                         //output error messages about any remaining user labels
 507                         set<string>::iterator it;
 508                         bool needToRun = false;
 509                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 510                                 m->mothurOut("Your file does not include the label " + *it);
 511                                 if (processedLabels.count(lastLabel) != 1) {
 512                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 513                                         needToRun = true;
 514                                 }else {
 515                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 516                                 }
 517                         }
 518
 519                         //run last label if you need to
 520                         if (needToRun == true)  {
 521                                 if (sabund != NULL) {   delete sabund;  }
 522                                 sabund = input->getSAbundVector(lastLabel);
 523
 524                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 525                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 526                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 527
 528                                 delete sabund;
 529
 530                         }
 531
 532                         if (m->control_pressed) {
 533                                         delete venn; delete input;
 534                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 535                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 536                                         return 0;
 537                         }
 538                 }
 539
 540                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 541                 delete venn; delete input;
 542
 543                 m->mothurOutEndLine();
 544                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 545                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 546                 m->mothurOutEndLine();
 547
 548
 549                 return 0;
 550         }
 551         catch(exception& e) {
 552                 m->errorOut(e, "VennCommand", "execute");
 553                 exit(1);
 554         }
 555 }
 556 //**********************************************************************************************************************
 557 //returns a vector of sets containing the 4 group combinations
 558 set< set<int> > VennCommand::findCombinations(int lookupSize){
 559         try {
 560                 set< set<int> > combos;
 561
 562                 set<int> possibles;
 563                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 564
 565                 getCombos(possibles, combos);
 566
 567                 return combos;
 568
 569         }
 570         catch(exception& e) {
 571                 m->errorOut(e, "VennCommand", "findCombinations");
 572                 exit(1);
 573         }
 574 }
 575 //**********************************************************************************************************************
 576 //recusively finds combos of 4
 577 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 578         try {
 579
 580                 if (possibles.size() == 4) { //done
 581                         if (combos.count(possibles) == 0) { //no dups
 582                                 combos.insert(possibles);
 583                         }
 584                 }else { //we still have work to do
 585                         set<int>::iterator it;
 586                         set<int>::iterator it2;
 587                         for (it = possibles.begin(); it != possibles.end(); it++) {
 588
 589                                 set<int> newPossibles;
 590                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 591                                         if (*it != *it2) {
 592                                                 newPossibles.insert(*it2);
 593                                         }
 594                                 }
 595                                 getCombos(newPossibles, combos);
 596                         }
 597                 }
 598
 599                 return 0;
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "VennCommand", "getCombos");
 603                 exit(1);
 604         }
 605 }
 606
 607 //**********************************************************************************************************************