removeotulabelscommand.cpp

   1 //
   2 //  removeotulabels.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 "removeotulabelscommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> RemoveOtuLabelsCommand::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); parameters.push_back(pconstaxonomy);
  16                 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
  17         CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
  18         CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
  19         CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
  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, "RemoveOtuLabelsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string RemoveOtuLabelsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes. It can also be used to select a set of otus from a shared or list file.\n";
  38                 helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, shared, list, label and accnos.\n";
  39                 helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
  40         helpString += "The otucorr parameter is input the results of the otu.association command.\n";
  41         helpString += "The corraxes parameter is 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 remove.otulabels commmand should be in the following format: \n";
  44                 helpString += "remove.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "RemoveOtuLabelsCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string RemoveOtuLabelsCommand::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, "RemoveOtuLabelsCommand", "getOutputPattern");
  68         exit(1);
  69     }
  70 }
  71 //**********************************************************************************************************************
  72 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76         vector<string> tempOutNames;
  77                 outputTypes["constaxonomy"] = tempOutNames;
  78         outputTypes["otucorr"] = tempOutNames;
  79         outputTypes["corraxes"] = tempOutNames;
  80         outputTypes["shared"] = tempOutNames;
  81         outputTypes["list"] = tempOutNames;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(string option)  {
  90         try {
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  96
  97                 else {
  98                         //valid paramters for this command
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string,string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter;
 105                         map<string,string>::iterator it;
 106                         //check to make sure all parameters are valid for command
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111
 112                         //if the user changes the input directory command factory will send this info to us in the output parameter
 113                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 114                         if (inputDir == "not found"){   inputDir = "";          }
 115                         else {
 116
 117                 //edit file types below to include only the types you added as parameters
 118
 119                                 string path;
 120                 it = parameters.find("constaxonomy");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["constaxonomy"] = inputDir + it->second;             }
 126                                 }
 127
 128                 it = parameters.find("accnos");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 134                                 }
 135
 136                 it = parameters.find("corraxes");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["corraxes"] = inputDir + it->second;         }
 142                                 }
 143
 144                 it = parameters.find("otucorr");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["otucorr"] = inputDir + it->second;          }
 150                                 }
 151
 152                 it = parameters.find("list");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 158                                 }
 159
 160                 it = parameters.find("shared");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 166                                 }
 167             }
 168
 169             vector<string> tempOutNames;
 170             outputTypes["constaxonomy"] = tempOutNames;
 171             outputTypes["otucorr"] = tempOutNames;
 172             outputTypes["corraxes"] = tempOutNames;
 173             outputTypes["shared"] = tempOutNames;
 174             outputTypes["list"] = tempOutNames;
 175
 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, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
 225                 exit(1);
 226         }
 227 }
 228 //**********************************************************************************************************************
 229
 230 int RemoveOtuLabelsCommand::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 RemoveOtuLabelsCommand::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                 ofstream out;
 283                 m->openOutputFile(outputFileName, out);
 284
 285                 ifstream in;
 286                 m->openInputFile(constaxonomyfile, in);
 287
 288                 bool wroteSomething = false;
 289                 int removedCount = 0;
 290
 291         //read headers
 292         string headers = m->getline(in);
 293         out << headers << endl;
 294
 295         while (!in.eof()) {
 296
 297             if (m->control_pressed) { break; }
 298
 299             string otu = ""; string tax = "unknown";
 300             int size = 0;
 301
 302             in >> otu >> size >> tax; m->gobble(in);
 303
 304             if (labels.count(otu) == 0) {
 305                                 wroteSomething = true;
 306                 out << otu << '\t' << size << '\t' << tax << endl;
 307             }else {  removedCount++;  }
 308         }
 309         in.close();
 310         out.close();
 311
 312                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 313                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 314
 315                 m->mothurOut("Removed " + toString(removedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 316
 317                 return 0;
 318
 319         }
 320         catch(exception& e) {
 321                 m->errorOut(e, "RemoveOtuLabelsCommand", "readClassifyOtu");
 322                 exit(1);
 323         }
 324 }
 325 //**********************************************************************************************************************
 326 int RemoveOtuLabelsCommand::readOtuAssociation(){
 327         try {
 328                 string thisOutputDir = outputDir;
 329                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 330         map<string, string> variables;
 331         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
 332         variables["[extension]"] = m->getExtension(otucorrfile);
 333                 string outputFileName = getOutputFileName("otucorr", variables);
 334                 ofstream out;
 335                 m->openOutputFile(outputFileName, out);
 336
 337                 ifstream in;
 338                 m->openInputFile(otucorrfile, in);
 339
 340                 bool wroteSomething = false;
 341                 int removedCount = 0;
 342
 343         //read headers
 344         string headers = m->getline(in);
 345         out << headers << endl;
 346
 347         while (!in.eof()) {
 348
 349             if (m->control_pressed) { break; }
 350
 351             string otu1 = "";
 352             string otu2 = "";
 353             in >> otu1 >> otu2;
 354             string line = m->getline(in); m->gobble(in);
 355
 356             if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
 357                                 wroteSomething = true;
 358
 359                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 360             }else { removedCount++; }
 361         }
 362         in.close();
 363         out.close();
 364
 365                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 366                 outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
 367
 368                 m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 369
 370                 return 0;
 371
 372         }
 373         catch(exception& e) {
 374                 m->errorOut(e, "RemoveOtuLabelsCommand", "readOtuAssociation");
 375                 exit(1);
 376         }
 377 }
 378 //**********************************************************************************************************************
 379 int RemoveOtuLabelsCommand::readCorrAxes(){
 380         try {
 381                 string thisOutputDir = outputDir;
 382                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 383         map<string, string> variables;
 384         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
 385         variables["[extension]"] = m->getExtension(corraxesfile);
 386                 string outputFileName = getOutputFileName("corraxes", variables);
 387                 ofstream out;
 388                 m->openOutputFile(outputFileName, out);
 389
 390
 391                 ifstream in;
 392                 m->openInputFile(corraxesfile, in);
 393
 394                 bool wroteSomething = false;
 395                 int removedCount = 0;
 396
 397         //read headers
 398         string headers = m->getline(in);
 399         out << headers << endl;
 400
 401         while (!in.eof()) {
 402
 403             if (m->control_pressed) { break; }
 404
 405             string otu = "";
 406             in >> otu;
 407             string line = m->getline(in); m->gobble(in);
 408
 409             if (labels.count(otu) == 0) {
 410                                 wroteSomething = true;
 411
 412                 out << otu << '\t' << line << endl;
 413             }else { removedCount++; }
 414         }
 415         in.close();
 416         out.close();
 417
 418                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 419                 outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
 420
 421                 m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 422
 423                 return 0;
 424
 425         }
 426         catch(exception& e) {
 427                 m->errorOut(e, "RemoveOtuLabelsCommand", "readCorrAxes");
 428                 exit(1);
 429         }
 430 }
 431 //**********************************************************************************************************************
 432 int RemoveOtuLabelsCommand::readShared(){
 433         try {
 434
 435         getShared();
 436
 437         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 438
 439         vector<string> newLabels;
 440
 441         //create new "filtered" lookup
 442         vector<SharedRAbundVector*> newLookup;
 443         for (int i = 0; i < lookup.size(); i++) {
 444             SharedRAbundVector* temp = new SharedRAbundVector();
 445                         temp->setLabel(lookup[i]->getLabel());
 446                         temp->setGroup(lookup[i]->getGroup());
 447                         newLookup.push_back(temp);
 448         }
 449
 450         bool wroteSomething = false;
 451         int numRemoved = 0;
 452         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 453
 454             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; }
 455
 456             //is this otu on the list
 457             if (labels.count(m->currentBinLabels[i]) == 0) {
 458                 wroteSomething = true;
 459                 newLabels.push_back(m->currentBinLabels[i]);
 460                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
 461                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
 462                 }
 463             }else { numRemoved++; }
 464         }
 465
 466         string thisOutputDir = outputDir;
 467                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 468         map<string, string> variables;
 469                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 470         variables["[extension]"] = m->getExtension(sharedfile);
 471         variables["[distance]"] = lookup[0]->getLabel();
 472                 string outputFileName = getOutputFileName("shared", variables);
 473         ofstream out;
 474                 m->openOutputFile(outputFileName, out);
 475                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 476
 477                 for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
 478
 479         m->currentBinLabels = newLabels;
 480
 481                 newLookup[0]->printHeaders(out);
 482
 483                 for (int i = 0; i < newLookup.size(); i++) {
 484                         out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
 485                         newLookup[i]->print(out);
 486                 }
 487                 out.close();
 488
 489         for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
 490
 491         if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 492
 493                 m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine();
 494
 495         return 0;
 496     }
 497         catch(exception& e) {
 498                 m->errorOut(e, "RemoveOtuLabelsCommand", "readShared");
 499                 exit(1);
 500         }
 501 }
 502 //**********************************************************************************************************************
 503 int RemoveOtuLabelsCommand::readList(){
 504         try {
 505         getListVector();
 506
 507         if (m->control_pressed) { delete list; return 0;}
 508
 509         ListVector newList;
 510         newList.setLabel(list->getLabel());
 511         int removedCount = 0;
 512         bool wroteSomething = false;
 513         string snumBins = toString(list->getNumBins());
 514
 515         for (int i = 0; i < list->getNumBins(); i++) {
 516
 517             if (m->control_pressed) { delete list; return 0;}
 518
 519             //create a label for this otu
 520             string otuLabel = "Otu";
 521             string sbinNumber = toString(i+1);
 522             if (sbinNumber.length() < snumBins.length()) {
 523                 int diff = snumBins.length() - sbinNumber.length();
 524                 for (int h = 0; h < diff; h++) { otuLabel += "0"; }
 525             }
 526             otuLabel += sbinNumber;
 527
 528             if (labels.count(otuLabel) == 0) {
 529                 newList.push_back(list->get(i));
 530             }else { removedCount++; }
 531         }
 532
 533         string thisOutputDir = outputDir;
 534                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 535         map<string, string> variables;
 536                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 537         variables["[extension]"] = m->getExtension(listfile);
 538         variables["[distance]"] = list->getLabel();
 539                 string outputFileName = getOutputFileName("list", variables);
 540                 ofstream out;
 541                 m->openOutputFile(outputFileName, out);
 542
 543                 delete list;
 544         //print new listvector
 545         if (newList.getNumBins() != 0) {
 546             wroteSomething = true;
 547             newList.print(out);
 548         }
 549                 out.close();
 550
 551                 if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine();  }
 552                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 553
 554                 m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine();
 555
 556         return 0;
 557     }
 558     catch(exception& e) {
 559         m->errorOut(e, "RemoveOtuLabelsCommand", "readList");
 560         exit(1);
 561     }
 562 }
 563 //**********************************************************************************************************************
 564 int RemoveOtuLabelsCommand::getListVector(){
 565         try {
 566                 InputData input(listfile, "list");
 567                 list = input.getListVector();
 568                 string lastLabel = list->getLabel();
 569
 570                 if (label == "") { label = lastLabel;  return 0; }
 571
 572                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 573                 set<string> labels; labels.insert(label);
 574                 set<string> processedLabels;
 575                 set<string> userLabels = labels;
 576
 577                 //as long as you are not at the end of the file or done wih the lines you want
 578                 while((list != NULL) && (userLabels.size() != 0)) {
 579                         if (m->control_pressed) {  return 0;  }
 580
 581                         if(labels.count(list->getLabel()) == 1){
 582                                 processedLabels.insert(list->getLabel());
 583                                 userLabels.erase(list->getLabel());
 584                                 break;
 585                         }
 586
 587                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 588                                 string saveLabel = list->getLabel();
 589
 590                                 delete list;
 591                                 list = input.getListVector(lastLabel);
 592
 593                                 processedLabels.insert(list->getLabel());
 594                                 userLabels.erase(list->getLabel());
 595
 596                                 //restore real lastlabel to save below
 597                                 list->setLabel(saveLabel);
 598                                 break;
 599                         }
 600
 601                         lastLabel = list->getLabel();
 602
 603                         //get next line to process
 604                         //prevent memory leak
 605                         delete list;
 606                         list = input.getListVector();
 607                 }
 608
 609
 610                 if (m->control_pressed) {  return 0;  }
 611
 612                 //output error messages about any remaining user labels
 613                 set<string>::iterator it;
 614                 bool needToRun = false;
 615                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 616                         m->mothurOut("Your file does not include the label " + *it);
 617                         if (processedLabels.count(lastLabel) != 1) {
 618                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 619                                 needToRun = true;
 620                         }else {
 621                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 622                         }
 623                 }
 624
 625                 //run last label if you need to
 626                 if (needToRun == true)  {
 627                         delete list;
 628                         list = input.getListVector(lastLabel);
 629                 }
 630
 631                 return 0;
 632         }
 633         catch(exception& e) {
 634                 m->errorOut(e, "RemoveOtuLabelsCommand", "getListVector");
 635                 exit(1);
 636         }
 637 }
 638 //**********************************************************************************************************************
 639 int RemoveOtuLabelsCommand::getShared(){
 640         try {
 641                 InputData input(sharedfile, "sharedfile");
 642                 lookup = input.getSharedRAbundVectors();
 643                 string lastLabel = lookup[0]->getLabel();
 644
 645                 if (label == "") { label = lastLabel;  return 0; }
 646
 647                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 648                 set<string> labels; labels.insert(label);
 649                 set<string> processedLabels;
 650                 set<string> userLabels = labels;
 651
 652                 //as long as you are not at the end of the file or done wih the lines you want
 653                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 654                         if (m->control_pressed) {   return 0;  }
 655
 656                         if(labels.count(lookup[0]->getLabel()) == 1){
 657                                 processedLabels.insert(lookup[0]->getLabel());
 658                                 userLabels.erase(lookup[0]->getLabel());
 659                                 break;
 660                         }
 661
 662                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 663                                 string saveLabel = lookup[0]->getLabel();
 664
 665                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 666                                 lookup = input.getSharedRAbundVectors(lastLabel);
 667
 668                                 processedLabels.insert(lookup[0]->getLabel());
 669                                 userLabels.erase(lookup[0]->getLabel());
 670
 671                                 //restore real lastlabel to save below
 672                                 lookup[0]->setLabel(saveLabel);
 673                                 break;
 674                         }
 675
 676                         lastLabel = lookup[0]->getLabel();
 677
 678                         //get next line to process
 679                         //prevent memory leak
 680                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 681                         lookup = input.getSharedRAbundVectors();
 682                 }
 683
 684
 685                 if (m->control_pressed) {  return 0;  }
 686
 687                 //output error messages about any remaining user labels
 688                 set<string>::iterator it;
 689                 bool needToRun = false;
 690                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 691                         m->mothurOut("Your file does not include the label " + *it);
 692                         if (processedLabels.count(lastLabel) != 1) {
 693                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 694                                 needToRun = true;
 695                         }else {
 696                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 697                         }
 698                 }
 699
 700                 //run last label if you need to
 701                 if (needToRun == true)  {
 702                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 703                         lookup = input.getSharedRAbundVectors(lastLabel);
 704                 }
 705
 706                 return 0;
 707         }
 708         catch(exception& e) {
 709                 m->errorOut(e, "RemoveOtuLabelsCommand", "getShared");
 710                 exit(1);
 711         }
 712 }
 713 //**********************************************************************************************************************
 714
 715
 716