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 #include "shannonrange.h"
  37
  38
  39 //**********************************************************************************************************************
  40 vector<string> CollectCommand::setParameters(){
  41         try {
  42                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
  43                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund);
  44                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund);
  45                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
  46                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  47                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
  48                 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-shannonrange", "", "", "","",true,false,true); parameters.push_back(pcalc);
  49                 CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
  50         CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
  51         CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
  52                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  53                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  54
  55                 vector<string> myArray;
  56                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "CollectCommand", "setParameters");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 string CollectCommand::getHelpString(){
  66         try {
  67                 string helpString = "";
  68                 ValidCalculators validCalculator;
  69                 helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc, alpha and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
  70                 helpString += "The collect.single command should be in the following format: \n";
  71                 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";
  72                 helpString += "collect.single(label=yourLabel, freq=yourFreq, calc=yourEstimators).\n";
  73                 helpString += "Example collect(label=unique-.01-.03, freq=10, calc=sobs-chao-ace-jack).\n";
  74                 helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
  75         helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
  76                 helpString += validCalculator.printCalc("single");
  77                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  78                 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
  79                 return helpString;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "CollectCommand", "getHelpString");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87 string CollectCommand::getOutputPattern(string type) {
  88     try {
  89         string pattern = "";
  90
  91         if (type == "sobs")             {  pattern =  "[filename],sobs";            }
  92         else if (type == "chao")        {  pattern =  "[filename],chao";            }
  93         else if (type == "nseqs")       {  pattern =  "[filename],nseqs";           }
  94         else if (type == "coverage")    {  pattern =  "[filename],coverage";        }
  95         else if (type == "ace")         {  pattern =  "[filename],ace";             }
  96         else if (type == "jack")        {  pattern =  "[filename],jack";            }
  97         else if (type == "shannon")     {  pattern =  "[filename],shannon";         }
  98         else if (type == "shannoneven") {  pattern =  "[filename],shannoneven";     }
  99         else if (type == "shannonrange"){  pattern =  "[filename],shannonrange";    }
 100         else if (type == "npshannon")   {  pattern =  "[filename],npshannon";       }
 101         else if (type == "heip")        {  pattern =  "[filename],heip";            }
 102         else if (type == "smithwilson") {  pattern =  "[filename],smithwilson";     }
 103         else if (type == "simpson")     {  pattern =  "[filename],simpson";         }
 104         else if (type == "simpsoneven") {  pattern =  "[filename],simpsoneven";     }
 105         else if (type == "invsimpson")  {  pattern =  "[filename],invsimpson";      }
 106         else if (type == "bootstrap")   {  pattern =  "[filename],bootstrap";       }
 107         else if (type == "geometric")   {  pattern =  "[filename],geometric";       }
 108         else if (type == "qstat")       {  pattern =  "[filename],qstat";           }
 109         else if (type == "logseries")   {  pattern =  "[filename],logseries";       }
 110         else if (type == "bergerparker") {  pattern =  "[filename],bergerparker";   }
 111         else if (type == "bstick")      {  pattern =  "[filename],bstick";          }
 112         else if (type == "goodscoverage") {  pattern =  "[filename],goodscoverage"; }
 113         else if (type == "efron")       {  pattern =  "[filename],efron";           }
 114         else if (type == "boneh")       {  pattern =  "[filename],boneh";           }
 115         else if (type == "solow")       {  pattern =  "[filename],solow";           }
 116         else if (type == "shen")        {  pattern =  "[filename],shen";            }
 117         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 118
 119         return pattern;
 120     }
 121     catch(exception& e) {
 122         m->errorOut(e, "CollectCommand", "getOutputPattern");
 123         exit(1);
 124     }
 125 }
 126 //**********************************************************************************************************************
 127 CollectCommand::CollectCommand(){
 128         try {
 129                 abort = true; calledHelp = true;
 130                 setParameters();
 131                 vector<string> tempOutNames;
 132                 outputTypes["sobs"] = tempOutNames;
 133                 outputTypes["chao"] = tempOutNames;
 134                 outputTypes["nseqs"] = tempOutNames;
 135                 outputTypes["coverage"] = tempOutNames;
 136                 outputTypes["ace"] = tempOutNames;
 137                 outputTypes["jack"] = tempOutNames;
 138                 outputTypes["shannon"] = tempOutNames;
 139                 outputTypes["shannoneven"] = tempOutNames;
 140         outputTypes["shannonrange"] = tempOutNames;
 141                 outputTypes["npshannon"] = tempOutNames;
 142                 outputTypes["heip"] = tempOutNames;
 143                 outputTypes["smithwilson"] = tempOutNames;
 144                 outputTypes["simpson"] = tempOutNames;
 145                 outputTypes["simpsoneven"] = tempOutNames;
 146                 outputTypes["invsimpson"] = tempOutNames;
 147                 outputTypes["bootstrap"] = tempOutNames;
 148                 outputTypes["geometric"] = tempOutNames;
 149                 outputTypes["qstat"] = tempOutNames;
 150                 outputTypes["logseries"] = tempOutNames;
 151                 outputTypes["bergerparker"] = tempOutNames;
 152                 outputTypes["bstick"] = tempOutNames;
 153                 outputTypes["goodscoverage"] = tempOutNames;
 154                 outputTypes["efron"] = tempOutNames;
 155                 outputTypes["boneh"] = tempOutNames;
 156                 outputTypes["solow"] = tempOutNames;
 157                 outputTypes["shen"] = tempOutNames;
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "CollectCommand", "CollectCommand");
 161                 exit(1);
 162         }
 163 }
 164 //**********************************************************************************************************************
 165 CollectCommand::CollectCommand(string option)  {
 166         try {
 167                 abort = false; calledHelp = false;
 168                 allLines = 1;
 169
 170                 //allow user to run help
 171                 if(option == "help") { help(); calledHelp = true; abort = true; }
 172                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 173
 174                 else {
 175                         vector<string> myArray = setParameters();
 176
 177                         OptionParser parser(option);
 178                         map<string,string> parameters = parser.getParameters();
 179                         map<string,string>::iterator it;
 180
 181                         ValidParameters validParameter;
 182
 183                         //check to make sure all parameters are valid for command
 184                         for (it = parameters.begin(); it != parameters.end(); it++) {
 185                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 186                         }
 187
 188                         //initialize outputTypes
 189                         vector<string> tempOutNames;
 190                         outputTypes["sobs"] = tempOutNames;
 191                         outputTypes["chao"] = tempOutNames;
 192                         outputTypes["nseqs"] = tempOutNames;
 193                         outputTypes["coverage"] = tempOutNames;
 194                         outputTypes["ace"] = tempOutNames;
 195                         outputTypes["jack"] = tempOutNames;
 196                         outputTypes["shannon"] = tempOutNames;
 197                         outputTypes["shannoneven"] = tempOutNames;
 198                         outputTypes["npshannon"] = tempOutNames;
 199                         outputTypes["heip"] = tempOutNames;
 200                         outputTypes["smithwilson"] = tempOutNames;
 201                         outputTypes["simpson"] = tempOutNames;
 202                         outputTypes["simpsoneven"] = tempOutNames;
 203             outputTypes["shannonrange"] = tempOutNames;
 204                         outputTypes["invsimpson"] = tempOutNames;
 205                         outputTypes["bootstrap"] = tempOutNames;
 206                         outputTypes["geometric"] = tempOutNames;
 207                         outputTypes["qstat"] = tempOutNames;
 208                         outputTypes["logseries"] = tempOutNames;
 209                         outputTypes["bergerparker"] = tempOutNames;
 210                         outputTypes["bstick"] = tempOutNames;
 211                         outputTypes["goodscoverage"] = tempOutNames;
 212                         outputTypes["efron"] = tempOutNames;
 213                         outputTypes["boneh"] = tempOutNames;
 214                         outputTypes["solow"] = tempOutNames;
 215                         outputTypes["shen"] = tempOutNames;
 216
 217                         //if the user changes the input directory command factory will send this info to us in the output parameter
 218                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 219                         if (inputDir == "not found"){   inputDir = "";          }
 220                         else {
 221                                 string path;
 222                                 it = parameters.find("shared");
 223                                 //user has given a template file
 224                                 if(it != parameters.end()){
 225                                         path = m->hasPath(it->second);
 226                                         //if the user has not given a path then, add inputdir. else leave path alone.
 227                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 228                                 }
 229
 230                                 it = parameters.find("rabund");
 231                                 //user has given a template file
 232                                 if(it != parameters.end()){
 233                                         path = m->hasPath(it->second);
 234                                         //if the user has not given a path then, add inputdir. else leave path alone.
 235                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 236                                 }
 237
 238                                 it = parameters.find("sabund");
 239                                 //user has given a template file
 240                                 if(it != parameters.end()){
 241                                         path = m->hasPath(it->second);
 242                                         //if the user has not given a path then, add inputdir. else leave path alone.
 243                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 244                                 }
 245
 246                                 it = parameters.find("list");
 247                                 //user has given a template file
 248                                 if(it != parameters.end()){
 249                                         path = m->hasPath(it->second);
 250                                         //if the user has not given a path then, add inputdir. else leave path alone.
 251                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 252                                 }
 253                         }
 254
 255                         //check for required parameters
 256                         listfile = validParameter.validFile(parameters, "list", true);
 257                         if (listfile == "not open") { listfile = ""; abort = true; }
 258                         else if (listfile == "not found") { listfile = ""; }
 259                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 260
 261                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 262                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 263                         else if (sabundfile == "not found") { sabundfile = ""; }
 264                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 265
 266                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 267                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 268                         else if (rabundfile == "not found") { rabundfile = ""; }
 269                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 270
 271                         sharedfile = validParameter.validFile(parameters, "shared", true);
 272                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 273                         else if (sharedfile == "not found") { sharedfile = ""; }
 274                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 275
 276
 277                         //if the user changes the output directory command factory will send this info to us in the output parameter
 278                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 279
 280                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 281                                 //is there are current file available for any of these?
 282                                 //give priority to shared, then list, then rabund, then sabund
 283                                 //if there is a current shared file, use it
 284                                 sharedfile = m->getSharedFile();
 285                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 286                                 else {
 287                                         listfile = m->getListFile();
 288                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 289                                         else {
 290                                                 rabundfile = m->getRabundFile();
 291                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 292                                                 else {
 293                                                         sabundfile = m->getSabundFile();
 294                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 295                                                         else {
 296                                                                 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();
 297                                                                 abort = true;
 298                                                         }
 299                                                 }
 300                                         }
 301                                 }
 302                         }
 303
 304                         //check for optional parameter and set defaults
 305                         // ...at some point should added some additional type checking...
 306                         label = validParameter.validFile(parameters, "label", false);
 307                         if (label == "not found") { label = ""; }
 308                         else {
 309                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 310                                 else { allLines = 1;  }
 311                         }
 312
 313                         //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
 314                         calc = validParameter.validFile(parameters, "calc", false);
 315                         if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 316                         else {
 317                                  if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 318                         }
 319                         m->splitAtDash(calc, Estimators);
 320                         if (m->inUsersGroups("citation", Estimators)) {
 321                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 322                                 //remove citation from list of calcs
 323                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 324                         }
 325
 326                         string temp;
 327                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 328                         m->mothurConvert(temp, freq);
 329
 330             temp = validParameter.validFile(parameters, "alpha", false);                if (temp == "not found") { temp = "1"; }
 331                         m->mothurConvert(temp, alpha);
 332
 333             if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; }
 334
 335                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 336                         m->mothurConvert(temp, abund);
 337
 338                         temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
 339                         m->mothurConvert(temp, size);
 340                 }
 341
 342         }
 343         catch(exception& e) {
 344                 m->errorOut(e, "CollectCommand", "CollectCommand");
 345                 exit(1);
 346         }
 347 }
 348 //**********************************************************************************************************************
 349
 350 int CollectCommand::execute(){
 351         try {
 352
 353                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 354
 355                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 356                 else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
 357
 358                 for (int p = 0; p < inputFileNames.size(); p++) {
 359
 360                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
 361
 362                         if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 363                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 364             map<string, string> variables;
 365             variables["[filename]"] = fileNameRoot;
 366                         //globaldata->inputFileName = inputFileNames[p];
 367
 368                         if (inputFileNames.size() > 1) {
 369                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 370                         }
 371
 372                         ValidCalculators validCalculator;
 373
 374                         for (int i=0; i<Estimators.size(); i++) {
 375                                 if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
 376                                         if (Estimators[i] == "sobs") {
 377                                                 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables))));
 378                                                 outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables));
 379                                         }else if (Estimators[i] == "chao") {
 380                                                 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables))));
 381                                                 outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables));
 382                                         }else if (Estimators[i] == "nseqs") {
 383                                                 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables))));
 384                                                 outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables));
 385                                         }else if (Estimators[i] == "coverage") {
 386                                                 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables))));
 387                                                 outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables));
 388                                         }else if (Estimators[i] == "ace") {
 389                                                 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables))));
 390                                                 outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables));
 391                                         }else if (Estimators[i] == "jack") {
 392                                                 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables))));
 393                                                 outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables));
 394                                         }else if (Estimators[i] == "shannon") {
 395                                                 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables))));
 396                                                 outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables));
 397                                         }else if (Estimators[i] == "shannoneven") {
 398                                                 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables))));
 399                                                 outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables));
 400                     }else if (Estimators[i] == "shannonrange") {
 401                             cDisplays.push_back(new CollectDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("shannonrange", variables))));
 402                             outputNames.push_back(getOutputFileName("shannonrange", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannonrange", variables));
 403                                         }else if (Estimators[i] == "npshannon") {
 404                                                 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables))));
 405                                                 outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables));
 406                                         }else if (Estimators[i] == "heip") {
 407                                                 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables))));
 408                                                 outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables));
 409                                         }else if (Estimators[i] == "smithwilson") {
 410                                                 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables))));
 411                                                 outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables));
 412                                         }else if (Estimators[i] == "simpson") {
 413                                                 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables))));
 414                                                 outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables));
 415                                         }else if (Estimators[i] == "simpsoneven") {
 416                                                 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables))));
 417                                                 outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables));
 418                                         }else if (Estimators[i] == "invsimpson") {
 419                                                 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables))));
 420                                                 outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables));
 421                                         }else if (Estimators[i] == "bootstrap") {
 422                                                 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables))));
 423                                                 outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables));
 424                                         }else if (Estimators[i] == "geometric") {
 425                                                 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables))));
 426                                                 outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables));
 427                                         }else if (Estimators[i] == "qstat") {
 428                                                 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables))));
 429                                                 outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables));
 430                                         }else if (Estimators[i] == "logseries") {
 431                                                 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables))));
 432                                                 outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables));
 433                                         }else if (Estimators[i] == "bergerparker") {
 434                                                 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables))));
 435                                                 outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables));
 436                                         }else if (Estimators[i] == "bstick") {
 437                                                 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables))));
 438                                                 outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables));
 439                                         }else if (Estimators[i] == "goodscoverage") {
 440                                                 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables))));
 441                                                 outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables));
 442                                         }else if (Estimators[i] == "efron") {
 443                                                 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables))));
 444                                                 outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables));
 445                                         }else if (Estimators[i] == "boneh") {
 446                                                 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables))));
 447                                                 outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables));
 448                                         }else if (Estimators[i] == "solow") {
 449                                                 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables))));
 450                                                 outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables));
 451                                         }else if (Estimators[i] == "shen") {
 452                                                 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables))));
 453                                                 outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables));
 454                                         }
 455                                 }
 456                         }
 457
 458                         //if the users entered no valid calculators don't execute command
 459                         if (cDisplays.size() == 0) { return 0; }
 460
 461                         input = new InputData(inputFileNames[p], format);
 462                         order = input->getOrderVector();
 463                         string lastLabel = order->getLabel();
 464
 465                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 466                         set<string> processedLabels;
 467                         set<string> userLabels = labels;
 468
 469                         if (m->control_pressed) {
 470                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 471                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 472                                 delete input;
 473                                 delete order;
 474                                 m->clearGroups();
 475                                 return 0;
 476                         }
 477
 478
 479                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 480
 481                                 if (m->control_pressed) {
 482                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 483                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 484                                         delete input;
 485                                         delete order;
 486                                         m->clearGroups();
 487                                         return 0;
 488                                 }
 489
 490
 491                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 492
 493                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 494                                         cCurve = new Collect(order, cDisplays);
 495                                         cCurve->getCurve(freq);
 496                                         delete cCurve;
 497
 498                                         processedLabels.insert(order->getLabel());
 499                                         userLabels.erase(order->getLabel());
 500
 501
 502                                 }
 503                                 //you have a label the user want that is smaller than this label and the last label has not already been processed
 504                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 505                                         string saveLabel = order->getLabel();
 506
 507                                         delete order;
 508                                         order = (input->getOrderVector(lastLabel));
 509
 510                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 511                                         cCurve = new Collect(order, cDisplays);
 512                                         cCurve->getCurve(freq);
 513                                         delete cCurve;
 514
 515
 516                                         processedLabels.insert(order->getLabel());
 517                                         userLabels.erase(order->getLabel());
 518
 519                                         //restore real lastlabel to save below
 520                                         order->setLabel(saveLabel);
 521                                 }
 522
 523                                 lastLabel = order->getLabel();
 524
 525                                 delete order;
 526                                 order = (input->getOrderVector());
 527                         }
 528
 529
 530                         if (m->control_pressed) {
 531                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 532                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 533                                         delete input;
 534                                         m->clearGroups();
 535                                         return 0;
 536                         }
 537
 538                         //output error messages about any remaining user labels
 539                         set<string>::iterator it;
 540                         bool needToRun = false;
 541                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 542                                 m->mothurOut("Your file does not include the label " + *it);
 543                                 if (processedLabels.count(lastLabel) != 1) {
 544                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 545                                         needToRun = true;
 546                                 }else {
 547                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 548                                 }
 549                         }
 550
 551                         //run last label if you need to
 552                         if (needToRun == true)  {
 553                                 if (order != NULL) {    delete order;   }
 554                                 order = (input->getOrderVector(lastLabel));
 555
 556                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 557
 558                                 cCurve = new Collect(order, cDisplays);
 559                                 cCurve->getCurve(freq);
 560                                 delete cCurve;
 561
 562                                 if (m->control_pressed) {
 563                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 564                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
 565                                         delete input;
 566                                         delete order;
 567                                         m->clearGroups();
 568                                         return 0;
 569                                 }
 570                                 delete order;
 571                         }
 572
 573                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 574                         cDisplays.clear();
 575                         delete input;
 576                 }
 577
 578                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 579
 580                 m->mothurOutEndLine();
 581                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 582                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 583                 m->mothurOutEndLine();
 584
 585
 586                 return 0;
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "CollectCommand", "execute");
 590                 exit(1);
 591         }
 592 }
 593
 594 //**********************************************************************************************************************
 595 vector<string> CollectCommand::parseSharedFile(string filename) {
 596         try {
 597                 vector<string> filenames;
 598
 599                 map<string, ofstream*> filehandles;
 600                 map<string, ofstream*>::iterator it3;
 601
 602                 input = new InputData(filename, "sharedfile");
 603                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 604
 605                 string sharedFileRoot = m->getRootName(filename);
 606
 607                 //clears file before we start to write to it below
 608                 for (int i=0; i<lookup.size(); i++) {
 609                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 610                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 611                 }
 612
 613                 ofstream* temp;
 614                 for (int i=0; i<lookup.size(); i++) {
 615                         temp = new ofstream;
 616                         filehandles[lookup[i]->getGroup()] = temp;
 617                         groups.push_back(lookup[i]->getGroup());
 618                 }
 619
 620                 while(lookup[0] != NULL) {
 621
 622                         for (int i = 0; i < lookup.size(); i++) {
 623                                 RAbundVector rav = lookup[i]->getRAbundVector();
 624                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 625                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 626                                 (*(filehandles[lookup[i]->getGroup()])).close();
 627                         }
 628
 629                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 630                         lookup = input->getSharedRAbundVectors();
 631                 }
 632
 633                 //free memory
 634                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 635                         delete it3->second;
 636                 }
 637
 638                 delete input;
 639
 640                 return filenames;
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "CollectCommand", "parseSharedFile");
 644                 exit(1);
 645         }
 646 }
 647 //**********************************************************************************************************************
 648