venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18 #include "nseqs.h"
  19
  20 //**********************************************************************************************************************
  21 vector<string> VennCommand::setParameters(){
  22         try {
  23                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
  24                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
  25                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  27                 CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc);
  28                 CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
  29                 CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs);
  30         CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
  31                 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
  32                 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
  33                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  34                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  35
  36                 vector<string> myArray;
  37                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "VennCommand", "setParameters");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string VennCommand::getHelpString(){
  47         try {
  48                 string helpString = "";
  49                 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  50                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
  51                 helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
  52                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  53                 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
  54                 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
  55                 helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
  56                 helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
  57                 helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
  58                 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
  59                 helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n";
  60                 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
  61                 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
  62                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  63                 return helpString;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "VennCommand", "getHelpString");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 string VennCommand::getOutputPattern(string type) {
  72     try {
  73         string pattern = "";
  74
  75         if (type == "svg") {  pattern = "[filename],svg"; }
  76         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  77
  78         return pattern;
  79     }
  80     catch(exception& e) {
  81         m->errorOut(e, "VennCommand", "getOutputPattern");
  82         exit(1);
  83     }
  84 }
  85
  86 //**********************************************************************************************************************
  87 VennCommand::VennCommand(){
  88         try {
  89                 abort = true; calledHelp = true;
  90                 setParameters();
  91                 vector<string> tempOutNames;
  92                 outputTypes["svg"] = tempOutNames;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "VennCommand", "VennCommand");
  96                 exit(1);
  97         }
  98 }
  99 //**********************************************************************************************************************
 100
 101 VennCommand::VennCommand(string option)  {
 102         try {
 103                 abort = false; calledHelp = false;
 104                 allLines = 1;
 105
 106                 //allow user to run help
 107                 if(option == "help") { help(); abort = true; calledHelp = true; }
 108                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 109
 110                 else {
 111                         vector<string> myArray = setParameters();
 112
 113                         OptionParser parser(option);
 114                         map<string,string> parameters = parser.getParameters();
 115                         map<string,string>::iterator it;
 116
 117                         ValidParameters validParameter;
 118
 119                         //check to make sure all parameters are valid for command
 120                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 121                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 122                         }
 123
 124                         //if the user changes the input directory command factory will send this info to us in the output parameter
 125                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 126                         if (inputDir == "not found"){   inputDir = "";          }
 127                         else {
 128                                 string path;
 129                                 it = parameters.find("shared");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 135                                 }
 136
 137                                 it = parameters.find("list");
 138                                 //user has given a template file
 139                                 if(it != parameters.end()){
 140                                         path = m->hasPath(it->second);
 141                                         //if the user has not given a path then, add inputdir. else leave path alone.
 142                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 143                                 }
 144                         }
 145
 146                         //check for required parameters
 147                         listfile = validParameter.validFile(parameters, "list", true);
 148                         if (listfile == "not open") { listfile = ""; abort = true; }
 149                         else if (listfile == "not found") { listfile = ""; }
 150                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 151
 152                         sharedfile = validParameter.validFile(parameters, "shared", true);
 153                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 154                         else if (sharedfile == "not found") { sharedfile = ""; }
 155                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 156
 157                         if ((sharedfile == "") && (listfile == "")) {
 158                                 //is there are current file available for any of these?
 159                                 //give priority to shared, then list, then rabund, then sabund
 160                                 //if there is a current shared file, use it
 161                                 sharedfile = m->getSharedFile();
 162                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 163                                 else {
 164                                         listfile = m->getListFile();
 165                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 166                                         else {
 167                                                 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
 168                                                 abort = true;
 169                                         }
 170                                 }
 171                         }
 172
 173                         //if the user changes the output directory command factory will send this info to us in the output parameter
 174                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 175
 176                         //check for optional parameter and set defaults
 177                         // ...at some point should added some additional type checking...
 178                         label = validParameter.validFile(parameters, "label", false);
 179                         if (label == "not found") { label = ""; }
 180                         else {
 181                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 182                                 else { allLines = 1;  }
 183                         }
 184
 185                         groups = validParameter.validFile(parameters, "groups", false);
 186                         if (groups == "not found") { groups = ""; }
 187                         else {
 188                                 m->splitAtDash(groups, Groups);
 189                                 m->setGroups(Groups);
 190                         }
 191
 192                         calc = validParameter.validFile(parameters, "calc", false);
 193                         if (calc == "not found") {
 194                                 if(format == "list") { calc = "sobs"; }
 195                                 else { calc = "sharedsobs"; }
 196                         }
 197                         else {
 198                                  if (calc == "default")  {
 199                                         if(format == "list") { calc = "sobs"; }
 200                                         else { calc = "sharedsobs"; }
 201                                 }
 202                         }
 203                         m->splitAtDash(calc, Estimators);
 204                         if (m->inUsersGroups("citation", Estimators)) {
 205                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 206                                 //remove citation from list of calcs
 207                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 208                         }
 209
 210                         string temp;
 211                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 212                         m->mothurConvert(temp, abund);
 213
 214                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 215                         nseqs = m->isTrue(temp);
 216
 217                         temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "f";                             }
 218                         perm = m->isTrue(temp);
 219
 220             temp = validParameter.validFile(parameters, "sharedotus", false);           if (temp == "not found"){       temp = "t";                             }
 221                         sharedOtus = m->isTrue(temp);
 222
 223                         temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
 224                         m->mothurConvert(temp, fontsize);
 225
 226                 }
 227
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "VennCommand", "VennCommand");
 231                 exit(1);
 232         }
 233 }
 234 //**********************************************************************************************************************
 235
 236 int VennCommand::execute(){
 237         try {
 238
 239                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 240
 241                 ValidCalculators validCalculator;
 242
 243                 if (format == "list") {
 244                         for (int i=0; i<Estimators.size(); i++) {
 245                                 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
 246                                         if (Estimators[i] == "sobs") {
 247                                                 vennCalculators.push_back(new Sobs());
 248                                         }else if (Estimators[i] == "chao") {
 249                                                 vennCalculators.push_back(new Chao1());
 250                                         }else if (Estimators[i] == "ace") {
 251                                                 if(abund < 5) { abund = 10; }
 252                                                 vennCalculators.push_back(new Ace(abund));
 253                                         }
 254                                 }
 255                         }
 256                 }else {
 257                         for (int i=0; i<Estimators.size(); i++) {
 258                                 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
 259                                         if (Estimators[i] == "sharedsobs") {
 260                                                 vennCalculators.push_back(new SharedSobsCS());
 261                                         }else if (Estimators[i] == "sharedchao") {
 262                                                 vennCalculators.push_back(new SharedChao1());
 263                                         }else if (Estimators[i] == "sharedace") {
 264                                                 vennCalculators.push_back(new SharedAce());
 265                                         }
 266                                 }
 267                         }
 268                 }
 269
 270                 //if the users entered no valid calculators don't execute command
 271                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0;  }
 272
 273                 venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
 274                 input = new InputData(inputfile, format);
 275
 276                 string lastLabel;
 277
 278                 if (format == "sharedfile") {
 279                         lookup = input->getSharedRAbundVectors();
 280                         lastLabel = lookup[0]->getLabel();
 281
 282                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 283                 }else if (format == "list") {
 284                         sabund = input->getSAbundVector();
 285                         lastLabel = sabund->getLabel();
 286                 }
 287
 288                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 289                 set<string> processedLabels;
 290                 set<string> userLabels = labels;
 291
 292                 if (format != "list") {
 293
 294                         //as long as you are not at the end of the file or done wih the lines you want
 295                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 296
 297                                 if (m->control_pressed) {
 298                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 299                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 300                                         m->clearGroups(); delete venn; delete input;
 301                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 302                                         return 0;
 303                                 }
 304
 305                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 306                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 307                                         processedLabels.insert(lookup[0]->getLabel());
 308                                         userLabels.erase(lookup[0]->getLabel());
 309
 310                                         if ((lookup.size() > 4) && (!perm)){
 311                                                 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();
 312                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 313
 314                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 315                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  } }
 316
 317                                         }else if ((lookup.size() > 4) && (perm)) {
 318                                                 set< set<int> >::iterator it3;
 319                                                 set<int>::iterator it2;
 320                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 321
 322                                                         set<int> poss = *it3;
 323                                                         vector<SharedRAbundVector*> subset;
 324                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 325
 326                                                         vector<string> outfilenames = venn->getPic(subset, 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 {
 330                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 331                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 332                                         }
 333                                 }
 334
 335                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 336                                         string saveLabel = lookup[0]->getLabel();
 337
 338                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 339                                         lookup = input->getSharedRAbundVectors(lastLabel);
 340
 341                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 342                                         processedLabels.insert(lookup[0]->getLabel());
 343                                         userLabels.erase(lookup[0]->getLabel());
 344
 345                                         if ((lookup.size() > 4) && (!perm)){
 346                                                 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();
 347                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 348
 349                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 350                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 351
 352                                         }else if ((lookup.size() > 4) && (perm)) {
 353                                                 set< set<int> >::iterator it3;
 354                                                 set<int>::iterator it2;
 355                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 356
 357                                                         set<int> poss = *it3;
 358                                                         vector<SharedRAbundVector*> subset;
 359                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 360
 361                                                         vector<string> outfilenames = venn->getPic(subset, 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                                         }else {
 365                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 366                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 367                                         }
 368
 369                                         //restore real lastlabel to save below
 370                                         lookup[0]->setLabel(saveLabel);
 371                                 }
 372
 373
 374                                 lastLabel = lookup[0]->getLabel();
 375
 376                                 //get next line to process
 377                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 378                                 lookup = input->getSharedRAbundVectors();
 379                         }
 380
 381                         if (m->control_pressed) {
 382                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 383                                         m->clearGroups(); delete venn; delete input;
 384                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 385                                         return 0;
 386                         }
 387
 388
 389                         //output error messages about any remaining user labels
 390                         set<string>::iterator it;
 391                         bool needToRun = false;
 392                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 393                                 m->mothurOut("Your file does not include the label " + *it);
 394                                 if (processedLabels.count(lastLabel) != 1) {
 395                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 396                                         needToRun = true;
 397                                 }else {
 398                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 399                                 }
 400                         }
 401
 402                         //run last label if you need to
 403                         if (needToRun == true)  {
 404                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 405                                         lookup = input->getSharedRAbundVectors(lastLabel);
 406
 407                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 408                                         processedLabels.insert(lookup[0]->getLabel());
 409                                         userLabels.erase(lookup[0]->getLabel());
 410
 411                                         if ((lookup.size() > 4) && (!perm)){
 412                                                 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();
 413                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 414
 415                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 416                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }  }
 417
 418                                         }else if ((lookup.size() > 4) && (perm)) {
 419                                                 set< set<int> >::iterator it3;
 420                                                 set<int>::iterator it2;
 421                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 422
 423                                                         set<int> poss = *it3;
 424                                                         vector<SharedRAbundVector*> subset;
 425                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 426
 427                                                         vector<string> outfilenames = venn->getPic(subset, 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                                         }else {
 431                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 432                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 433                                         }
 434
 435                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 436                         }
 437
 438
 439                         //reset groups parameter
 440                         m->clearGroups();
 441
 442                         if (m->control_pressed) {
 443                                         m->clearGroups(); delete venn; delete input;
 444                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 445                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 446                                         return 0;
 447                         }
 448
 449
 450                 }else{
 451
 452                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 453
 454                                 if (m->control_pressed) {
 455                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 456                                         delete sabund; delete venn; delete input;
 457                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 458                                         return 0;
 459                                 }
 460
 461                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 462
 463                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 464                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 465                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 466
 467
 468                                         processedLabels.insert(sabund->getLabel());
 469                                         userLabels.erase(sabund->getLabel());
 470                                 }
 471
 472                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 473                                         string saveLabel = sabund->getLabel();
 474
 475                                         delete sabund;
 476                                         sabund = input->getSAbundVector(lastLabel);
 477
 478                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 479                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 480                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 481
 482
 483                                         processedLabels.insert(sabund->getLabel());
 484                                         userLabels.erase(sabund->getLabel());
 485
 486                                         //restore real lastlabel to save below
 487                                         sabund->setLabel(saveLabel);
 488                                 }
 489
 490                                 lastLabel = sabund->getLabel();
 491
 492                                 delete sabund;
 493                                 sabund = input->getSAbundVector();
 494                         }
 495
 496                         if (m->control_pressed) {
 497                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 498                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 499                                         delete venn; delete input;
 500                                         return 0;
 501                         }
 502
 503                         //output error messages about any remaining user labels
 504                         set<string>::iterator it;
 505                         bool needToRun = false;
 506                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 507                                 m->mothurOut("Your file does not include the label " + *it);
 508                                 if (processedLabels.count(lastLabel) != 1) {
 509                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 510                                         needToRun = true;
 511                                 }else {
 512                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 513                                 }
 514                         }
 515
 516                         //run last label if you need to
 517                         if (needToRun == true)  {
 518                                 if (sabund != NULL) {   delete sabund;  }
 519                                 sabund = input->getSAbundVector(lastLabel);
 520
 521                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 522                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 523                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]);  }  }
 524
 525                                 delete sabund;
 526
 527                         }
 528
 529                         if (m->control_pressed) {
 530                                         delete venn; delete input;
 531                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 532                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 533                                         return 0;
 534                         }
 535                 }
 536
 537                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 538                 delete venn; delete input;
 539
 540                 m->mothurOutEndLine();
 541                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 542                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 543                 m->mothurOutEndLine();
 544
 545
 546                 return 0;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "VennCommand", "execute");
 550                 exit(1);
 551         }
 552 }
 553 //**********************************************************************************************************************
 554 //returns a vector of sets containing the 4 group combinations
 555 set< set<int> > VennCommand::findCombinations(int lookupSize){
 556         try {
 557                 set< set<int> > combos;
 558
 559                 set<int> possibles;
 560                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 561
 562                 getCombos(possibles, combos);
 563
 564                 return combos;
 565
 566         }
 567         catch(exception& e) {
 568                 m->errorOut(e, "VennCommand", "findCombinations");
 569                 exit(1);
 570         }
 571 }
 572 //**********************************************************************************************************************
 573 //recusively finds combos of 4
 574 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 575         try {
 576
 577                 if (possibles.size() == 4) { //done
 578                         if (combos.count(possibles) == 0) { //no dups
 579                                 combos.insert(possibles);
 580                         }
 581                 }else { //we still have work to do
 582                         set<int>::iterator it;
 583                         set<int>::iterator it2;
 584                         for (it = possibles.begin(); it != possibles.end(); it++) {
 585
 586                                 set<int> newPossibles;
 587                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 588                                         if (*it != *it2) {
 589                                                 newPossibles.insert(*it2);
 590                                         }
 591                                 }
 592                                 getCombos(newPossibles, combos);
 593                         }
 594                 }
 595
 596                 return 0;
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "VennCommand", "getCombos");
 600                 exit(1);
 601         }
 602 }
 603
 604 //**********************************************************************************************************************