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,true); parameters.push_back(plist);
  42                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund);
  43                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund);
  44                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); 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-npshannon-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,true); 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, freq=yourFreq, calc=yourEstimators).\n";
  71                 helpString += "Example collect(label=unique-.01-.03, 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 string CollectCommand::getOutputPattern(string type) {
  85     try {
  86         string pattern = "";
  87
  88         if (type == "sobs")             {  pattern =  "[filename],sobs";            }
  89         else if (type == "chao")        {  pattern =  "[filename],chao";            }
  90         else if (type == "nseqs")       {  pattern =  "[filename],nseqs";           }
  91         else if (type == "coverage")    {  pattern =  "[filename],coverage";        }
  92         else if (type == "ace")         {  pattern =  "[filename],ace";             }
  93         else if (type == "jack")        {  pattern =  "[filename],jack";            }
  94         else if (type == "shannon")     {  pattern =  "[filename],shannon";         }
  95         else if (type == "shannoneven") {  pattern =  "[filename],shannoneven";     }
  96         else if (type == "npshannon")   {  pattern =  "[filename],npshannon";       }
  97         else if (type == "heip")        {  pattern =  "[filename],heip";            }
  98         else if (type == "smithwilson") {  pattern =  "[filename],smithwilson";     }
  99         else if (type == "simpson")     {  pattern =  "[filename],simpson";         }
 100         else if (type == "simpsoneven") {  pattern =  "[filename],simpsoneven";     }
 101         else if (type == "invsimpson")  {  pattern =  "[filename],invsimpson";      }
 102         else if (type == "bootstrap")   {  pattern =  "[filename],bootstrap";       }
 103         else if (type == "geometric")   {  pattern =  "[filename],geometric";       }
 104         else if (type == "qstat")       {  pattern =  "[filename],qstat";           }
 105         else if (type == "logseries")   {  pattern =  "[filename],logseries";       }
 106         else if (type == "bergerparker") {  pattern =  "[filename],bergerparker";   }
 107         else if (type == "bstick")      {  pattern =  "[filename],bstick";          }
 108         else if (type == "goodscoverage") {  pattern =  "[filename],goodscoverage"; }
 109         else if (type == "efron")       {  pattern =  "[filename],efron";           }
 110         else if (type == "boneh")       {  pattern =  "[filename],boneh";           }
 111         else if (type == "solow")       {  pattern =  "[filename],solow";           }
 112         else if (type == "shen")        {  pattern =  "[filename],shen";            }
 113         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 114
 115         return pattern;
 116     }
 117     catch(exception& e) {
 118         m->errorOut(e, "CollectCommand", "getOutputPattern");
 119         exit(1);
 120     }
 121 }
 122 //**********************************************************************************************************************
 123 CollectCommand::CollectCommand(){
 124         try {
 125                 abort = true; calledHelp = true;
 126                 setParameters();
 127                 vector<string> tempOutNames;
 128                 outputTypes["sobs"] = tempOutNames;
 129                 outputTypes["chao"] = tempOutNames;
 130                 outputTypes["nseqs"] = tempOutNames;
 131                 outputTypes["coverage"] = tempOutNames;
 132                 outputTypes["ace"] = tempOutNames;
 133                 outputTypes["jack"] = tempOutNames;
 134                 outputTypes["shannon"] = tempOutNames;
 135                 outputTypes["shannoneven"] = tempOutNames;
 136                 outputTypes["npshannon"] = tempOutNames;
 137                 outputTypes["heip"] = tempOutNames;
 138                 outputTypes["smithwilson"] = tempOutNames;
 139                 outputTypes["simpson"] = tempOutNames;
 140                 outputTypes["simpsoneven"] = tempOutNames;
 141                 outputTypes["invsimpson"] = tempOutNames;
 142                 outputTypes["bootstrap"] = tempOutNames;
 143                 outputTypes["geometric"] = tempOutNames;
 144                 outputTypes["qstat"] = tempOutNames;
 145                 outputTypes["logseries"] = tempOutNames;
 146                 outputTypes["bergerparker"] = tempOutNames;
 147                 outputTypes["bstick"] = tempOutNames;
 148                 outputTypes["goodscoverage"] = tempOutNames;
 149                 outputTypes["efron"] = tempOutNames;
 150                 outputTypes["boneh"] = tempOutNames;
 151                 outputTypes["solow"] = tempOutNames;
 152                 outputTypes["shen"] = tempOutNames;
 153         }
 154         catch(exception& e) {
 155                 m->errorOut(e, "CollectCommand", "CollectCommand");
 156                 exit(1);
 157         }
 158 }
 159 //**********************************************************************************************************************
 160 CollectCommand::CollectCommand(string option)  {
 161         try {
 162                 abort = false; calledHelp = false;
 163                 allLines = 1;
 164
 165                 //allow user to run help
 166                 if(option == "help") { help(); calledHelp = true; abort = true; }
 167                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 168
 169                 else {
 170                         vector<string> myArray = setParameters();
 171
 172                         OptionParser parser(option);
 173                         map<string,string> parameters = parser.getParameters();
 174                         map<string,string>::iterator it;
 175
 176                         ValidParameters validParameter;
 177
 178                         //check to make sure all parameters are valid for command
 179                         for (it = parameters.begin(); it != parameters.end(); it++) {
 180                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 181                         }
 182
 183                         //initialize outputTypes
 184                         vector<string> tempOutNames;
 185                         outputTypes["sobs"] = tempOutNames;
 186                         outputTypes["chao"] = tempOutNames;
 187                         outputTypes["nseqs"] = tempOutNames;
 188                         outputTypes["coverage"] = tempOutNames;
 189                         outputTypes["ace"] = tempOutNames;
 190                         outputTypes["jack"] = tempOutNames;
 191                         outputTypes["shannon"] = tempOutNames;
 192                         outputTypes["shannoneven"] = tempOutNames;
 193                         outputTypes["npshannon"] = tempOutNames;
 194                         outputTypes["heip"] = tempOutNames;
 195                         outputTypes["smithwilson"] = tempOutNames;
 196                         outputTypes["simpson"] = tempOutNames;
 197                         outputTypes["simpsoneven"] = tempOutNames;
 198                         outputTypes["invsimpson"] = tempOutNames;
 199                         outputTypes["bootstrap"] = tempOutNames;
 200                         outputTypes["geometric"] = tempOutNames;
 201                         outputTypes["qstat"] = tempOutNames;
 202                         outputTypes["logseries"] = tempOutNames;
 203                         outputTypes["bergerparker"] = tempOutNames;
 204                         outputTypes["bstick"] = tempOutNames;
 205                         outputTypes["goodscoverage"] = tempOutNames;
 206                         outputTypes["efron"] = tempOutNames;
 207                         outputTypes["boneh"] = tempOutNames;
 208                         outputTypes["solow"] = tempOutNames;
 209                         outputTypes["shen"] = tempOutNames;
 210
 211                         //if the user changes the input directory command factory will send this info to us in the output parameter
 212                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 213                         if (inputDir == "not found"){   inputDir = "";          }
 214                         else {
 215                                 string path;
 216                                 it = parameters.find("shared");
 217                                 //user has given a template file
 218                                 if(it != parameters.end()){
 219                                         path = m->hasPath(it->second);
 220                                         //if the user has not given a path then, add inputdir. else leave path alone.
 221                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 222                                 }
 223
 224                                 it = parameters.find("rabund");
 225                                 //user has given a template file
 226                                 if(it != parameters.end()){
 227                                         path = m->hasPath(it->second);
 228                                         //if the user has not given a path then, add inputdir. else leave path alone.
 229                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 230                                 }
 231
 232                                 it = parameters.find("sabund");
 233                                 //user has given a template file
 234                                 if(it != parameters.end()){
 235                                         path = m->hasPath(it->second);
 236                                         //if the user has not given a path then, add inputdir. else leave path alone.
 237                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 238                                 }
 239
 240                                 it = parameters.find("list");
 241                                 //user has given a template file
 242                                 if(it != parameters.end()){
 243                                         path = m->hasPath(it->second);
 244                                         //if the user has not given a path then, add inputdir. else leave path alone.
 245                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 246                                 }
 247                         }
 248
 249                         //check for required parameters
 250                         listfile = validParameter.validFile(parameters, "list", true);
 251                         if (listfile == "not open") { listfile = ""; abort = true; }
 252                         else if (listfile == "not found") { listfile = ""; }
 253                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 254
 255                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 256                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 257                         else if (sabundfile == "not found") { sabundfile = ""; }
 258                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 259
 260                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 261                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 262                         else if (rabundfile == "not found") { rabundfile = ""; }
 263                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 264
 265                         sharedfile = validParameter.validFile(parameters, "shared", true);
 266                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 267                         else if (sharedfile == "not found") { sharedfile = ""; }
 268                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 269
 270
 271                         //if the user changes the output directory command factory will send this info to us in the output parameter
 272                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 273
 274                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 275                                 //is there are current file available for any of these?
 276                                 //give priority to shared, then list, then rabund, then sabund
 277                                 //if there is a current shared file, use it
 278                                 sharedfile = m->getSharedFile();
 279                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 280                                 else {
 281                                         listfile = m->getListFile();
 282                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 283                                         else {
 284                                                 rabundfile = m->getRabundFile();
 285                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 286                                                 else {
 287                                                         sabundfile = m->getSabundFile();
 288                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 289                                                         else {
 290                                                                 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();
 291                                                                 abort = true;
 292                                                         }
 293                                                 }
 294                                         }
 295                                 }
 296                         }
 297
 298                         //check for optional parameter and set defaults
 299                         // ...at some point should added some additional type checking...
 300                         label = validParameter.validFile(parameters, "label", false);
 301                         if (label == "not found") { label = ""; }
 302                         else {
 303                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 304                                 else { allLines = 1;  }
 305                         }
 306
 307                         //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
 308                         calc = validParameter.validFile(parameters, "calc", false);
 309                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 310                         else {
 311                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 312                         }
 313                         m->splitAtDash(calc, Estimators);
 314                         if (m->inUsersGroups("citation", Estimators)) {
 315                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 316                                 //remove citation from list of calcs
 317                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 318                         }
 319
 320                         string temp;
 321                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 322                         m->mothurConvert(temp, freq);
 323
 324                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 325                         m->mothurConvert(temp, abund);
 326
 327                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 328                         m->mothurConvert(temp, size);
 329                 }
 330
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "CollectCommand", "CollectCommand");
 334                 exit(1);
 335         }
 336 }
 337 //**********************************************************************************************************************
 338
 339 int CollectCommand::execute(){
 340         try {
 341
 342                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 343
 344                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 345                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 346
 347                 for (int p = 0; p < inputFileNames.size(); p++) {
 348
 349                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
 350
 351                         if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 352                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 353             map<string, string> variables;
 354             variables["[filename]"] = fileNameRoot;
 355                         //globaldata->inputFileName = inputFileNames[p];
 356
 357                         if (inputFileNames.size() > 1) {
 358                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 359                         }
 360
 361                         ValidCalculators validCalculator;
 362
 363                         for (int i=0; i<Estimators.size(); i++) {
 364                                 if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
 365                                         if (Estimators[i] == "sobs") {
 366                                                 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables))));
 367                                                 outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables));
 368                                         }else if (Estimators[i] == "chao") {
 369                                                 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables))));
 370                                                 outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables));
 371                                         }else if (Estimators[i] == "nseqs") {
 372                                                 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables))));
 373                                                 outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables));
 374                                         }else if (Estimators[i] == "coverage") {
 375                                                 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables))));
 376                                                 outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables));
 377                                         }else if (Estimators[i] == "ace") {
 378                                                 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables))));
 379                                                 outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables));
 380                                         }else if (Estimators[i] == "jack") {
 381                                                 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables))));
 382                                                 outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables));
 383                                         }else if (Estimators[i] == "shannon") {
 384                                                 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables))));
 385                                                 outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables));
 386                                         }else if (Estimators[i] == "shannoneven") {
 387                                                 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables))));
 388                                                 outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables));
 389                                         }else if (Estimators[i] == "npshannon") {
 390                                                 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables))));
 391                                                 outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables));
 392                                         }else if (Estimators[i] == "heip") {
 393                                                 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables))));
 394                                                 outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables));
 395                                         }else if (Estimators[i] == "smithwilson") {
 396                                                 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables))));
 397                                                 outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables));
 398                                         }else if (Estimators[i] == "simpson") {
 399                                                 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables))));
 400                                                 outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables));
 401                                         }else if (Estimators[i] == "simpsoneven") {
 402                                                 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables))));
 403                                                 outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables));
 404                                         }else if (Estimators[i] == "invsimpson") {
 405                                                 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables))));
 406                                                 outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables));
 407                                         }else if (Estimators[i] == "bootstrap") {
 408                                                 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables))));
 409                                                 outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables));
 410                                         }else if (Estimators[i] == "geometric") {
 411                                                 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables))));
 412                                                 outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables));
 413                                         }else if (Estimators[i] == "qstat") {
 414                                                 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables))));
 415                                                 outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables));
 416                                         }else if (Estimators[i] == "logseries") {
 417                                                 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables))));
 418                                                 outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables));
 419                                         }else if (Estimators[i] == "bergerparker") {
 420                                                 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables))));
 421                                                 outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables));
 422                                         }else if (Estimators[i] == "bstick") {
 423                                                 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables))));
 424                                                 outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables));
 425                                         }else if (Estimators[i] == "goodscoverage") {
 426                                                 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables))));
 427                                                 outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables));
 428                                         }else if (Estimators[i] == "efron") {
 429                                                 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables))));
 430                                                 outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables));
 431                                         }else if (Estimators[i] == "boneh") {
 432                                                 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables))));
 433                                                 outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables));
 434                                         }else if (Estimators[i] == "solow") {
 435                                                 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables))));
 436                                                 outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables));
 437                                         }else if (Estimators[i] == "shen") {
 438                                                 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables))));
 439                                                 outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables));
 440                                         }
 441                                 }
 442                         }
 443
 444                         //if the users entered no valid calculators don't execute command
 445                         if (cDisplays.size() == 0) { return 0; }
 446
 447                         input = new InputData(inputFileNames[p], format);
 448                         order = input->getOrderVector();
 449                         string lastLabel = order->getLabel();
 450
 451                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 452                         set<string> processedLabels;
 453                         set<string> userLabels = labels;
 454
 455                         if (m->control_pressed) {
 456                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 457                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 458                                 delete input;
 459                                 delete order;
 460                                 m->clearGroups();
 461                                 return 0;
 462                         }
 463
 464
 465                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 466
 467                                 if (m->control_pressed) {
 468                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 469                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 470                                         delete input;
 471                                         delete order;
 472                                         m->clearGroups();
 473                                         return 0;
 474                                 }
 475
 476
 477                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 478
 479                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 480                                         cCurve = new Collect(order, cDisplays);
 481                                         cCurve->getCurve(freq);
 482                                         delete cCurve;
 483
 484                                         processedLabels.insert(order->getLabel());
 485                                         userLabels.erase(order->getLabel());
 486
 487
 488                                 }
 489                                 //you have a label the user want that is smaller than this label and the last label has not already been processed
 490                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 491                                         string saveLabel = order->getLabel();
 492
 493                                         delete order;
 494                                         order = (input->getOrderVector(lastLabel));
 495
 496                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 497                                         cCurve = new Collect(order, cDisplays);
 498                                         cCurve->getCurve(freq);
 499                                         delete cCurve;
 500
 501
 502                                         processedLabels.insert(order->getLabel());
 503                                         userLabels.erase(order->getLabel());
 504
 505                                         //restore real lastlabel to save below
 506                                         order->setLabel(saveLabel);
 507                                 }
 508
 509                                 lastLabel = order->getLabel();
 510
 511                                 delete order;
 512                                 order = (input->getOrderVector());
 513                         }
 514
 515
 516                         if (m->control_pressed) {
 517                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 518                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 519                                         delete input;
 520                                         m->clearGroups();
 521                                         return 0;
 522                         }
 523
 524                         //output error messages about any remaining user labels
 525                         set<string>::iterator it;
 526                         bool needToRun = false;
 527                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 528                                 m->mothurOut("Your file does not include the label " + *it);
 529                                 if (processedLabels.count(lastLabel) != 1) {
 530                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 531                                         needToRun = true;
 532                                 }else {
 533                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 534                                 }
 535                         }
 536
 537                         //run last label if you need to
 538                         if (needToRun == true)  {
 539                                 if (order != NULL) {    delete order;   }
 540                                 order = (input->getOrderVector(lastLabel));
 541
 542                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 543
 544                                 cCurve = new Collect(order, cDisplays);
 545                                 cCurve->getCurve(freq);
 546                                 delete cCurve;
 547
 548                                 if (m->control_pressed) {
 549                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 550                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 551                                         delete input;
 552                                         delete order;
 553                                         m->clearGroups();
 554                                         return 0;
 555                                 }
 556                                 delete order;
 557                         }
 558
 559                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 560                         cDisplays.clear();
 561                         delete input;
 562                 }
 563
 564                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 565
 566                 m->mothurOutEndLine();
 567                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 568                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 569                 m->mothurOutEndLine();
 570
 571
 572                 return 0;
 573         }
 574         catch(exception& e) {
 575                 m->errorOut(e, "CollectCommand", "execute");
 576                 exit(1);
 577         }
 578 }
 579
 580 //**********************************************************************************************************************
 581 vector<string> CollectCommand::parseSharedFile(string filename) {
 582         try {
 583                 vector<string> filenames;
 584
 585                 map<string, ofstream*> filehandles;
 586                 map<string, ofstream*>::iterator it3;
 587
 588                 input = new InputData(filename, "sharedfile");
 589                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 590
 591                 string sharedFileRoot = m->getRootName(filename);
 592
 593                 //clears file before we start to write to it below
 594                 for (int i=0; i<lookup.size(); i++) {
 595                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 596                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 597                 }
 598
 599                 ofstream* temp;
 600                 for (int i=0; i<lookup.size(); i++) {
 601                         temp = new ofstream;
 602                         filehandles[lookup[i]->getGroup()] = temp;
 603                         groups.push_back(lookup[i]->getGroup());
 604                 }
 605
 606                 while(lookup[0] != NULL) {
 607
 608                         for (int i = 0; i < lookup.size(); i++) {
 609                                 RAbundVector rav = lookup[i]->getRAbundVector();
 610                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 611                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 612                                 (*(filehandles[lookup[i]->getGroup()])).close();
 613                         }
 614
 615                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 616                         lookup = input->getSharedRAbundVectors();
 617                 }
 618
 619                 //free memory
 620                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 621                         delete it3->second;
 622                 }
 623
 624                 delete input;
 625
 626                 return filenames;
 627         }
 628         catch(exception& e) {
 629                 m->errorOut(e, "CollectCommand", "parseSharedFile");
 630                 exit(1);
 631         }
 632 }
 633 //**********************************************************************************************************************
 634