getotulabelscommand.cpp

   1 //
   2 //  getotulabelscommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 5/21/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "getotulabelscommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> GetOtuLabelsCommand::setParameters(){
  13         try {
  14         CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true, true); parameters.push_back(paccnos);
  15         CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy);
  16         CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
  17         CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
  18                 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false, true); parameters.push_back(potucorr);
  19         CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false, true); parameters.push_back(pcorraxes);
  20         CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  21         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "GetOtuLabelsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string GetOtuLabelsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The get.otulabels command can be used to select specific otus with the output from classify.otu, otu.association, or corr.axes commands.  It can also be used to select a set of otus from a shared or list file.\n";
  38                 helpString += "The get.otulabels parameters are: constaxonomy, otucorr, corraxes, shared, list, label and accnos.\n";
  39                 helpString += "The constaxonomy parameter is used to input the results of the classify.otu command.\n";
  40         helpString += "The otucorr parameter is used to input the results of the otu.association command.\n";
  41         helpString += "The corraxes parameter is used to input the results of the corr.axes command.\n";
  42         helpString += "The label parameter is used to analyze specific labels in your input. \n";
  43                 helpString += "The get.otulabels commmand should be in the following format: \n";
  44                 helpString += "get.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "GetOtuLabelsCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string GetOtuLabelsCommand::getOutputPattern(string type) {
  54     try {
  55         string pattern = "";
  56
  57         if (type == "constaxonomy")         {   pattern = "[filename],pick,[extension]";    }
  58         else if (type == "otucorr")         {   pattern = "[filename],pick,[extension]";    }
  59         else if (type == "corraxes")        {   pattern = "[filename],pick,[extension]";    }
  60         else if (type == "list")            {   pattern = "[filename],[distance],pick,[extension]";    }
  61         else if (type == "shared")          {   pattern = "[filename],[distance],pick,[extension]";    }
  62         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  63
  64         return pattern;
  65     }
  66     catch(exception& e) {
  67         m->errorOut(e, "GetOtuLabelsCommand", "getOutputPattern");
  68         exit(1);
  69     }
  70 }
  71
  72 //**********************************************************************************************************************
  73 GetOtuLabelsCommand::GetOtuLabelsCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77         vector<string> tempOutNames;
  78                 outputTypes["constaxonomy"] = tempOutNames;
  79         outputTypes["otucorr"] = tempOutNames;
  80         outputTypes["corraxes"] = tempOutNames;
  81         outputTypes["shared"] = tempOutNames;
  82         outputTypes["list"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
  86                 exit(1);
  87         }
  88 }
  89 //**********************************************************************************************************************
  90 GetOtuLabelsCommand::GetOtuLabelsCommand(string option)  {
  91         try {
  92                 abort = false; calledHelp = false;
  93
  94                 //allow user to run help
  95                 if(option == "help") { help(); abort = true; calledHelp = true; }
  96                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  97
  98                 else {
  99                         //valid paramters for this command
 100                         vector<string> myArray = setParameters();
 101
 102                         OptionParser parser(option);
 103                         map<string,string> parameters = parser.getParameters();
 104
 105                         ValidParameters validParameter;
 106                         map<string,string>::iterator it;
 107                         //check to make sure all parameters are valid for command
 108                         for (it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112
 113                         //if the user changes the input directory command factory will send this info to us in the output parameter
 114                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 115                         if (inputDir == "not found"){   inputDir = "";          }
 116                         else {
 117
 118                 //edit file types below to include only the types you added as parameters
 119
 120                                 string path;
 121                 it = parameters.find("constaxonomy");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["constaxonomy"] = inputDir + it->second;             }
 127                                 }
 128
 129                 it = parameters.find("accnos");
 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["accnos"] = inputDir + it->second;           }
 135                                 }
 136
 137                 it = parameters.find("corraxes");
 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["corraxes"] = inputDir + it->second;         }
 143                                 }
 144
 145                 it = parameters.find("otucorr");
 146                                 //user has given a template file
 147                                 if(it != parameters.end()){
 148                                         path = m->hasPath(it->second);
 149                                         //if the user has not given a path then, add inputdir. else leave path alone.
 150                                         if (path == "") {       parameters["otucorr"] = inputDir + it->second;          }
 151                                 }
 152
 153                 it = parameters.find("list");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 159                                 }
 160
 161                 it = parameters.find("shared");
 162                                 //user has given a template file
 163                                 if(it != parameters.end()){
 164                                         path = m->hasPath(it->second);
 165                                         //if the user has not given a path then, add inputdir. else leave path alone.
 166                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 167                                 }
 168             }
 169
 170             vector<string> tempOutNames;
 171             outputTypes["constaxonomy"] = tempOutNames;
 172             outputTypes["otucorr"] = tempOutNames;
 173             outputTypes["corraxes"] = tempOutNames;
 174             outputTypes["shared"] = tempOutNames;
 175             outputTypes["list"] = tempOutNames;
 176
 177                         //check for parameters
 178             accnosfile = validParameter.validFile(parameters, "accnos", true);
 179                         if (accnosfile == "not open") { abort = true; }
 180                         else if (accnosfile == "not found") {
 181                                 accnosfile = m->getAccnosFile();
 182                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 183                                 else {
 184                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 185                                         abort = true;
 186                                 }
 187                         }else { m->setAccnosFile(accnosfile); }
 188
 189                         constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
 190                         if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
 191                         else if (constaxonomyfile == "not found") {  constaxonomyfile = "";  }
 192
 193             corraxesfile = validParameter.validFile(parameters, "corraxes", true);
 194                         if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
 195                         else if (corraxesfile == "not found") {  corraxesfile = "";  }
 196
 197             otucorrfile = validParameter.validFile(parameters, "otucorr", true);
 198                         if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
 199                         else if (otucorrfile == "not found") {  otucorrfile = "";  }
 200
 201             listfile = validParameter.validFile(parameters, "list", true);
 202                         if (listfile == "not open") { listfile = ""; abort = true; }
 203                         else if (listfile == "not found") {  listfile = "";  }
 204             else { m->setListFile(listfile); }
 205
 206             sharedfile = validParameter.validFile(parameters, "shared", true);
 207                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 208                         else if (sharedfile == "not found") {  sharedfile = "";  }
 209             else { m->setSharedFile(sharedfile); }
 210
 211             //if the user changes the output directory command factory will send this info to us in the output parameter
 212                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){   outputDir = "";        }
 213
 214             if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "") && (sharedfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: constaxonomy, corraxes, otucorr, shared or list."); m->mothurOutEndLine(); abort = true; }
 215
 216             if ((sharedfile != "") || (listfile != "")) {
 217                 label = validParameter.validFile(parameters, "label", false);
 218                 if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
 219             }
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
 225                 exit(1);
 226         }
 227 }
 228 //**********************************************************************************************************************
 229
 230 int GetOtuLabelsCommand::execute(){
 231         try {
 232
 233                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 234
 235         //get labels you want to keep
 236                 labels = m->readAccnos(accnosfile);
 237         //simplfy labels
 238         set<string> newLabels;
 239         for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {  newLabels.insert(m->getSimpleLabel(*it)); }
 240         labels = newLabels;
 241
 242                 if (m->control_pressed) { return 0; }
 243
 244                 //read through the correct file and output lines you want to keep
 245                 if (constaxonomyfile != "")     {               readClassifyOtu();      }
 246                 if (corraxesfile != "")         {               readCorrAxes();         }
 247                 if (otucorrfile != "")          {               readOtuAssociation();   }
 248         if (listfile != "")         {           readList();             }
 249         if (sharedfile != "")           {               readShared();           }
 250
 251         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 252
 253         //output files created by command
 254                 m->mothurOutEndLine();
 255                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 256                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 257                 m->mothurOutEndLine();
 258
 259         string current = "";
 260         itTypes = outputTypes.find("list");
 261         if (itTypes != outputTypes.end()) {
 262             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 263         }
 264
 265         itTypes = outputTypes.find("shared");
 266         if (itTypes != outputTypes.end()) {
 267             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 268         }
 269
 270         return 0;
 271     }
 272         catch(exception& e) {
 273                 m->errorOut(e, "GetOtuLabelsCommand", "execute");
 274                 exit(1);
 275         }
 276 }
 277 //**********************************************************************************************************************
 278 int GetOtuLabelsCommand::readClassifyOtu(){
 279         try {
 280                 string thisOutputDir = outputDir;
 281                 if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
 282         map<string, string> variables;
 283         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
 284         variables["[extension]"] = m->getExtension(constaxonomyfile);
 285                 string outputFileName = getOutputFileName("constaxonomy", variables);
 286
 287                 ofstream out;
 288                 m->openOutputFile(outputFileName, out);
 289
 290                 ifstream in;
 291                 m->openInputFile(constaxonomyfile, in);
 292
 293                 bool wroteSomething = false;
 294                 int selectedCount = 0;
 295
 296         //read headers
 297         string headers = m->getline(in);
 298         out << headers << endl;
 299
 300         while (!in.eof()) {
 301
 302             if (m->control_pressed) { break; }
 303
 304             string otu = ""; string tax = "unknown";
 305             int size = 0;
 306
 307             in >> otu >> size >> tax; m->gobble(in);
 308
 309             if (labels.count(m->getSimpleLabel(otu)) != 0) {
 310                                 wroteSomething = true;
 311                                 selectedCount++;
 312
 313                 out << otu << '\t' << size << '\t' << tax << endl;
 314             }
 315         }
 316         in.close();
 317         out.close();
 318
 319                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 320                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 321
 322                 m->mothurOut("Selected " + toString(selectedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 323
 324                 return 0;
 325
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "GetOtuLabelsCommand", "readClassifyOtu");
 329                 exit(1);
 330         }
 331 }
 332 //**********************************************************************************************************************
 333 int GetOtuLabelsCommand::readOtuAssociation(){
 334         try {
 335                 string thisOutputDir = outputDir;
 336                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 337         map<string, string> variables;
 338         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
 339         variables["[extension]"] = m->getExtension(otucorrfile);
 340                 string outputFileName = getOutputFileName("otucorr", variables);
 341
 342                 ofstream out;
 343                 m->openOutputFile(outputFileName, out);
 344
 345                 ifstream in;
 346                 m->openInputFile(otucorrfile, in);
 347
 348                 bool wroteSomething = false;
 349                 int selectedCount = 0;
 350
 351         //read headers
 352         string headers = m->getline(in);
 353         out << headers << endl;
 354
 355         while (!in.eof()) {
 356
 357             if (m->control_pressed) { break; }
 358
 359             string otu1 = "";
 360             string otu2 = "";
 361             in >> otu1 >> otu2;
 362             string line = m->getline(in); m->gobble(in);
 363
 364             if ((labels.count(m->getSimpleLabel(otu1)) != 0) && (labels.count(m->getSimpleLabel(otu2)) != 0)){
 365                                 wroteSomething = true;
 366                                 selectedCount++;
 367
 368                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 369             }
 370         }
 371         in.close();
 372         out.close();
 373
 374                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 375                 outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
 376
 377                 m->mothurOut("Selected " + toString(selectedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 378
 379                 return 0;
 380
 381         }
 382         catch(exception& e) {
 383                 m->errorOut(e, "GetOtuLabelsCommand", "readOtuAssociation");
 384                 exit(1);
 385         }
 386 }
 387 //**********************************************************************************************************************
 388 int GetOtuLabelsCommand::readCorrAxes(){
 389         try {
 390                 string thisOutputDir = outputDir;
 391                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 392         map<string, string> variables;
 393         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
 394         variables["[extension]"] = m->getExtension(corraxesfile);
 395                 string outputFileName = getOutputFileName("corraxes", variables);
 396
 397                 ofstream out;
 398                 m->openOutputFile(outputFileName, out);
 399
 400
 401                 ifstream in;
 402                 m->openInputFile(corraxesfile, in);
 403
 404                 bool wroteSomething = false;
 405                 int selectedCount = 0;
 406
 407         //read headers
 408         string headers = m->getline(in);
 409         out << headers << endl;
 410
 411         while (!in.eof()) {
 412
 413             if (m->control_pressed) { break; }
 414
 415             string otu = "";
 416             in >> otu;
 417             string line = m->getline(in); m->gobble(in);
 418
 419             if (labels.count(m->getSimpleLabel(otu)) != 0) {
 420                                 wroteSomething = true;
 421                                 selectedCount++;
 422
 423                 out << otu << '\t' << line << endl;
 424             }
 425         }
 426         in.close();
 427         out.close();
 428
 429                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 430                 outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
 431
 432                 m->mothurOut("Selected " + toString(selectedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 433
 434                 return 0;
 435
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "GetOtuLabelsCommand", "readCorrAxes");
 439                 exit(1);
 440         }
 441 }
 442 //**********************************************************************************************************************
 443 int GetOtuLabelsCommand::readShared(){
 444         try {
 445
 446         getShared();
 447
 448         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 449
 450         vector<string> newLabels;
 451
 452         //create new "filtered" lookup
 453         vector<SharedRAbundVector*> newLookup;
 454         for (int i = 0; i < lookup.size(); i++) {
 455             SharedRAbundVector* temp = new SharedRAbundVector();
 456                         temp->setLabel(lookup[i]->getLabel());
 457                         temp->setGroup(lookup[i]->getGroup());
 458                         newLookup.push_back(temp);
 459         }
 460
 461         bool wroteSomething = false;
 462         int numSelected = 0;
 463         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 464
 465             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
 466
 467             //is this otu on the list
 468             if (labels.count(m->getSimpleLabel(m->currentSharedBinLabels[i])) != 0) {
 469                 numSelected++; wroteSomething = true;
 470                 newLabels.push_back(m->currentSharedBinLabels[i]);
 471                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
 472                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
 473                 }
 474             }
 475         }
 476
 477         string thisOutputDir = outputDir;
 478                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 479         map<string, string> variables;
 480                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 481         variables["[extension]"] = m->getExtension(sharedfile);
 482         variables["[distance]"] = lookup[0]->getLabel();
 483                 string outputFileName = getOutputFileName("shared", variables);
 484         ofstream out;
 485                 m->openOutputFile(outputFileName, out);
 486                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 487
 488                 for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
 489
 490         m->currentSharedBinLabels = newLabels;
 491
 492                 newLookup[0]->printHeaders(out);
 493
 494                 for (int i = 0; i < newLookup.size(); i++) {
 495                         out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
 496                         newLookup[i]->print(out);
 497                 }
 498                 out.close();
 499
 500         for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
 501
 502         if (wroteSomething == false) { m->mothurOut("Your file does not contain any OTUs from the .accnos file."); m->mothurOutEndLine();  }
 503
 504                 m->mothurOut("Selected " + toString(numSelected) + " OTUs from your shared file."); m->mothurOutEndLine();
 505
 506         return 0;
 507     }
 508         catch(exception& e) {
 509                 m->errorOut(e, "GetOtuLabelsCommand", "readShared");
 510                 exit(1);
 511         }
 512 }
 513 //**********************************************************************************************************************
 514 int GetOtuLabelsCommand::readList(){
 515         try {
 516         getListVector();
 517
 518         if (m->control_pressed) { delete list; return 0;}
 519
 520         ListVector newList;
 521         newList.setLabel(list->getLabel());
 522         int selectedCount = 0;
 523         bool wroteSomething = false;
 524
 525         vector<string> binLabels = list->getLabels();
 526         vector<string> newLabels;
 527         for (int i = 0; i < list->getNumBins(); i++) {
 528
 529             if (m->control_pressed) { delete list; return 0;}
 530
 531             if (labels.count(m->getSimpleLabel(binLabels[i])) != 0) {
 532                                 selectedCount++;
 533                 newList.push_back(list->get(i));
 534                 newLabels.push_back(binLabels[i]);
 535             }
 536         }
 537
 538         string thisOutputDir = outputDir;
 539                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 540         map<string, string> variables;
 541                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 542         variables["[extension]"] = m->getExtension(listfile);
 543         variables["[distance]"] = list->getLabel();
 544                 string outputFileName = getOutputFileName("list", variables);
 545                 ofstream out;
 546                 m->openOutputFile(outputFileName, out);
 547
 548                 delete list;
 549         //print new listvector
 550         if (newList.getNumBins() != 0) {
 551             wroteSomething = true;
 552             newList.setLabels(newLabels);
 553             newList.printHeaders(out);
 554             newList.print(out);
 555         }
 556                 out.close();
 557
 558                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any OTUs from the .accnos file."); m->mothurOutEndLine();  }
 559                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 560
 561                 m->mothurOut("Selected " + toString(selectedCount) + " OTUs from your list file."); m->mothurOutEndLine();
 562
 563         return 0;
 564     }
 565     catch(exception& e) {
 566             m->errorOut(e, "GetOtuLabelsCommand", "readList");
 567             exit(1);
 568         }
 569     }
 570 //**********************************************************************************************************************
 571 int GetOtuLabelsCommand::getListVector(){
 572         try {
 573                 InputData input(listfile, "list");
 574                 list = input.getListVector();
 575                 string lastLabel = list->getLabel();
 576
 577                 if (label == "") { label = lastLabel;  return 0; }
 578
 579                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 580                 set<string> labels; labels.insert(label);
 581                 set<string> processedLabels;
 582                 set<string> userLabels = labels;
 583
 584                 //as long as you are not at the end of the file or done wih the lines you want
 585                 while((list != NULL) && (userLabels.size() != 0)) {
 586                         if (m->control_pressed) {  return 0;  }
 587
 588                         if(labels.count(list->getLabel()) == 1){
 589                                 processedLabels.insert(list->getLabel());
 590                                 userLabels.erase(list->getLabel());
 591                                 break;
 592                         }
 593
 594                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 595                                 string saveLabel = list->getLabel();
 596
 597                                 delete list;
 598                                 list = input.getListVector(lastLabel);
 599
 600                                 processedLabels.insert(list->getLabel());
 601                                 userLabels.erase(list->getLabel());
 602
 603                                 //restore real lastlabel to save below
 604                                 list->setLabel(saveLabel);
 605                                 break;
 606                         }
 607
 608                         lastLabel = list->getLabel();
 609
 610                         //get next line to process
 611                         //prevent memory leak
 612                         delete list;
 613                         list = input.getListVector();
 614                 }
 615
 616
 617                 if (m->control_pressed) {  return 0;  }
 618
 619                 //output error messages about any remaining user labels
 620                 set<string>::iterator it;
 621                 bool needToRun = false;
 622                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 623                         m->mothurOut("Your file does not include the label " + *it);
 624                         if (processedLabels.count(lastLabel) != 1) {
 625                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 626                                 needToRun = true;
 627                         }else {
 628                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 629                         }
 630                 }
 631
 632                 //run last label if you need to
 633                 if (needToRun == true)  {
 634                         delete list;
 635                         list = input.getListVector(lastLabel);
 636                 }
 637
 638                 return 0;
 639         }
 640         catch(exception& e) {
 641                 m->errorOut(e, "GetOtuLabelsCommand", "getListVector");
 642                 exit(1);
 643         }
 644 }
 645 //**********************************************************************************************************************
 646 int GetOtuLabelsCommand::getShared(){
 647         try {
 648                 InputData input(sharedfile, "sharedfile");
 649                 lookup = input.getSharedRAbundVectors();
 650                 string lastLabel = lookup[0]->getLabel();
 651
 652                 if (label == "") { label = lastLabel;  return 0; }
 653
 654                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 655                 set<string> labels; labels.insert(label);
 656                 set<string> processedLabels;
 657                 set<string> userLabels = labels;
 658
 659                 //as long as you are not at the end of the file or done wih the lines you want
 660                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 661                         if (m->control_pressed) {   return 0;  }
 662
 663                         if(labels.count(lookup[0]->getLabel()) == 1){
 664                                 processedLabels.insert(lookup[0]->getLabel());
 665                                 userLabels.erase(lookup[0]->getLabel());
 666                                 break;
 667                         }
 668
 669                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 670                                 string saveLabel = lookup[0]->getLabel();
 671
 672                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 673                                 lookup = input.getSharedRAbundVectors(lastLabel);
 674
 675                                 processedLabels.insert(lookup[0]->getLabel());
 676                                 userLabels.erase(lookup[0]->getLabel());
 677
 678                                 //restore real lastlabel to save below
 679                                 lookup[0]->setLabel(saveLabel);
 680                                 break;
 681                         }
 682
 683                         lastLabel = lookup[0]->getLabel();
 684
 685                         //get next line to process
 686                         //prevent memory leak
 687                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 688                         lookup = input.getSharedRAbundVectors();
 689                 }
 690
 691
 692                 if (m->control_pressed) {  return 0;  }
 693
 694                 //output error messages about any remaining user labels
 695                 set<string>::iterator it;
 696                 bool needToRun = false;
 697                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 698                         m->mothurOut("Your file does not include the label " + *it);
 699                         if (processedLabels.count(lastLabel) != 1) {
 700                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 701                                 needToRun = true;
 702                         }else {
 703                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 704                         }
 705                 }
 706
 707                 //run last label if you need to
 708                 if (needToRun == true)  {
 709                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 710                         lookup = input.getSharedRAbundVectors(lastLabel);
 711                 }
 712
 713                 return 0;
 714         }
 715         catch(exception& e) {
 716                 m->errorOut(e, "GetOtuLabelsCommand", "getShared");
 717                 exit(1);
 718         }
 719 }
 720 //**********************************************************************************************************************