collectcommand.cpp

   1 /*
   2  *  collectcommand.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 "collectcommand.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 "invsimpson.h"
  19 #include "npshannon.h"
  20 #include "shannon.h"
  21 #include "smithwilson.h"
  22 #include "heip.h"
  23 #include "shannoneven.h"
  24 #include "jackknife.h"
  25 #include "geom.h"
  26 #include "qstat.h"
  27 #include "logsd.h"
  28 #include "bergerparker.h"
  29 #include "bstick.h"
  30 #include "goodscoverage.h"
  31 #include "efron.h"
  32 #include "boneh.h"
  33 #include "solow.h"
  34 #include "shen.h"
  35 #include "coverage.h"
  36
  37 //**********************************************************************************************************************
  38 vector<string> CollectCommand::getValidParameters(){
  39         try {
  40                 string AlignArray[] =  {"freq","label","calc","abund","size","outputdir","inputdir"};
  41                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "CollectCommand", "getValidParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> CollectCommand::getRequiredParameters(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "CollectCommand", "getRequiredParameters");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 vector<string> CollectCommand::getRequiredFiles(){
  62         try {
  63                 string AlignArray[] =  {"shared","list","rabund","sabund","or"};
  64                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  65                 return myArray;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "CollectCommand", "getRequiredFiles");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 CollectCommand::CollectCommand(){
  74         try {
  75                 //initialize outputTypes
  76                 vector<string> tempOutNames;
  77                 outputTypes["sobs"] = tempOutNames;
  78                 outputTypes["chao"] = tempOutNames;
  79                 outputTypes["nseqs"] = tempOutNames;
  80                 outputTypes["coverage"] = tempOutNames;
  81                 outputTypes["ace"] = tempOutNames;
  82                 outputTypes["jack"] = tempOutNames;
  83                 outputTypes["shannon"] = tempOutNames;
  84                 outputTypes["shannoneven"] = tempOutNames;
  85                 outputTypes["np_shannon"] = tempOutNames;
  86                 outputTypes["heip"] = tempOutNames;
  87                 outputTypes["smithwilson"] = tempOutNames;
  88                 outputTypes["simpson"] = tempOutNames;
  89                 outputTypes["simpsoneven"] = tempOutNames;
  90                 outputTypes["invsimpson"] = tempOutNames;
  91                 outputTypes["bootstrap"] = tempOutNames;
  92                 outputTypes["geometric"] = tempOutNames;
  93                 outputTypes["qstat"] = tempOutNames;
  94                 outputTypes["logseries"] = tempOutNames;
  95                 outputTypes["bergerparker"] = tempOutNames;
  96                 outputTypes["bstick"] = tempOutNames;
  97                 outputTypes["goodscoverage"] = tempOutNames;
  98                 outputTypes["efron"] = tempOutNames;
  99                 outputTypes["boneh"] = tempOutNames;
 100                 outputTypes["solow"] = tempOutNames;
 101                 outputTypes["shen"] = tempOutNames;
 102         }
 103         catch(exception& e) {
 104                 m->errorOut(e, "CollectCommand", "CollectCommand");
 105                 exit(1);
 106         }
 107 }
 108 //**********************************************************************************************************************
 109 CollectCommand::CollectCommand(string option)  {
 110         try {
 111                 globaldata = GlobalData::getInstance();
 112                 abort = false;
 113                 allLines = 1;
 114                 labels.clear();
 115                 Estimators.clear();
 116
 117                 //allow user to run help
 118                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
 119
 120                 else {
 121                         //valid paramters for this command
 122                         string Array[] =  {"freq","label","calc","abund","size","outputdir","inputdir"};
 123                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 124
 125                         OptionParser parser(option);
 126                         map<string,string> parameters = parser.getParameters();
 127
 128                         ValidParameters validParameter;
 129
 130                         //check to make sure all parameters are valid for command
 131                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 132                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["sobs"] = tempOutNames;
 138                         outputTypes["chao"] = tempOutNames;
 139                         outputTypes["nseqs"] = tempOutNames;
 140                         outputTypes["coverage"] = tempOutNames;
 141                         outputTypes["ace"] = tempOutNames;
 142                         outputTypes["jack"] = tempOutNames;
 143                         outputTypes["shannon"] = tempOutNames;
 144                         outputTypes["shannoneven"] = tempOutNames;
 145                         outputTypes["np_shannon"] = tempOutNames;
 146                         outputTypes["heip"] = tempOutNames;
 147                         outputTypes["smithwilson"] = tempOutNames;
 148                         outputTypes["simpson"] = tempOutNames;
 149                         outputTypes["simpsoneven"] = tempOutNames;
 150                         outputTypes["invsimpson"] = tempOutNames;
 151                         outputTypes["bootstrap"] = tempOutNames;
 152                         outputTypes["geometric"] = tempOutNames;
 153                         outputTypes["qstat"] = tempOutNames;
 154                         outputTypes["logseries"] = tempOutNames;
 155                         outputTypes["bergerparker"] = tempOutNames;
 156                         outputTypes["bstick"] = tempOutNames;
 157                         outputTypes["goodscoverage"] = tempOutNames;
 158                         outputTypes["efron"] = tempOutNames;
 159                         outputTypes["boneh"] = tempOutNames;
 160                         outputTypes["solow"] = tempOutNames;
 161                         outputTypes["shen"] = tempOutNames;
 162
 163                         //if the user changes the output directory command factory will send this info to us in the output parameter
 164                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 165
 166                         //make sure the user has already run the read.otu command
 167                         if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); abort = true; }
 168
 169                         //check for optional parameter and set defaults
 170                         // ...at some point should added some additional type checking...
 171                         label = validParameter.validFile(parameters, "label", false);
 172                         if (label == "not found") { label = ""; }
 173                         else {
 174                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 175                                 else { allLines = 1;  }
 176                         }
 177
 178                         //if the user has not specified any labels use the ones from read.otu
 179                         if (label == "") {
 180                                 allLines = globaldata->allLines;
 181                                 labels = globaldata->labels;
 182                         }
 183
 184                         calc = validParameter.validFile(parameters, "calc", false);
 185                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 186                         else {
 187                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 188                         }
 189                         m->splitAtDash(calc, Estimators);
 190
 191                         string temp;
 192                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 193                         convert(temp, freq);
 194
 195                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 196                         convert(temp, abund);
 197
 198                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 199                         convert(temp, size);
 200                 }
 201
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "CollectCommand", "CollectCommand");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 void CollectCommand::help(){
 211         try {
 212                 m->mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
 213                 m->mothurOut("The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 214                 m->mothurOut("The collect.single command parameters are label, freq, calc and abund.  No parameters are required. \n");
 215                 m->mothurOut("The collect.single command should be in the following format: \n");
 216                 m->mothurOut("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");
 217                 m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 218                 m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
 219                 m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
 220                 validCalculator->printCalc("single", cout);
 221                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 222                 m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "CollectCommand", "help");
 226                 exit(1);
 227         }
 228 }
 229
 230 //**********************************************************************************************************************
 231
 232 CollectCommand::~CollectCommand(){}
 233
 234 //**********************************************************************************************************************
 235
 236 int CollectCommand::execute(){
 237         try {
 238
 239                 if (abort == true) { return 0; }
 240
 241                 string hadShared = "";
 242                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 243                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 244
 245                 for (int p = 0; p < inputFileNames.size(); p++) {
 246
 247                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  globaldata->Groups.clear(); if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 248
 249                         if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 250                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 251                         globaldata->inputFileName = inputFileNames[p];
 252
 253                         if (inputFileNames.size() > 1) {
 254                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 255                         }
 256
 257                         validCalculator = new ValidCalculators();
 258
 259                         for (int i=0; i<Estimators.size(); i++) {
 260                                 if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
 261                                         if (Estimators[i] == "sobs") {
 262                                                 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
 263                                                 outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
 264                                         }else if (Estimators[i] == "chao") {
 265                                                 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
 266                                                 outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
 267                                         }else if (Estimators[i] == "nseqs") {
 268                                                 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
 269                                                 outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
 270                                         }else if (Estimators[i] == "coverage") {
 271                                                 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
 272                                                 outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
 273                                         }else if (Estimators[i] == "ace") {
 274                                                 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
 275                                                 outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
 276                                         }else if (Estimators[i] == "jack") {
 277                                                 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
 278                                                 outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
 279                                         }else if (Estimators[i] == "shannon") {
 280                                                 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
 281                                                 outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
 282                                         }else if (Estimators[i] == "shannoneven") {
 283                                                 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
 284                                                 outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
 285                                         }else if (Estimators[i] == "npshannon") {
 286                                                 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
 287                                                 outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
 288                                         }else if (Estimators[i] == "heip") {
 289                                                 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
 290                                                 outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
 291                                         }else if (Estimators[i] == "smithwilson") {
 292                                                 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
 293                                                 outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
 294                                         }else if (Estimators[i] == "simpson") {
 295                                                 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
 296                                                 outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
 297                                         }else if (Estimators[i] == "simpsoneven") {
 298                                                 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
 299                                                 outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
 300                                         }else if (Estimators[i] == "invsimpson") {
 301                                                 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
 302                                                 outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
 303                                         }else if (Estimators[i] == "bootstrap") {
 304                                                 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
 305                                                 outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
 306                                         }else if (Estimators[i] == "geometric") {
 307                                                 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
 308                                                 outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
 309                                         }else if (Estimators[i] == "qstat") {
 310                                                 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
 311                                                 outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
 312                                         }else if (Estimators[i] == "logseries") {
 313                                                 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
 314                                                 outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
 315                                         }else if (Estimators[i] == "bergerparker") {
 316                                                 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
 317                                                 outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
 318                                         }else if (Estimators[i] == "bstick") {
 319                                                 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
 320                                                 outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
 321                                         }else if (Estimators[i] == "goodscoverage") {
 322                                                 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
 323                                                 outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
 324                                         }else if (Estimators[i] == "efron") {
 325                                                 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
 326                                                 outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
 327                                         }else if (Estimators[i] == "boneh") {
 328                                                 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
 329                                                 outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
 330                                         }else if (Estimators[i] == "solow") {
 331                                                 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
 332                                                 outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
 333                                         }else if (Estimators[i] == "shen") {
 334                                                 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
 335                                                 outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
 336                                         }
 337                                 }
 338                         }
 339
 340                         //if the users entered no valid calculators don't execute command
 341                         if (cDisplays.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 342
 343                         read = new ReadOTUFile(inputFileNames[p]);
 344                         read->read(&*globaldata);
 345
 346                         order = globaldata->gorder;
 347                         string lastLabel = order->getLabel();
 348                         input = globaldata->ginput;
 349
 350                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 351                         set<string> processedLabels;
 352                         set<string> userLabels = labels;
 353
 354                         if (m->control_pressed) {
 355                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 356                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 357                                 delete input;  globaldata->ginput = NULL;
 358                                 delete read;
 359                                 delete order; globaldata->gorder = NULL;
 360                                 delete validCalculator;
 361                                 globaldata->Groups.clear();
 362                                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 363                                 return 0;
 364                         }
 365
 366
 367                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 368
 369                                 if (m->control_pressed) {
 370                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 371                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 372                                         delete input;  globaldata->ginput = NULL;
 373                                         delete read;
 374                                         delete order; globaldata->gorder = NULL;
 375                                         delete validCalculator;
 376                                         globaldata->Groups.clear();
 377                                         if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 378                                         return 0;
 379                                 }
 380
 381
 382                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 383
 384                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 385                                         cCurve = new Collect(order, cDisplays);
 386                                         cCurve->getCurve(freq);
 387                                         delete cCurve;
 388
 389                                         processedLabels.insert(order->getLabel());
 390                                         userLabels.erase(order->getLabel());
 391
 392
 393                                 }
 394                                 //you have a label the user want that is smaller than this label and the last label has not already been processed
 395                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 396                                         string saveLabel = order->getLabel();
 397
 398                                         delete order;
 399                                         order = (input->getOrderVector(lastLabel));
 400
 401                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 402                                         cCurve = new Collect(order, cDisplays);
 403                                         cCurve->getCurve(freq);
 404                                         delete cCurve;
 405
 406
 407                                         processedLabels.insert(order->getLabel());
 408                                         userLabels.erase(order->getLabel());
 409
 410                                         //restore real lastlabel to save below
 411                                         order->setLabel(saveLabel);
 412                                 }
 413
 414                                 lastLabel = order->getLabel();
 415
 416                                 delete order;
 417                                 order = (input->getOrderVector());
 418                         }
 419
 420
 421                         if (m->control_pressed) {
 422                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 423                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 424                                         delete input;  globaldata->ginput = NULL;
 425                                         delete read;
 426                                         delete validCalculator;
 427                                         globaldata->Groups.clear();
 428                                         if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 429                                         return 0;
 430                         }
 431
 432                         //output error messages about any remaining user labels
 433                         set<string>::iterator it;
 434                         bool needToRun = false;
 435                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 436                                 m->mothurOut("Your file does not include the label " + *it);
 437                                 if (processedLabels.count(lastLabel) != 1) {
 438                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 439                                         needToRun = true;
 440                                 }else {
 441                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 442                                 }
 443                         }
 444
 445                         //run last label if you need to
 446                         if (needToRun == true)  {
 447                                 if (order != NULL) {    delete order;   }
 448                                 order = (input->getOrderVector(lastLabel));
 449
 450                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 451
 452                                 cCurve = new Collect(order, cDisplays);
 453                                 cCurve->getCurve(freq);
 454                                 delete cCurve;
 455
 456                                 if (m->control_pressed) {
 457                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 458                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 459                                         delete input;  globaldata->ginput = NULL;
 460                                         delete read;
 461                                         delete order; globaldata->gorder = NULL;
 462                                         delete validCalculator;
 463                                         globaldata->Groups.clear();
 464                                         if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 465                                         return 0;
 466                                 }
 467                                 delete order;
 468                         }
 469
 470                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 471                         cDisplays.clear();
 472                         delete input;  globaldata->ginput = NULL;
 473                         delete read;
 474                         globaldata->gorder = NULL;
 475                         delete validCalculator;
 476                 }
 477
 478                 //return to shared mode if you changed above
 479                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 480
 481                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
 482
 483                 m->mothurOutEndLine();
 484                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 485                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 486                 m->mothurOutEndLine();
 487
 488
 489                 return 0;
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "CollectCommand", "execute");
 493                 exit(1);
 494         }
 495 }
 496
 497 //**********************************************************************************************************************
 498 vector<string> CollectCommand::parseSharedFile(string filename) {
 499         try {
 500                 vector<string> filenames;
 501
 502                 map<string, ofstream*> filehandles;
 503                 map<string, ofstream*>::iterator it3;
 504
 505
 506                 //read first line
 507                 read = new ReadOTUFile(filename);
 508                 read->read(&*globaldata);
 509
 510                 input = globaldata->ginput;
 511                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 512
 513                 string sharedFileRoot = m->getRootName(filename);
 514
 515                 //clears file before we start to write to it below
 516                 for (int i=0; i<lookup.size(); i++) {
 517                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 518                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 519                 }
 520
 521                 ofstream* temp;
 522                 for (int i=0; i<lookup.size(); i++) {
 523                         temp = new ofstream;
 524                         filehandles[lookup[i]->getGroup()] = temp;
 525                         groups.push_back(lookup[i]->getGroup());
 526                 }
 527
 528                 while(lookup[0] != NULL) {
 529
 530                         for (int i = 0; i < lookup.size(); i++) {
 531                                 RAbundVector rav = lookup[i]->getRAbundVector();
 532                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 533                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 534                                 (*(filehandles[lookup[i]->getGroup()])).close();
 535                         }
 536
 537                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 538                         lookup = input->getSharedRAbundVectors();
 539                 }
 540
 541                 //free memory
 542                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 543                         delete it3->second;
 544                 }
 545                 delete read;
 546                 delete input;
 547                 globaldata->ginput = NULL;
 548
 549                 return filenames;
 550         }
 551         catch(exception& e) {
 552                 m->errorOut(e, "CollectCommand", "parseSharedFile");
 553                 exit(1);
 554         }
 555 }
 556 //**********************************************************************************************************************
 557