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 //**********************************************************************************************************************
  39 vector<string> CollectCommand::setParameters(){
  40         try {
  41                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  42                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  43                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  44                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  45                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  46                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
  47                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
  48                 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
  49                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  50                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  51                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  52
  53                 vector<string> myArray;
  54                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "CollectCommand", "setParameters");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 string CollectCommand::getHelpString(){
  64         try {
  65                 string helpString = "";
  66                 ValidCalculators validCalculator;
  67                 helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
  68                 helpString += "The collect.single command should be in the following format: \n";
  69                 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";
  70                 helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
  71                 helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
  72                 helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
  73                 helpString += validCalculator.printCalc("single");
  74                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  75                 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
  76                 return helpString;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "CollectCommand", "getHelpString");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 CollectCommand::CollectCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["sobs"] = tempOutNames;
  90                 outputTypes["chao"] = tempOutNames;
  91                 outputTypes["nseqs"] = tempOutNames;
  92                 outputTypes["coverage"] = tempOutNames;
  93                 outputTypes["ace"] = tempOutNames;
  94                 outputTypes["jack"] = tempOutNames;
  95                 outputTypes["shannon"] = tempOutNames;
  96                 outputTypes["shannoneven"] = tempOutNames;
  97                 outputTypes["np_shannon"] = tempOutNames;
  98                 outputTypes["heip"] = tempOutNames;
  99                 outputTypes["smithwilson"] = tempOutNames;
 100                 outputTypes["simpson"] = tempOutNames;
 101                 outputTypes["simpsoneven"] = tempOutNames;
 102                 outputTypes["invsimpson"] = tempOutNames;
 103                 outputTypes["bootstrap"] = tempOutNames;
 104                 outputTypes["geometric"] = tempOutNames;
 105                 outputTypes["qstat"] = tempOutNames;
 106                 outputTypes["logseries"] = tempOutNames;
 107                 outputTypes["bergerparker"] = tempOutNames;
 108                 outputTypes["bstick"] = tempOutNames;
 109                 outputTypes["goodscoverage"] = tempOutNames;
 110                 outputTypes["efron"] = tempOutNames;
 111                 outputTypes["boneh"] = tempOutNames;
 112                 outputTypes["solow"] = tempOutNames;
 113                 outputTypes["shen"] = tempOutNames;
 114         }
 115         catch(exception& e) {
 116                 m->errorOut(e, "CollectCommand", "CollectCommand");
 117                 exit(1);
 118         }
 119 }
 120 //**********************************************************************************************************************
 121 CollectCommand::CollectCommand(string option)  {
 122         try {
 123                 abort = false; calledHelp = false;
 124                 allLines = 1;
 125
 126                 //allow user to run help
 127                 if(option == "help") { help(); calledHelp = true; abort = true; }
 128                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 129
 130                 else {
 131                         vector<string> myArray = setParameters();
 132
 133                         OptionParser parser(option);
 134                         map<string,string> parameters = parser.getParameters();
 135                         map<string,string>::iterator it;
 136
 137                         ValidParameters validParameter;
 138
 139                         //check to make sure all parameters are valid for command
 140                         for (it = parameters.begin(); it != parameters.end(); it++) {
 141                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 142                         }
 143
 144                         //initialize outputTypes
 145                         vector<string> tempOutNames;
 146                         outputTypes["sobs"] = tempOutNames;
 147                         outputTypes["chao"] = tempOutNames;
 148                         outputTypes["nseqs"] = tempOutNames;
 149                         outputTypes["coverage"] = tempOutNames;
 150                         outputTypes["ace"] = tempOutNames;
 151                         outputTypes["jack"] = tempOutNames;
 152                         outputTypes["shannon"] = tempOutNames;
 153                         outputTypes["shannoneven"] = tempOutNames;
 154                         outputTypes["np_shannon"] = tempOutNames;
 155                         outputTypes["heip"] = tempOutNames;
 156                         outputTypes["smithwilson"] = tempOutNames;
 157                         outputTypes["simpson"] = tempOutNames;
 158                         outputTypes["simpsoneven"] = tempOutNames;
 159                         outputTypes["invsimpson"] = tempOutNames;
 160                         outputTypes["bootstrap"] = tempOutNames;
 161                         outputTypes["geometric"] = tempOutNames;
 162                         outputTypes["qstat"] = tempOutNames;
 163                         outputTypes["logseries"] = tempOutNames;
 164                         outputTypes["bergerparker"] = tempOutNames;
 165                         outputTypes["bstick"] = tempOutNames;
 166                         outputTypes["goodscoverage"] = tempOutNames;
 167                         outputTypes["efron"] = tempOutNames;
 168                         outputTypes["boneh"] = tempOutNames;
 169                         outputTypes["solow"] = tempOutNames;
 170                         outputTypes["shen"] = tempOutNames;
 171
 172                         //if the user changes the input directory command factory will send this info to us in the output parameter
 173                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 174                         if (inputDir == "not found"){   inputDir = "";          }
 175                         else {
 176                                 string path;
 177                                 it = parameters.find("shared");
 178                                 //user has given a template file
 179                                 if(it != parameters.end()){
 180                                         path = m->hasPath(it->second);
 181                                         //if the user has not given a path then, add inputdir. else leave path alone.
 182                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 183                                 }
 184
 185                                 it = parameters.find("rabund");
 186                                 //user has given a template file
 187                                 if(it != parameters.end()){
 188                                         path = m->hasPath(it->second);
 189                                         //if the user has not given a path then, add inputdir. else leave path alone.
 190                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 191                                 }
 192
 193                                 it = parameters.find("sabund");
 194                                 //user has given a template file
 195                                 if(it != parameters.end()){
 196                                         path = m->hasPath(it->second);
 197                                         //if the user has not given a path then, add inputdir. else leave path alone.
 198                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 199                                 }
 200
 201                                 it = parameters.find("list");
 202                                 //user has given a template file
 203                                 if(it != parameters.end()){
 204                                         path = m->hasPath(it->second);
 205                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 207                                 }
 208                         }
 209
 210                         //check for required parameters
 211                         listfile = validParameter.validFile(parameters, "list", true);
 212                         if (listfile == "not open") { listfile = ""; abort = true; }
 213                         else if (listfile == "not found") { listfile = ""; }
 214                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 215
 216                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 217                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 218                         else if (sabundfile == "not found") { sabundfile = ""; }
 219                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 220
 221                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 222                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 223                         else if (rabundfile == "not found") { rabundfile = ""; }
 224                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 225
 226                         sharedfile = validParameter.validFile(parameters, "shared", true);
 227                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 228                         else if (sharedfile == "not found") { sharedfile = ""; }
 229                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 230
 231
 232                         //if the user changes the output directory command factory will send this info to us in the output parameter
 233                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 234
 235                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 236                                 //is there are current file available for any of these?
 237                                 //give priority to shared, then list, then rabund, then sabund
 238                                 //if there is a current shared file, use it
 239                                 sharedfile = m->getSharedFile();
 240                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 241                                 else {
 242                                         listfile = m->getListFile();
 243                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 244                                         else {
 245                                                 rabundfile = m->getRabundFile();
 246                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 247                                                 else {
 248                                                         sabundfile = m->getSabundFile();
 249                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 250                                                         else {
 251                                                                 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();
 252                                                                 abort = true;
 253                                                         }
 254                                                 }
 255                                         }
 256                                 }
 257                         }
 258
 259                         //check for optional parameter and set defaults
 260                         // ...at some point should added some additional type checking...
 261                         label = validParameter.validFile(parameters, "label", false);
 262                         if (label == "not found") { label = ""; }
 263                         else {
 264                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 265                                 else { allLines = 1;  }
 266                         }
 267
 268                         //NOTE: if you add new calc options, don't forget to add them to the parameter initialize in setParameters or the gui won't be able to use them
 269                         calc = validParameter.validFile(parameters, "calc", false);
 270                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 271                         else {
 272                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 273                         }
 274                         m->splitAtDash(calc, Estimators);
 275                         if (m->inUsersGroups("citation", Estimators)) {
 276                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 277                                 //remove citation from list of calcs
 278                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 279                         }
 280
 281                         string temp;
 282                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 283                         convert(temp, freq);
 284
 285                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 286                         convert(temp, abund);
 287
 288                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 289                         convert(temp, size);
 290                 }
 291
 292         }
 293         catch(exception& e) {
 294                 m->errorOut(e, "CollectCommand", "CollectCommand");
 295                 exit(1);
 296         }
 297 }
 298 //**********************************************************************************************************************
 299
 300 int CollectCommand::execute(){
 301         try {
 302
 303                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 304
 305                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 306                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 307
 308                 for (int p = 0; p < inputFileNames.size(); p++) {
 309
 310                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  m->Groups.clear();  return 0; }
 311
 312                         if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 313                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 314                         //globaldata->inputFileName = inputFileNames[p];
 315
 316                         if (inputFileNames.size() > 1) {
 317                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 318                         }
 319
 320                         ValidCalculators validCalculator;
 321
 322                         for (int i=0; i<Estimators.size(); i++) {
 323                                 if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
 324                                         if (Estimators[i] == "sobs") {
 325                                                 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
 326                                                 outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
 327                                         }else if (Estimators[i] == "chao") {
 328                                                 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
 329                                                 outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
 330                                         }else if (Estimators[i] == "nseqs") {
 331                                                 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
 332                                                 outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
 333                                         }else if (Estimators[i] == "coverage") {
 334                                                 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
 335                                                 outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
 336                                         }else if (Estimators[i] == "ace") {
 337                                                 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
 338                                                 outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
 339                                         }else if (Estimators[i] == "jack") {
 340                                                 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
 341                                                 outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
 342                                         }else if (Estimators[i] == "shannon") {
 343                                                 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
 344                                                 outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
 345                                         }else if (Estimators[i] == "shannoneven") {
 346                                                 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
 347                                                 outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
 348                                         }else if (Estimators[i] == "npshannon") {
 349                                                 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
 350                                                 outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
 351                                         }else if (Estimators[i] == "heip") {
 352                                                 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
 353                                                 outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
 354                                         }else if (Estimators[i] == "smithwilson") {
 355                                                 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
 356                                                 outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
 357                                         }else if (Estimators[i] == "simpson") {
 358                                                 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
 359                                                 outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
 360                                         }else if (Estimators[i] == "simpsoneven") {
 361                                                 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
 362                                                 outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
 363                                         }else if (Estimators[i] == "invsimpson") {
 364                                                 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
 365                                                 outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
 366                                         }else if (Estimators[i] == "bootstrap") {
 367                                                 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
 368                                                 outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
 369                                         }else if (Estimators[i] == "geometric") {
 370                                                 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
 371                                                 outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
 372                                         }else if (Estimators[i] == "qstat") {
 373                                                 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
 374                                                 outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
 375                                         }else if (Estimators[i] == "logseries") {
 376                                                 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
 377                                                 outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
 378                                         }else if (Estimators[i] == "bergerparker") {
 379                                                 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
 380                                                 outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
 381                                         }else if (Estimators[i] == "bstick") {
 382                                                 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
 383                                                 outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
 384                                         }else if (Estimators[i] == "goodscoverage") {
 385                                                 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
 386                                                 outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
 387                                         }else if (Estimators[i] == "efron") {
 388                                                 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
 389                                                 outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
 390                                         }else if (Estimators[i] == "boneh") {
 391                                                 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
 392                                                 outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
 393                                         }else if (Estimators[i] == "solow") {
 394                                                 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
 395                                                 outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
 396                                         }else if (Estimators[i] == "shen") {
 397                                                 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
 398                                                 outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
 399                                         }
 400                                 }
 401                         }
 402
 403                         //if the users entered no valid calculators don't execute command
 404                         if (cDisplays.size() == 0) { return 0; }
 405
 406                         input = new InputData(inputFileNames[p], format);
 407                         order = input->getOrderVector();
 408                         string lastLabel = order->getLabel();
 409
 410                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 411                         set<string> processedLabels;
 412                         set<string> userLabels = labels;
 413
 414                         if (m->control_pressed) {
 415                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 416                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 417                                 delete input;
 418                                 delete order;
 419                                 m->Groups.clear();
 420                                 return 0;
 421                         }
 422
 423
 424                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 425
 426                                 if (m->control_pressed) {
 427                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 428                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 429                                         delete input;
 430                                         delete order;
 431                                         m->Groups.clear();
 432                                         return 0;
 433                                 }
 434
 435
 436                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 437
 438                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 439                                         cCurve = new Collect(order, cDisplays);
 440                                         cCurve->getCurve(freq);
 441                                         delete cCurve;
 442
 443                                         processedLabels.insert(order->getLabel());
 444                                         userLabels.erase(order->getLabel());
 445
 446
 447                                 }
 448                                 //you have a label the user want that is smaller than this label and the last label has not already been processed
 449                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 450                                         string saveLabel = order->getLabel();
 451
 452                                         delete order;
 453                                         order = (input->getOrderVector(lastLabel));
 454
 455                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 456                                         cCurve = new Collect(order, cDisplays);
 457                                         cCurve->getCurve(freq);
 458                                         delete cCurve;
 459
 460
 461                                         processedLabels.insert(order->getLabel());
 462                                         userLabels.erase(order->getLabel());
 463
 464                                         //restore real lastlabel to save below
 465                                         order->setLabel(saveLabel);
 466                                 }
 467
 468                                 lastLabel = order->getLabel();
 469
 470                                 delete order;
 471                                 order = (input->getOrderVector());
 472                         }
 473
 474
 475                         if (m->control_pressed) {
 476                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 477                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 478                                         delete input;
 479                                         m->Groups.clear();
 480                                         return 0;
 481                         }
 482
 483                         //output error messages about any remaining user labels
 484                         set<string>::iterator it;
 485                         bool needToRun = false;
 486                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 487                                 m->mothurOut("Your file does not include the label " + *it);
 488                                 if (processedLabels.count(lastLabel) != 1) {
 489                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 490                                         needToRun = true;
 491                                 }else {
 492                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 493                                 }
 494                         }
 495
 496                         //run last label if you need to
 497                         if (needToRun == true)  {
 498                                 if (order != NULL) {    delete order;   }
 499                                 order = (input->getOrderVector(lastLabel));
 500
 501                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 502
 503                                 cCurve = new Collect(order, cDisplays);
 504                                 cCurve->getCurve(freq);
 505                                 delete cCurve;
 506
 507                                 if (m->control_pressed) {
 508                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 509                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 510                                         delete input;
 511                                         delete order;
 512                                         m->Groups.clear();
 513                                         return 0;
 514                                 }
 515                                 delete order;
 516                         }
 517
 518                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 519                         cDisplays.clear();
 520                         delete input;
 521                 }
 522
 523                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
 524
 525                 m->mothurOutEndLine();
 526                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 527                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 528                 m->mothurOutEndLine();
 529
 530
 531                 return 0;
 532         }
 533         catch(exception& e) {
 534                 m->errorOut(e, "CollectCommand", "execute");
 535                 exit(1);
 536         }
 537 }
 538
 539 //**********************************************************************************************************************
 540 vector<string> CollectCommand::parseSharedFile(string filename) {
 541         try {
 542                 vector<string> filenames;
 543
 544                 map<string, ofstream*> filehandles;
 545                 map<string, ofstream*>::iterator it3;
 546
 547                 input = new InputData(filename, "sharedfile");
 548                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 549
 550                 string sharedFileRoot = m->getRootName(filename);
 551
 552                 //clears file before we start to write to it below
 553                 for (int i=0; i<lookup.size(); i++) {
 554                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 555                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 556                 }
 557
 558                 ofstream* temp;
 559                 for (int i=0; i<lookup.size(); i++) {
 560                         temp = new ofstream;
 561                         filehandles[lookup[i]->getGroup()] = temp;
 562                         groups.push_back(lookup[i]->getGroup());
 563                 }
 564
 565                 while(lookup[0] != NULL) {
 566
 567                         for (int i = 0; i < lookup.size(); i++) {
 568                                 RAbundVector rav = lookup[i]->getRAbundVector();
 569                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 570                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 571                                 (*(filehandles[lookup[i]->getGroup()])).close();
 572                         }
 573
 574                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 575                         lookup = input->getSharedRAbundVectors();
 576                 }
 577
 578                 //free memory
 579                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 580                         delete it3->second;
 581                 }
 582
 583                 delete input;
 584
 585                 return filenames;
 586         }
 587         catch(exception& e) {
 588                 m->errorOut(e, "CollectCommand", "parseSharedFile");
 589                 exit(1);
 590         }
 591 }
 592 //**********************************************************************************************************************
 593