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 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 string VennCommand::getOutputPattern(string type) {
  71     try {
  72         string pattern = "";
  73
  74         if (type == "svg") {  pattern = "[filename],svg"; }
  75         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  76
  77         return pattern;
  78     }
  79     catch(exception& e) {
  80         m->errorOut(e, "VennCommand", "getOutputPattern");
  81         exit(1);
  82     }
  83 }
  84
  85 //**********************************************************************************************************************
  86 VennCommand::VennCommand(){
  87         try {
  88                 abort = true; calledHelp = true;
  89                 setParameters();
  90                 vector<string> tempOutNames;
  91                 outputTypes["svg"] = tempOutNames;
  92         }
  93         catch(exception& e) {
  94                 m->errorOut(e, "VennCommand", "VennCommand");
  95                 exit(1);
  96         }
  97 }
  98 //**********************************************************************************************************************
  99
 100 VennCommand::VennCommand(string option)  {
 101         try {
 102                 abort = false; calledHelp = false;
 103                 allLines = 1;
 104
 105                 //allow user to run help
 106                 if(option == "help") { help(); abort = true; calledHelp = true; }
 107                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 108
 109                 else {
 110                         vector<string> myArray = setParameters();
 111
 112                         OptionParser parser(option);
 113                         map<string,string> parameters = parser.getParameters();
 114                         map<string,string>::iterator it;
 115
 116                         ValidParameters validParameter;
 117
 118                         //check to make sure all parameters are valid for command
 119                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 120                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 121                         }
 122
 123                         //if the user changes the input directory command factory will send this info to us in the output parameter
 124                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 125                         if (inputDir == "not found"){   inputDir = "";          }
 126                         else {
 127                                 string path;
 128                                 it = parameters.find("shared");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 134                                 }
 135
 136                                 it = parameters.find("list");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 142                                 }
 143                         }
 144
 145                         //check for required parameters
 146                         listfile = validParameter.validFile(parameters, "list", true);
 147                         if (listfile == "not open") { listfile = ""; abort = true; }
 148                         else if (listfile == "not found") { listfile = ""; }
 149                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 150
 151                         sharedfile = validParameter.validFile(parameters, "shared", true);
 152                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 153                         else if (sharedfile == "not found") { sharedfile = ""; }
 154                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 155
 156                         if ((sharedfile == "") && (listfile == "")) {
 157                                 //is there are current file available for any of these?
 158                                 //give priority to shared, then list, then rabund, then sabund
 159                                 //if there is a current shared file, use it
 160                                 sharedfile = m->getSharedFile();
 161                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 162                                 else {
 163                                         listfile = m->getListFile();
 164                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 165                                         else {
 166                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 167                                                 abort = true;
 168                                         }
 169                                 }
 170                         }
 171
 172                         //if the user changes the output directory command factory will send this info to us in the output parameter
 173                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 174
 175                         //check for optional parameter and set defaults
 176                         // ...at some point should added some additional type checking...
 177                         label = validParameter.validFile(parameters, "label", false);
 178                         if (label == "not found") { label = ""; }
 179                         else {
 180                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 181                                 else { allLines = 1;  }
 182                         }
 183
 184                         groups = validParameter.validFile(parameters, "groups", false);
 185                         if (groups == "not found") { groups = ""; }
 186                         else {
 187                                 m->splitAtDash(groups, Groups);
 188                                 m->setGroups(Groups);
 189                         }
 190
 191                         calc = validParameter.validFile(parameters, "calc", false);
 192                         if (calc == "not found") {
 193                                 if(format == "list") { calc = "sobs"; }
 194                                 else { calc = "sharedsobs"; }
 195                         }
 196                         else {
 197                                  if (calc == "default")  {
 198                                         if(format == "list") { calc = "sobs"; }
 199                                         else { calc = "sharedsobs"; }
 200                                 }
 201                         }
 202                         m->splitAtDash(calc, Estimators);
 203                         if (m->inUsersGroups("citation", Estimators)) {
 204                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 205                                 //remove citation from list of calcs
 206                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 207                         }
 208
 209                         string temp;
 210                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 211                         m->mothurConvert(temp, abund);
 212
 213                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 214                         nseqs = m->isTrue(temp);
 215
 216                         temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "f";                             }
 217                         perm = m->isTrue(temp);
 218
 219                         temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
 220                         m->mothurConvert(temp, fontsize);
 221
 222                 }
 223
 224         }
 225         catch(exception& e) {
 226                 m->errorOut(e, "VennCommand", "VennCommand");
 227                 exit(1);
 228         }
 229 }
 230 //**********************************************************************************************************************
 231
 232 int VennCommand::execute(){
 233         try {
 234
 235                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 236
 237                 ValidCalculators validCalculator;
 238
 239                 if (format == "list") {
 240                         for (int i=0; i<Estimators.size(); i++) {
 241                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 242                                         if (Estimators[i] == "sobs") {
 243                                                 vennCalculators.push_back(new Sobs());
 244                                         }else if (Estimators[i] == "chao") {
 245                                                 vennCalculators.push_back(new Chao1());
 246                                         }else if (Estimators[i] == "ace") {
 247                                                 if(abund < 5) { abund = 10; }
 248                                                 vennCalculators.push_back(new Ace(abund));
 249                                         }
 250                                 }
 251                         }
 252                 }else {
 253                         for (int i=0; i<Estimators.size(); i++) {
 254                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 255                                         if (Estimators[i] == "sharedsobs") {
 256                                                 vennCalculators.push_back(new SharedSobsCS());
 257                                         }else if (Estimators[i] == "sharedchao") {
 258                                                 vennCalculators.push_back(new SharedChao1());
 259                                         }else if (Estimators[i] == "sharedace") {
 260                                                 vennCalculators.push_back(new SharedAce());
 261                                         }
 262                                 }
 263                         }
 264                 }
 265
 266                 //if the users entered no valid calculators don't execute command
 267                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 268
 269                 venn = new Venn(outputDir, nseqs, inputfile, fontsize);
 270                 input = new InputData(inputfile, format);
 271
 272                 string lastLabel;
 273
 274                 if (format == "sharedfile") {
 275                         lookup = input->getSharedRAbundVectors();
 276                         lastLabel = lookup[0]->getLabel();
 277
 278                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 279                 }else if (format == "list") {
 280                         sabund = input->getSAbundVector();
 281                         lastLabel = sabund->getLabel();
 282                 }
 283
 284                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 285                 set<string> processedLabels;
 286                 set<string> userLabels = labels;
 287
 288                 if (format != "list") {
 289
 290                         //as long as you are not at the end of the file or done wih the lines you want
 291                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 292
 293                                 if (m->control_pressed) {
 294                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 295                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 296                                         m->clearGroups(); delete venn; delete input;
 297                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 298                                         return 0;
 299                                 }
 300
 301                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 302                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 303                                         processedLabels.insert(lookup[0]->getLabel());
 304                                         userLabels.erase(lookup[0]->getLabel());
 305
 306                                         if ((lookup.size() > 4) && (!perm)){
 307                                                 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();
 308                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 309
 310                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 311                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 312
 313                                         }else if ((lookup.size() > 4) && (perm)) {
 314                                                 set< set<int> >::iterator it3;
 315                                                 set<int>::iterator it2;
 316                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 317
 318                                                         set<int> poss = *it3;
 319                                                         vector<SharedRAbundVector*> subset;
 320                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 321
 322                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 323                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 324                                                 }
 325                                         }else {
 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                                 }
 330
 331                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 332                                         string saveLabel = lookup[0]->getLabel();
 333
 334                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 335                                         lookup = input->getSharedRAbundVectors(lastLabel);
 336
 337                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 338                                         processedLabels.insert(lookup[0]->getLabel());
 339                                         userLabels.erase(lookup[0]->getLabel());
 340
 341                                         if ((lookup.size() > 4) && (!perm)){
 342                                                 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();
 343                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 344
 345                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 346                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 347
 348                                         }else if ((lookup.size() > 4) && (perm)) {
 349                                                 set< set<int> >::iterator it3;
 350                                                 set<int>::iterator it2;
 351                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 352
 353                                                         set<int> poss = *it3;
 354                                                         vector<SharedRAbundVector*> subset;
 355                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 356
 357                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 358                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 359                                                 }
 360                                         }else {
 361                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 362                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 363                                         }
 364
 365                                         //restore real lastlabel to save below
 366                                         lookup[0]->setLabel(saveLabel);
 367                                 }
 368
 369
 370                                 lastLabel = lookup[0]->getLabel();
 371
 372                                 //get next line to process
 373                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 374                                 lookup = input->getSharedRAbundVectors();
 375                         }
 376
 377                         if (m->control_pressed) {
 378                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 379                                         m->clearGroups(); delete venn; delete input;
 380                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 381                                         return 0;
 382                         }
 383
 384
 385                         //output error messages about any remaining user labels
 386                         set<string>::iterator it;
 387                         bool needToRun = false;
 388                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 389                                 m->mothurOut("Your file does not include the label " + *it);
 390                                 if (processedLabels.count(lastLabel) != 1) {
 391                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 392                                         needToRun = true;
 393                                 }else {
 394                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 395                                 }
 396                         }
 397
 398                         //run last label if you need to
 399                         if (needToRun == true)  {
 400                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 401                                         lookup = input->getSharedRAbundVectors(lastLabel);
 402
 403                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 404                                         processedLabels.insert(lookup[0]->getLabel());
 405                                         userLabels.erase(lookup[0]->getLabel());
 406
 407                                         if ((lookup.size() > 4) && (!perm)){
 408                                                 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();
 409                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 410
 411                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 412                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 413
 414                                         }else if ((lookup.size() > 4) && (perm)) {
 415                                                 set< set<int> >::iterator it3;
 416                                                 set<int>::iterator it2;
 417                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 418
 419                                                         set<int> poss = *it3;
 420                                                         vector<SharedRAbundVector*> subset;
 421                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 422
 423                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 424                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 425                                                 }
 426                                         }else {
 427                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 428                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 429                                         }
 430
 431                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 432                         }
 433
 434
 435                         //reset groups parameter
 436                         m->clearGroups();
 437
 438                         if (m->control_pressed) {
 439                                         m->clearGroups(); delete venn; delete input;
 440                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 441                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 442                                         return 0;
 443                         }
 444
 445
 446                 }else{
 447
 448                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 449
 450                                 if (m->control_pressed) {
 451                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 452                                         delete sabund; delete venn; delete input;
 453                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 454                                         return 0;
 455                                 }
 456
 457                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 458
 459                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 460                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 461                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 462
 463
 464                                         processedLabels.insert(sabund->getLabel());
 465                                         userLabels.erase(sabund->getLabel());
 466                                 }
 467
 468                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 469                                         string saveLabel = sabund->getLabel();
 470
 471                                         delete sabund;
 472                                         sabund = input->getSAbundVector(lastLabel);
 473
 474                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 475                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 476                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 477
 478
 479                                         processedLabels.insert(sabund->getLabel());
 480                                         userLabels.erase(sabund->getLabel());
 481
 482                                         //restore real lastlabel to save below
 483                                         sabund->setLabel(saveLabel);
 484                                 }
 485
 486                                 lastLabel = sabund->getLabel();
 487
 488                                 delete sabund;
 489                                 sabund = input->getSAbundVector();
 490                         }
 491
 492                         if (m->control_pressed) {
 493                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 494                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 495                                         delete venn; delete input;
 496                                         return 0;
 497                         }
 498
 499                         //output error messages about any remaining user labels
 500                         set<string>::iterator it;
 501                         bool needToRun = false;
 502                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 503                                 m->mothurOut("Your file does not include the label " + *it);
 504                                 if (processedLabels.count(lastLabel) != 1) {
 505                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 506                                         needToRun = true;
 507                                 }else {
 508                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 509                                 }
 510                         }
 511
 512                         //run last label if you need to
 513                         if (needToRun == true)  {
 514                                 if (sabund != NULL) {   delete sabund;  }
 515                                 sabund = input->getSAbundVector(lastLabel);
 516
 517                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 518                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 519                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 520
 521                                 delete sabund;
 522
 523                         }
 524
 525                         if (m->control_pressed) {
 526                                         delete venn; delete input;
 527                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 528                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 529                                         return 0;
 530                         }
 531                 }
 532
 533                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 534                 delete venn; delete input;
 535
 536                 m->mothurOutEndLine();
 537                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 538                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 539                 m->mothurOutEndLine();
 540
 541
 542                 return 0;
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "VennCommand", "execute");
 546                 exit(1);
 547         }
 548 }
 549 //**********************************************************************************************************************
 550 //returns a vector of sets containing the 4 group combinations
 551 set< set<int> > VennCommand::findCombinations(int lookupSize){
 552         try {
 553                 set< set<int> > combos;
 554
 555                 set<int> possibles;
 556                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 557
 558                 getCombos(possibles, combos);
 559
 560                 return combos;
 561
 562         }
 563         catch(exception& e) {
 564                 m->errorOut(e, "VennCommand", "findCombinations");
 565                 exit(1);
 566         }
 567 }
 568 //**********************************************************************************************************************
 569 //recusively finds combos of 4
 570 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 571         try {
 572
 573                 if (possibles.size() == 4) { //done
 574                         if (combos.count(possibles) == 0) { //no dups
 575                                 combos.insert(possibles);
 576                         }
 577                 }else { //we still have work to do
 578                         set<int>::iterator it;
 579                         set<int>::iterator it2;
 580                         for (it = possibles.begin(); it != possibles.end(); it++) {
 581
 582                                 set<int> newPossibles;
 583                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 584                                         if (*it != *it2) {
 585                                                 newPossibles.insert(*it2);
 586                                         }
 587                                 }
 588                                 getCombos(newPossibles, combos);
 589                         }
 590                 }
 591
 592                 return 0;
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "VennCommand", "getCombos");
 596                 exit(1);
 597         }
 598 }
 599
 600 //**********************************************************************************************************************