rarefactcommand.cpp

   1 /*
   2  *  rarefactcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "simpsoneven.h"
  18 #include "heip.h"
  19 #include "smithwilson.h"
  20 #include "invsimpson.h"
  21 #include "npshannon.h"
  22 #include "shannoneven.h"
  23 #include "shannon.h"
  24 #include "jackknife.h"
  25 #include "coverage.h"
  26
  27
  28 //**********************************************************************************************************************
  29 vector<string> RareFactCommand::setParameters(){
  30         try {
  31                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  32                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  33                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  34                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  35                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  36                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
  37                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  38                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "",true,false); parameters.push_back(pcalc);
  39                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  40                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  41                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  42                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  43
  44                 vector<string> myArray;
  45                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "RareFactCommand", "setParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 string RareFactCommand::getHelpString(){
  55         try {
  56                 ValidCalculators validCalculator;
  57                 string helpString = "";
  58                 helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
  59                 helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
  60                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  61                 helpString += "The rarefaction.single command should be in the following format: \n";
  62                 helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
  63                 helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
  64                 helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
  65                 validCalculator.printCalc("rarefaction");
  66                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  67                 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
  68                 return helpString;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "RareFactCommand", "getHelpString");
  72                 exit(1);
  73         }
  74 }
  75
  76 //**********************************************************************************************************************
  77 RareFactCommand::RareFactCommand(){
  78         try {
  79                 abort = true; calledHelp = true;
  80                 setParameters();
  81                 vector<string> tempOutNames;
  82                 outputTypes["rarefaction"] = tempOutNames;
  83                 outputTypes["r_chao"] = tempOutNames;
  84                 outputTypes["r_ace"] = tempOutNames;
  85                 outputTypes["r_jack"] = tempOutNames;
  86                 outputTypes["r_shannon"] = tempOutNames;
  87                 outputTypes["r_shannoneven"] = tempOutNames;
  88                 outputTypes["r_heip"] = tempOutNames;
  89                 outputTypes["r_smithwilson"] = tempOutNames;
  90                 outputTypes["r_npshannon"] = tempOutNames;
  91                 outputTypes["r_simpson"] = tempOutNames;
  92                 outputTypes["r_simpsoneven"] = tempOutNames;
  93                 outputTypes["r_invsimpson"] = tempOutNames;
  94                 outputTypes["r_bootstrap"] = tempOutNames;
  95                 outputTypes["r_coverage"] = tempOutNames;
  96                 outputTypes["r_nseqs"] = tempOutNames;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 RareFactCommand::RareFactCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107                 allLines = 1;
 108
 109                 //allow user to run help
 110                 if(option == "help") { help(); abort = true; calledHelp = true; }
 111                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 112
 113                 else {
 114                         vector<string> myArray = setParameters();
 115
 116                         OptionParser parser(option);
 117                         map<string,string> parameters = parser.getParameters();
 118                         map<string,string>::iterator it;
 119
 120                         ValidParameters validParameter;
 121
 122                         //check to make sure all parameters are valid for command
 123                         for (it = parameters.begin(); it != parameters.end(); it++) {
 124                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 125                         }
 126
 127                         //initialize outputTypes
 128                         vector<string> tempOutNames;
 129                         outputTypes["rarefaction"] = tempOutNames;
 130                         outputTypes["r_chao"] = tempOutNames;
 131                         outputTypes["r_ace"] = tempOutNames;
 132                         outputTypes["r_jack"] = tempOutNames;
 133                         outputTypes["r_shannon"] = tempOutNames;
 134                         outputTypes["r_shannoneven"] = tempOutNames;
 135                         outputTypes["r_heip"] = tempOutNames;
 136                         outputTypes["r_smithwilson"] = tempOutNames;
 137                         outputTypes["r_npshannon"] = tempOutNames;
 138                         outputTypes["r_simpson"] = tempOutNames;
 139                         outputTypes["r_simpsoneven"] = tempOutNames;
 140                         outputTypes["r_invsimpson"] = tempOutNames;
 141                         outputTypes["r_bootstrap"] = tempOutNames;
 142                         outputTypes["r_coverage"] = tempOutNames;
 143                         outputTypes["r_nseqs"] = tempOutNames;
 144
 145                         //if the user changes the input directory command factory will send this info to us in the output parameter
 146                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 147                         if (inputDir == "not found"){   inputDir = "";          }
 148                         else {
 149                                 string path;
 150                                 it = parameters.find("shared");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 156                                 }
 157
 158                                 it = parameters.find("rabund");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 164                                 }
 165
 166                                 it = parameters.find("sabund");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 172                                 }
 173
 174                                 it = parameters.find("list");
 175                                 //user has given a template file
 176                                 if(it != parameters.end()){
 177                                         path = m->hasPath(it->second);
 178                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 180                                 }
 181                         }
 182
 183                         //check for required parameters
 184                         listfile = validParameter.validFile(parameters, "list", true);
 185                         if (listfile == "not open") { listfile = ""; abort = true; }
 186                         else if (listfile == "not found") { listfile = ""; }
 187                         else {  format = "list"; inputfile = listfile; }
 188
 189                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 190                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 191                         else if (sabundfile == "not found") { sabundfile = ""; }
 192                         else {  format = "sabund"; inputfile = sabundfile; }
 193
 194                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 195                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 196                         else if (rabundfile == "not found") { rabundfile = ""; }
 197                         else {  format = "rabund"; inputfile = rabundfile; }
 198
 199                         sharedfile = validParameter.validFile(parameters, "shared", true);
 200                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 201                         else if (sharedfile == "not found") { sharedfile = ""; }
 202                         else {  format = "sharedfile"; inputfile = sharedfile; }
 203
 204                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 205                                 //is there are current file available for any of these?
 206                                 //give priority to shared, then list, then rabund, then sabund
 207                                 //if there is a current shared file, use it
 208                                 sharedfile = m->getSharedFile();
 209                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 210                                 else {
 211                                         listfile = m->getListFile();
 212                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 213                                         else {
 214                                                 rabundfile = m->getRabundFile();
 215                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 216                                                 else {
 217                                                         sabundfile = m->getSabundFile();
 218                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 219                                                         else {
 220                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
 221                                                                 abort = true;
 222                                                         }
 223                                                 }
 224                                         }
 225                                 }
 226                         }
 227
 228                         //if the user changes the output directory command factory will send this info to us in the output parameter
 229                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 230
 231                         //check for optional parameter and set defaults
 232                         // ...at some point should added some additional type checking...
 233                         label = validParameter.validFile(parameters, "label", false);
 234                         if (label == "not found") { label = ""; }
 235                         else {
 236                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 237                                 else { allLines = 1;  }
 238                         }
 239
 240                         calc = validParameter.validFile(parameters, "calc", false);
 241                         if (calc == "not found") { calc = "sobs";  }
 242                         else {
 243                                  if (calc == "default")  {  calc = "sobs";  }
 244                         }
 245                         m->splitAtDash(calc, Estimators);
 246
 247                         string temp;
 248                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 249                         convert(temp, freq);
 250
 251                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
 252                         convert(temp, abund);
 253
 254                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 255                         convert(temp, nIters);
 256
 257                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 258                         m->setProcessors(temp);
 259                         convert(temp, processors);
 260                 }
 261
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 265                 exit(1);
 266         }
 267 }
 268 //**********************************************************************************************************************
 269
 270 int RareFactCommand::execute(){
 271         try {
 272
 273                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 274
 275                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 276                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 277
 278                 if (m->control_pressed) { return 0; }
 279
 280                 for (int p = 0; p < inputFileNames.size(); p++) {
 281
 282                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 283
 284                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  m->Groups.clear();  return 0; }
 285
 286                         if (inputFileNames.size() > 1) {
 287                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 288                         }
 289                         int i;
 290                         ValidCalculators validCalculator;
 291
 292
 293                         for (i=0; i<Estimators.size(); i++) {
 294                                 if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
 295                                         if (Estimators[i] == "sobs") {
 296                                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
 297                                                 outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
 298                                         }else if (Estimators[i] == "chao") {
 299                                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
 300                                                 outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
 301                                         }else if (Estimators[i] == "ace") {
 302                                                 if(abund < 5)
 303                                                         abund = 10;
 304                                                 rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
 305                                                 outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
 306                                         }else if (Estimators[i] == "jack") {
 307                                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
 308                                                 outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
 309                                         }else if (Estimators[i] == "shannon") {
 310                                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
 311                                                 outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
 312                                         }else if (Estimators[i] == "shannoneven") {
 313                                                 rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
 314                                                 outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
 315                                         }else if (Estimators[i] == "heip") {
 316                                                 rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
 317                                                 outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
 318                                         }else if (Estimators[i] == "smithwilson") {
 319                                                 rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
 320                                                 outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
 321                                         }else if (Estimators[i] == "npshannon") {
 322                                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
 323                                                 outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
 324                                         }else if (Estimators[i] == "simpson") {
 325                                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
 326                                                 outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
 327                                         }else if (Estimators[i] == "simpsoneven") {
 328                                                 rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
 329                                                 outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
 330                                         }else if (Estimators[i] == "invsimpson") {
 331                                                 rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
 332                                                 outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
 333                                         }else if (Estimators[i] == "bootstrap") {
 334                                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
 335                                                 outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
 336                                         }else if (Estimators[i] == "coverage") {
 337                                                 rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
 338                                                 outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
 339                                         }else if (Estimators[i] == "nseqs") {
 340                                                 rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
 341                                                 outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
 342                                         }
 343                                 }
 344                         }
 345
 346
 347                         //if the users entered no valid calculators don't execute command
 348                         if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){       delete rDisplays[i];    }  return 0; }
 349
 350                         input = new InputData(inputFileNames[p], format);
 351                         order = input->getOrderVector();
 352                         string lastLabel = order->getLabel();
 353
 354                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 355                         set<string> processedLabels;
 356                         set<string> userLabels = labels;
 357
 358                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 359
 360                         //as long as you are not at the end of the file or done wih the lines you want
 361                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 362
 363                                 if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 364
 365
 366                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 367
 368                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 369                                         rCurve = new Rarefact(order, rDisplays, processors);
 370                                         rCurve->getCurve(freq, nIters);
 371                                         delete rCurve;
 372
 373                                         processedLabels.insert(order->getLabel());
 374                                         userLabels.erase(order->getLabel());
 375                                 }
 376
 377                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 378                                         string saveLabel = order->getLabel();
 379
 380                                         delete order;
 381                                         order = (input->getOrderVector(lastLabel));
 382
 383                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 384                                         rCurve = new Rarefact(order, rDisplays, processors);
 385                                         rCurve->getCurve(freq, nIters);
 386                                         delete rCurve;
 387
 388                                         processedLabels.insert(order->getLabel());
 389                                         userLabels.erase(order->getLabel());
 390
 391                                         //restore real lastlabel to save below
 392                                         order->setLabel(saveLabel);
 393                                 }
 394
 395                                 lastLabel = order->getLabel();
 396
 397                                 delete order;
 398                                 order = (input->getOrderVector());
 399                         }
 400
 401                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
 402
 403                         //output error messages about any remaining user labels
 404                         set<string>::iterator it;
 405                         bool needToRun = false;
 406                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 407                                 m->mothurOut("Your file does not include the label " + *it);
 408                                 if (processedLabels.count(lastLabel) != 1) {
 409                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 410                                         needToRun = true;
 411                                 }else {
 412                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 413                                 }
 414                         }
 415
 416                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
 417
 418                         //run last label if you need to
 419                         if (needToRun == true)  {
 420                                 if (order != NULL) {    delete order;   }
 421                                 order = (input->getOrderVector(lastLabel));
 422
 423                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 424                                 rCurve = new Rarefact(order, rDisplays, processors);
 425                                 rCurve->getCurve(freq, nIters);
 426                                 delete rCurve;
 427
 428                                 delete order;
 429                         }
 430
 431
 432                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 433                         rDisplays.clear();
 434                         delete input;
 435                 }
 436
 437
 438                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
 439
 440                 m->mothurOutEndLine();
 441                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 442                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 443                 m->mothurOutEndLine();
 444
 445                 return 0;
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "RareFactCommand", "execute");
 449                 exit(1);
 450         }
 451 }
 452 //**********************************************************************************************************************
 453 vector<string> RareFactCommand::parseSharedFile(string filename) {
 454         try {
 455                 vector<string> filenames;
 456
 457                 map<string, ofstream*> filehandles;
 458                 map<string, ofstream*>::iterator it3;
 459
 460                 input = new InputData(filename, "sharedfile");
 461                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 462
 463                 string sharedFileRoot = m->getRootName(filename);
 464
 465                 //clears file before we start to write to it below
 466                 for (int i=0; i<lookup.size(); i++) {
 467                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 468                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 469                 }
 470
 471                 ofstream* temp;
 472                 for (int i=0; i<lookup.size(); i++) {
 473                         temp = new ofstream;
 474                         filehandles[lookup[i]->getGroup()] = temp;
 475                         groups.push_back(lookup[i]->getGroup());
 476                 }
 477
 478                 while(lookup[0] != NULL) {
 479
 480                         for (int i = 0; i < lookup.size(); i++) {
 481                                 RAbundVector rav = lookup[i]->getRAbundVector();
 482                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 483                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 484                                 (*(filehandles[lookup[i]->getGroup()])).close();
 485                         }
 486
 487                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 488                         lookup = input->getSharedRAbundVectors();
 489                 }
 490
 491                 //free memory
 492                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 493                         delete it3->second;
 494                 }
 495
 496                 delete input;
 497                 m->Groups.clear();
 498
 499                 return filenames;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "RareFactCommand", "parseSharedFile");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507
 508
 509