venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18 #include "nseqs.h"
  19
  20 //**********************************************************************************************************************
  21 vector<string> VennCommand::setParameters(){
  22         try {
  23                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  24                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  25                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  27                 CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
  28                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  29                 CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
  30                 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "VennCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string VennCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  48                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
  49                 helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
  50                 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
  51                 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
  52                 helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
  53                 helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
  54                 helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
  55                 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
  56                 helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n";
  57                 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
  58                 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
  59                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "VennCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67
  68 //**********************************************************************************************************************
  69 VennCommand::VennCommand(){
  70         try {
  71                 abort = true; calledHelp = true;
  72                 setParameters();
  73                 vector<string> tempOutNames;
  74                 outputTypes["svg"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "VennCommand", "VennCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82
  83 VennCommand::VennCommand(string option)  {
  84         try {
  85                 abort = false; calledHelp = false;
  86                 allLines = 1;
  87
  88                 //allow user to run help
  89                 if(option == "help") { help(); abort = true; calledHelp = true; }
  90                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  91
  92                 else {
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string,string> parameters = parser.getParameters();
  97                         map<string,string>::iterator it;
  98
  99                         ValidParameters validParameter;
 100
 101                         //check to make sure all parameters are valid for command
 102                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 103                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 104                         }
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("shared");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 117                                 }
 118
 119                                 it = parameters.find("list");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 125                                 }
 126                         }
 127
 128                         //check for required parameters
 129                         listfile = validParameter.validFile(parameters, "list", true);
 130                         if (listfile == "not open") { listfile = ""; abort = true; }
 131                         else if (listfile == "not found") { listfile = ""; }
 132                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 133
 134                         sharedfile = validParameter.validFile(parameters, "shared", true);
 135                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 136                         else if (sharedfile == "not found") { sharedfile = ""; }
 137                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 138
 139                         if ((sharedfile == "") && (listfile == "")) {
 140                                 //is there are current file available for any of these?
 141                                 //give priority to shared, then list, then rabund, then sabund
 142                                 //if there is a current shared file, use it
 143                                 sharedfile = m->getSharedFile();
 144                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 145                                 else {
 146                                         listfile = m->getListFile();
 147                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 148                                         else {
 149                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 150                                                 abort = true;
 151                                         }
 152                                 }
 153                         }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 157
 158                         //check for optional parameter and set defaults
 159                         // ...at some point should added some additional type checking...
 160                         label = validParameter.validFile(parameters, "label", false);
 161                         if (label == "not found") { label = ""; }
 162                         else {
 163                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 164                                 else { allLines = 1;  }
 165                         }
 166
 167                         groups = validParameter.validFile(parameters, "groups", false);
 168                         if (groups == "not found") { groups = ""; }
 169                         else {
 170                                 m->splitAtDash(groups, Groups);
 171                                 m->setGroups(Groups);
 172                         }
 173
 174                         calc = validParameter.validFile(parameters, "calc", false);
 175                         if (calc == "not found") {
 176                                 if(format == "list") { calc = "sobs"; }
 177                                 else { calc = "sharedsobs"; }
 178                         }
 179                         else {
 180                                  if (calc == "default")  {
 181                                         if(format == "list") { calc = "sobs"; }
 182                                         else { calc = "sharedsobs"; }
 183                                 }
 184                         }
 185                         m->splitAtDash(calc, Estimators);
 186                         if (m->inUsersGroups("citation", Estimators)) {
 187                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 188                                 //remove citation from list of calcs
 189                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 190                         }
 191
 192                         string temp;
 193                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 194                         convert(temp, abund);
 195
 196                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 197                         nseqs = m->isTrue(temp);
 198
 199                         temp = validParameter.validFile(parameters, "permute", false);                  if (temp == "not found"){       temp = "f";                             }
 200                         perm = m->isTrue(temp);
 201
 202                 }
 203
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "VennCommand", "VennCommand");
 207                 exit(1);
 208         }
 209 }
 210 //**********************************************************************************************************************
 211
 212 int VennCommand::execute(){
 213         try {
 214
 215                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 216
 217                 ValidCalculators validCalculator;
 218
 219                 if (format == "list") {
 220                         for (int i=0; i<Estimators.size(); i++) {
 221                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 222                                         if (Estimators[i] == "sobs") {
 223                                                 vennCalculators.push_back(new Sobs());
 224                                         }else if (Estimators[i] == "chao") {
 225                                                 vennCalculators.push_back(new Chao1());
 226                                         }else if (Estimators[i] == "ace") {
 227                                                 if(abund < 5)
 228                                                         abund = 10;
 229                                                 vennCalculators.push_back(new Ace(abund));
 230                                         }
 231                                 }
 232                         }
 233                 }else {
 234                         for (int i=0; i<Estimators.size(); i++) {
 235                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 236                                         if (Estimators[i] == "sharedsobs") {
 237                                                 vennCalculators.push_back(new SharedSobsCS());
 238                                         }else if (Estimators[i] == "sharedchao") {
 239                                                 vennCalculators.push_back(new SharedChao1());
 240                                         }else if (Estimators[i] == "sharedace") {
 241                                                 vennCalculators.push_back(new SharedAce());
 242                                         }
 243                                 }
 244                         }
 245                 }
 246
 247                 //if the users entered no valid calculators don't execute command
 248                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 249
 250                 venn = new Venn(outputDir, nseqs, inputfile);
 251                 input = new InputData(inputfile, format);
 252
 253                 string lastLabel;
 254
 255                 if (format == "sharedfile") {
 256                         lookup = input->getSharedRAbundVectors();
 257                         lastLabel = lookup[0]->getLabel();
 258
 259                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 260                 }else if (format == "list") {
 261                         sabund = input->getSAbundVector();
 262                         lastLabel = sabund->getLabel();
 263                 }
 264
 265                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 266                 set<string> processedLabels;
 267                 set<string> userLabels = labels;
 268
 269                 if (format != "list") {
 270
 271                         //as long as you are not at the end of the file or done wih the lines you want
 272                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 273
 274                                 if (m->control_pressed) {
 275                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 276                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 277                                         m->clearGroups(); delete venn; delete input;
 278                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 279                                         return 0;
 280                                 }
 281
 282                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 283                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 284                                         processedLabels.insert(lookup[0]->getLabel());
 285                                         userLabels.erase(lookup[0]->getLabel());
 286
 287                                         if ((lookup.size() > 4) && (!perm)){
 288                                                 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();
 289                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 290
 291                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 292                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 293
 294                                         }else if ((lookup.size() > 4) && (perm)) {
 295                                                 set< set<int> >::iterator it3;
 296                                                 set<int>::iterator it2;
 297                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 298
 299                                                         set<int> poss = *it3;
 300                                                         vector<SharedRAbundVector*> subset;
 301                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 302
 303                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 304                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 305                                                 }
 306                                         }else {
 307                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 308                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 309                                         }
 310                                 }
 311
 312                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 313                                         string saveLabel = lookup[0]->getLabel();
 314
 315                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 316                                         lookup = input->getSharedRAbundVectors(lastLabel);
 317
 318                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 319                                         processedLabels.insert(lookup[0]->getLabel());
 320                                         userLabels.erase(lookup[0]->getLabel());
 321
 322                                         if ((lookup.size() > 4) && (!perm)){
 323                                                 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();
 324                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 325
 326                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 327                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 328
 329                                         }else if ((lookup.size() > 4) && (perm)) {
 330                                                 set< set<int> >::iterator it3;
 331                                                 set<int>::iterator it2;
 332                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 333
 334                                                         set<int> poss = *it3;
 335                                                         vector<SharedRAbundVector*> subset;
 336                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 337
 338                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 339                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 340                                                 }
 341                                         }else {
 342                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 343                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 344                                         }
 345
 346                                         //restore real lastlabel to save below
 347                                         lookup[0]->setLabel(saveLabel);
 348                                 }
 349
 350
 351                                 lastLabel = lookup[0]->getLabel();
 352
 353                                 //get next line to process
 354                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 355                                 lookup = input->getSharedRAbundVectors();
 356                         }
 357
 358                         if (m->control_pressed) {
 359                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 360                                         m->clearGroups(); delete venn; delete input;
 361                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 362                                         return 0;
 363                         }
 364
 365
 366                         //output error messages about any remaining user labels
 367                         set<string>::iterator it;
 368                         bool needToRun = false;
 369                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 370                                 m->mothurOut("Your file does not include the label " + *it);
 371                                 if (processedLabels.count(lastLabel) != 1) {
 372                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 373                                         needToRun = true;
 374                                 }else {
 375                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 376                                 }
 377                         }
 378
 379                         //run last label if you need to
 380                         if (needToRun == true)  {
 381                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 382                                         lookup = input->getSharedRAbundVectors(lastLabel);
 383
 384                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 385                                         processedLabels.insert(lookup[0]->getLabel());
 386                                         userLabels.erase(lookup[0]->getLabel());
 387
 388                                         if ((lookup.size() > 4) && (!perm)){
 389                                                 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();
 390                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 391
 392                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 393                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 394
 395                                         }else if ((lookup.size() > 4) && (perm)) {
 396                                                 set< set<int> >::iterator it3;
 397                                                 set<int>::iterator it2;
 398                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 399
 400                                                         set<int> poss = *it3;
 401                                                         vector<SharedRAbundVector*> subset;
 402                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 403
 404                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 405                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 406                                                 }
 407                                         }else {
 408                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 409                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 410                                         }
 411
 412                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 413                         }
 414
 415
 416                         //reset groups parameter
 417                         m->clearGroups();
 418
 419                         if (m->control_pressed) {
 420                                         m->clearGroups(); delete venn; delete input;
 421                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 422                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 423                                         return 0;
 424                         }
 425
 426
 427                 }else{
 428
 429                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 430
 431                                 if (m->control_pressed) {
 432                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 433                                         delete sabund; delete venn; delete input;
 434                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 435                                         return 0;
 436                                 }
 437
 438                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 439
 440                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 441                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 442                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 443
 444
 445                                         processedLabels.insert(sabund->getLabel());
 446                                         userLabels.erase(sabund->getLabel());
 447                                 }
 448
 449                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 450                                         string saveLabel = sabund->getLabel();
 451
 452                                         delete sabund;
 453                                         sabund = input->getSAbundVector(lastLabel);
 454
 455                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 456                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 457                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 458
 459
 460                                         processedLabels.insert(sabund->getLabel());
 461                                         userLabels.erase(sabund->getLabel());
 462
 463                                         //restore real lastlabel to save below
 464                                         sabund->setLabel(saveLabel);
 465                                 }
 466
 467                                 lastLabel = sabund->getLabel();
 468
 469                                 delete sabund;
 470                                 sabund = input->getSAbundVector();
 471                         }
 472
 473                         if (m->control_pressed) {
 474                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 475                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 476                                         delete venn; delete input;
 477                                         return 0;
 478                         }
 479
 480                         //output error messages about any remaining user labels
 481                         set<string>::iterator it;
 482                         bool needToRun = false;
 483                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 484                                 m->mothurOut("Your file does not include the label " + *it);
 485                                 if (processedLabels.count(lastLabel) != 1) {
 486                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 487                                         needToRun = true;
 488                                 }else {
 489                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 490                                 }
 491                         }
 492
 493                         //run last label if you need to
 494                         if (needToRun == true)  {
 495                                 if (sabund != NULL) {   delete sabund;  }
 496                                 sabund = input->getSAbundVector(lastLabel);
 497
 498                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 499                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 500                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 501
 502                                 delete sabund;
 503
 504                         }
 505
 506                         if (m->control_pressed) {
 507                                         delete venn; delete input;
 508                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 509                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 510                                         return 0;
 511                         }
 512                 }
 513
 514                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 515                 delete venn; delete input;
 516
 517                 m->mothurOutEndLine();
 518                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 519                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 520                 m->mothurOutEndLine();
 521
 522
 523                 return 0;
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "VennCommand", "execute");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531 //returns a vector of sets containing the 4 group combinations
 532 set< set<int> > VennCommand::findCombinations(int lookupSize){
 533         try {
 534                 set< set<int> > combos;
 535
 536                 set<int> possibles;
 537                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 538
 539                 getCombos(possibles, combos);
 540
 541                 return combos;
 542
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "VennCommand", "findCombinations");
 546                 exit(1);
 547         }
 548 }
 549 //**********************************************************************************************************************
 550 //recusively finds combos of 4
 551 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 552         try {
 553
 554                 if (possibles.size() == 4) { //done
 555                         if (combos.count(possibles) == 0) { //no dups
 556                                 combos.insert(possibles);
 557                         }
 558                 }else { //we still have work to do
 559                         set<int>::iterator it;
 560                         set<int>::iterator it2;
 561                         for (it = possibles.begin(); it != possibles.end(); it++) {
 562
 563                                 set<int> newPossibles;
 564                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 565                                         if (*it != *it2) {
 566                                                 newPossibles.insert(*it2);
 567                                         }
 568                                 }
 569                                 getCombos(newPossibles, combos);
 570                         }
 571                 }
 572
 573                 return 0;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "VennCommand", "getCombos");
 577                 exit(1);
 578         }
 579 }
 580
 581 //**********************************************************************************************************************