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
 238                 if (m->control_pressed) { return 0; }
 239
 240                 //read through the correct file and output lines you want to keep
 241                 if (constaxonomyfile != "")     {               readClassifyOtu();      }
 242                 if (corraxesfile != "")         {               readCorrAxes();         }
 243                 if (otucorrfile != "")          {               readOtuAssociation();   }
 244         if (listfile != "")         {           readList();             }
 245         if (sharedfile != "")           {               readShared();           }
 246
 247         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 248
 249         //output files created by command
 250                 m->mothurOutEndLine();
 251                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 252                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 253                 m->mothurOutEndLine();
 254
 255         string current = "";
 256         itTypes = outputTypes.find("list");
 257         if (itTypes != outputTypes.end()) {
 258             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 259         }
 260
 261         itTypes = outputTypes.find("shared");
 262         if (itTypes != outputTypes.end()) {
 263             if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 264         }
 265
 266         return 0;
 267     }
 268         catch(exception& e) {
 269                 m->errorOut(e, "GetOtuLabelsCommand", "execute");
 270                 exit(1);
 271         }
 272 }
 273 //**********************************************************************************************************************
 274 int GetOtuLabelsCommand::readClassifyOtu(){
 275         try {
 276                 string thisOutputDir = outputDir;
 277                 if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
 278         map<string, string> variables;
 279         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
 280         variables["[extension]"] = m->getExtension(constaxonomyfile);
 281                 string outputFileName = getOutputFileName("constaxonomy", variables);
 282
 283                 ofstream out;
 284                 m->openOutputFile(outputFileName, out);
 285
 286                 ifstream in;
 287                 m->openInputFile(constaxonomyfile, in);
 288
 289                 bool wroteSomething = false;
 290                 int selectedCount = 0;
 291
 292         //read headers
 293         string headers = m->getline(in);
 294         out << headers << endl;
 295
 296         while (!in.eof()) {
 297
 298             if (m->control_pressed) { break; }
 299
 300             string otu = ""; string tax = "unknown";
 301             int size = 0;
 302
 303             in >> otu >> size >> tax; m->gobble(in);
 304
 305             if (labels.count(otu) != 0) {
 306                                 wroteSomething = true;
 307                                 selectedCount++;
 308
 309                 out << otu << '\t' << size << '\t' << tax << endl;
 310             }
 311         }
 312         in.close();
 313         out.close();
 314
 315                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 316                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 317
 318                 m->mothurOut("Selected " + toString(selectedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 319
 320                 return 0;
 321
 322         }
 323         catch(exception& e) {
 324                 m->errorOut(e, "GetOtuLabelsCommand", "readClassifyOtu");
 325                 exit(1);
 326         }
 327 }
 328 //**********************************************************************************************************************
 329 int GetOtuLabelsCommand::readOtuAssociation(){
 330         try {
 331                 string thisOutputDir = outputDir;
 332                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 333         map<string, string> variables;
 334         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
 335         variables["[extension]"] = m->getExtension(otucorrfile);
 336                 string outputFileName = getOutputFileName("otucorr", variables);
 337
 338                 ofstream out;
 339                 m->openOutputFile(outputFileName, out);
 340
 341                 ifstream in;
 342                 m->openInputFile(otucorrfile, in);
 343
 344                 bool wroteSomething = false;
 345                 int selectedCount = 0;
 346
 347         //read headers
 348         string headers = m->getline(in);
 349         out << headers << endl;
 350
 351         while (!in.eof()) {
 352
 353             if (m->control_pressed) { break; }
 354
 355             string otu1 = "";
 356             string otu2 = "";
 357             in >> otu1 >> otu2;
 358             string line = m->getline(in); m->gobble(in);
 359
 360             if ((labels.count(otu1) != 0) && (labels.count(otu2) != 0)){
 361                                 wroteSomething = true;
 362                                 selectedCount++;
 363
 364                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 365             }
 366         }
 367         in.close();
 368         out.close();
 369
 370                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 371                 outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
 372
 373                 m->mothurOut("Selected " + toString(selectedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 374
 375                 return 0;
 376
 377         }
 378         catch(exception& e) {
 379                 m->errorOut(e, "GetOtuLabelsCommand", "readOtuAssociation");
 380                 exit(1);
 381         }
 382 }
 383 //**********************************************************************************************************************
 384 int GetOtuLabelsCommand::readCorrAxes(){
 385         try {
 386                 string thisOutputDir = outputDir;
 387                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 388         map<string, string> variables;
 389         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
 390         variables["[extension]"] = m->getExtension(corraxesfile);
 391                 string outputFileName = getOutputFileName("corraxes", variables);
 392
 393                 ofstream out;
 394                 m->openOutputFile(outputFileName, out);
 395
 396
 397                 ifstream in;
 398                 m->openInputFile(corraxesfile, in);
 399
 400                 bool wroteSomething = false;
 401                 int selectedCount = 0;
 402
 403         //read headers
 404         string headers = m->getline(in);
 405         out << headers << endl;
 406
 407         while (!in.eof()) {
 408
 409             if (m->control_pressed) { break; }
 410
 411             string otu = "";
 412             in >> otu;
 413             string line = m->getline(in); m->gobble(in);
 414
 415             if (labels.count(otu) != 0) {
 416                                 wroteSomething = true;
 417                                 selectedCount++;
 418
 419                 out << otu << '\t' << line << endl;
 420             }
 421         }
 422         in.close();
 423         out.close();
 424
 425                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine();  }
 426                 outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
 427
 428                 m->mothurOut("Selected " + toString(selectedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 429
 430                 return 0;
 431
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "GetOtuLabelsCommand", "readCorrAxes");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439 int GetOtuLabelsCommand::readShared(){
 440         try {
 441
 442         getShared();
 443
 444         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 445
 446         vector<string> newLabels;
 447
 448         //create new "filtered" lookup
 449         vector<SharedRAbundVector*> newLookup;
 450         for (int i = 0; i < lookup.size(); i++) {
 451             SharedRAbundVector* temp = new SharedRAbundVector();
 452                         temp->setLabel(lookup[i]->getLabel());
 453                         temp->setGroup(lookup[i]->getGroup());
 454                         newLookup.push_back(temp);
 455         }
 456
 457         bool wroteSomething = false;
 458         int numSelected = 0;
 459         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 460
 461             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; }
 462
 463             //is this otu on the list
 464             if (labels.count(m->currentBinLabels[i]) != 0) {
 465                 numSelected++; wroteSomething = true;
 466                 newLabels.push_back(m->currentBinLabels[i]);
 467                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
 468                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
 469                 }
 470             }
 471         }
 472
 473         string thisOutputDir = outputDir;
 474                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 475         map<string, string> variables;
 476                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 477         variables["[extension]"] = m->getExtension(sharedfile);
 478         variables["[distance]"] = lookup[0]->getLabel();
 479                 string outputFileName = getOutputFileName("shared", variables);
 480         ofstream out;
 481                 m->openOutputFile(outputFileName, out);
 482                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 483
 484                 for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
 485
 486         m->currentBinLabels = newLabels;
 487
 488                 newLookup[0]->printHeaders(out);
 489
 490                 for (int i = 0; i < newLookup.size(); i++) {
 491                         out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
 492                         newLookup[i]->print(out);
 493                 }
 494                 out.close();
 495
 496         for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
 497
 498         if (wroteSomething == false) { m->mothurOut("Your file does not contain any OTUs from the .accnos file."); m->mothurOutEndLine();  }
 499
 500                 m->mothurOut("Selected " + toString(numSelected) + " OTUs from your shared file."); m->mothurOutEndLine();
 501
 502         return 0;
 503     }
 504         catch(exception& e) {
 505                 m->errorOut(e, "GetOtuLabelsCommand", "readShared");
 506                 exit(1);
 507         }
 508 }
 509 //**********************************************************************************************************************
 510 int GetOtuLabelsCommand::readList(){
 511         try {
 512         getListVector();
 513
 514         if (m->control_pressed) { delete list; return 0;}
 515
 516         ListVector newList;
 517         newList.setLabel(list->getLabel());
 518         int selectedCount = 0;
 519         bool wroteSomething = false;
 520         string snumBins = toString(list->getNumBins());
 521
 522         for (int i = 0; i < list->getNumBins(); i++) {
 523
 524             if (m->control_pressed) { delete list; return 0;}
 525
 526             //create a label for this otu
 527             string otuLabel = "Otu";
 528             string sbinNumber = toString(i+1);
 529             if (sbinNumber.length() < snumBins.length()) {
 530                 int diff = snumBins.length() - sbinNumber.length();
 531                 for (int h = 0; h < diff; h++) { otuLabel += "0"; }
 532             }
 533             otuLabel += sbinNumber;
 534
 535             if (labels.count(otuLabel) != 0) {
 536                                 selectedCount++;
 537                 newList.push_back(list->get(i));
 538             }
 539         }
 540
 541         string thisOutputDir = outputDir;
 542                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 543         map<string, string> variables;
 544                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 545         variables["[extension]"] = m->getExtension(listfile);
 546         variables["[distance]"] = list->getLabel();
 547                 string outputFileName = getOutputFileName("list", variables);
 548                 ofstream out;
 549                 m->openOutputFile(outputFileName, out);
 550
 551                 delete list;
 552         //print new listvector
 553         if (newList.getNumBins() != 0) {
 554             wroteSomething = true;
 555             newList.print(out);
 556         }
 557                 out.close();
 558
 559                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any OTUs from the .accnos file."); m->mothurOutEndLine();  }
 560                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 561
 562                 m->mothurOut("Selected " + toString(selectedCount) + " OTUs from your list file."); m->mothurOutEndLine();
 563
 564         return 0;
 565     }
 566     catch(exception& e) {
 567             m->errorOut(e, "GetOtuLabelsCommand", "readList");
 568             exit(1);
 569         }
 570     }
 571 //**********************************************************************************************************************
 572 int GetOtuLabelsCommand::getListVector(){
 573         try {
 574                 InputData input(listfile, "list");
 575                 list = input.getListVector();
 576                 string lastLabel = list->getLabel();
 577
 578                 if (label == "") { label = lastLabel;  return 0; }
 579
 580                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 581                 set<string> labels; labels.insert(label);
 582                 set<string> processedLabels;
 583                 set<string> userLabels = labels;
 584
 585                 //as long as you are not at the end of the file or done wih the lines you want
 586                 while((list != NULL) && (userLabels.size() != 0)) {
 587                         if (m->control_pressed) {  return 0;  }
 588
 589                         if(labels.count(list->getLabel()) == 1){
 590                                 processedLabels.insert(list->getLabel());
 591                                 userLabels.erase(list->getLabel());
 592                                 break;
 593                         }
 594
 595                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 596                                 string saveLabel = list->getLabel();
 597
 598                                 delete list;
 599                                 list = input.getListVector(lastLabel);
 600
 601                                 processedLabels.insert(list->getLabel());
 602                                 userLabels.erase(list->getLabel());
 603
 604                                 //restore real lastlabel to save below
 605                                 list->setLabel(saveLabel);
 606                                 break;
 607                         }
 608
 609                         lastLabel = list->getLabel();
 610
 611                         //get next line to process
 612                         //prevent memory leak
 613                         delete list;
 614                         list = input.getListVector();
 615                 }
 616
 617
 618                 if (m->control_pressed) {  return 0;  }
 619
 620                 //output error messages about any remaining user labels
 621                 set<string>::iterator it;
 622                 bool needToRun = false;
 623                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 624                         m->mothurOut("Your file does not include the label " + *it);
 625                         if (processedLabels.count(lastLabel) != 1) {
 626                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 627                                 needToRun = true;
 628                         }else {
 629                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 630                         }
 631                 }
 632
 633                 //run last label if you need to
 634                 if (needToRun == true)  {
 635                         delete list;
 636                         list = input.getListVector(lastLabel);
 637                 }
 638
 639                 return 0;
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "GetOtuLabelsCommand", "getListVector");
 643                 exit(1);
 644         }
 645 }
 646 //**********************************************************************************************************************
 647 int GetOtuLabelsCommand::getShared(){
 648         try {
 649                 InputData input(sharedfile, "sharedfile");
 650                 lookup = input.getSharedRAbundVectors();
 651                 string lastLabel = lookup[0]->getLabel();
 652
 653                 if (label == "") { label = lastLabel;  return 0; }
 654
 655                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 656                 set<string> labels; labels.insert(label);
 657                 set<string> processedLabels;
 658                 set<string> userLabels = labels;
 659
 660                 //as long as you are not at the end of the file or done wih the lines you want
 661                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 662                         if (m->control_pressed) {   return 0;  }
 663
 664                         if(labels.count(lookup[0]->getLabel()) == 1){
 665                                 processedLabels.insert(lookup[0]->getLabel());
 666                                 userLabels.erase(lookup[0]->getLabel());
 667                                 break;
 668                         }
 669
 670                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 671                                 string saveLabel = lookup[0]->getLabel();
 672
 673                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 674                                 lookup = input.getSharedRAbundVectors(lastLabel);
 675
 676                                 processedLabels.insert(lookup[0]->getLabel());
 677                                 userLabels.erase(lookup[0]->getLabel());
 678
 679                                 //restore real lastlabel to save below
 680                                 lookup[0]->setLabel(saveLabel);
 681                                 break;
 682                         }
 683
 684                         lastLabel = lookup[0]->getLabel();
 685
 686                         //get next line to process
 687                         //prevent memory leak
 688                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 689                         lookup = input.getSharedRAbundVectors();
 690                 }
 691
 692
 693                 if (m->control_pressed) {  return 0;  }
 694
 695                 //output error messages about any remaining user labels
 696                 set<string>::iterator it;
 697                 bool needToRun = false;
 698                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 699                         m->mothurOut("Your file does not include the label " + *it);
 700                         if (processedLabels.count(lastLabel) != 1) {
 701                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 702                                 needToRun = true;
 703                         }else {
 704                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 705                         }
 706                 }
 707
 708                 //run last label if you need to
 709                 if (needToRun == true)  {
 710                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 711                         lookup = input.getSharedRAbundVectors(lastLabel);
 712                 }
 713
 714                 return 0;
 715         }
 716         catch(exception& e) {
 717                 m->errorOut(e, "GetOtuLabelsCommand", "getShared");
 718                 exit(1);
 719         }
 720 }
 721 //**********************************************************************************************************************