collectsharedcommand.cpp

   1 /*
   2  *  collectsharedcommand.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 "collectsharedcommand.h"
  11 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22 #include "sharedkstest.h"
  23 #include "whittaker.h"
  24 #include "sharednseqs.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "whittaker.h"
  34 #include "odum.h"
  35 #include "canberra.h"
  36 #include "structeuclidean.h"
  37 #include "structchord.h"
  38 #include "hellinger.h"
  39 #include "manhattan.h"
  40 #include "structpearson.h"
  41 #include "soergel.h"
  42 #include "spearman.h"
  43 #include "structkulczynski.h"
  44 #include "structchi2.h"
  45 #include "speciesprofile.h"
  46 #include "hamming.h"
  47 #include "gower.h"
  48 #include "memchi2.h"
  49 #include "memchord.h"
  50 #include "memeuclidean.h"
  51 #include "mempearson.h"
  52 #include "sharedjsd.h"
  53
  54
  55 //**********************************************************************************************************************
  56 vector<string> CollectSharedCommand::setParameters(){
  57         try {
  58                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
  59                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  60                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
  61                 CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
  62                 CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
  63                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  64                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  65                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  66
  67                 vector<string> myArray;
  68                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  69                 return myArray;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "CollectSharedCommand", "setParameters");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77 string CollectSharedCommand::getHelpString(){
  78         try {
  79                 string helpString = "";
  80                 ValidCalculators validCalculator;
  81                 helpString += "The collect.shared command parameters are shared, label, freq, calc and groups.  shared is required if there is no current sharedfile. \n";
  82                 helpString += "The collect.shared command should be in the following format: \n";
  83                 helpString += "collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n";
  84                 helpString += "Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
  85                 helpString += "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n";
  86                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  87                 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";
  88                 helpString += validCalculator.printCalc("shared");
  89                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  90                 helpString += "The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
  91                 helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
  92                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
  93                 helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedfile).\n";
  94                 return helpString;
  95         }
  96         catch(exception& e) {
  97                 m->errorOut(e, "CollectSharedCommand", "getHelpString");
  98                 exit(1);
  99         }
 100 }
 101 //**********************************************************************************************************************
 102 string CollectSharedCommand::getOutputPattern(string type) {
 103     try {
 104         string pattern = "";
 105
 106         if (type == "sharedchao")               {  pattern =  "[filename],shared.chao";     }
 107         else if (type == "sharedsobs")          {  pattern =  "[filename],shared.sobs";     }
 108         else if (type == "sharedace")           {  pattern =  "[filename],shared.ace";      }
 109         else if (type == "jabund")              {  pattern =  "[filename],jabund";          }
 110         else if (type == "sorabund")            {  pattern =  "[filename],sorabund";        }
 111         else if (type == "jclass")              {  pattern =  "[filename],jclass";          }
 112         else if (type == "sorclass")            {  pattern =  "[filename],sorclass";        }
 113         else if (type == "jest")                {  pattern =  "[filename],jest";            }
 114         else if (type == "sorest")              {  pattern =  "[filename],sorest";          }
 115         else if (type == "thetayc")             {  pattern =  "[filename],thetayc";         }
 116         else if (type == "thetan")              {  pattern =  "[filename],thetan";          }
 117         else if (type == "kstest")              {  pattern =  "[filename],kstest";          }
 118         else if (type == "whittaker")           {  pattern =  "[filename],whittaker";       }
 119         else if (type == "sharednseqs")         {  pattern =  "[filename],shared.nseqs";    }
 120         else if (type == "ochiai")              {  pattern =  "[filename],ochiai";          }
 121         else if (type == "anderberg")           {  pattern =  "[filename],anderberg";       }
 122         else if (type == "kulczynski")          {  pattern =  "[filename],kulczynski";      }
 123         else if (type == "kulczynskicody")      {  pattern =  "[filename],kulczynskicody";  }
 124         else if (type == "lennon")              {  pattern =  "[filename],lennon";          }
 125         else if (type == "morisitahorn")        {  pattern =  "[filename],morisitahorn";    }
 126         else if (type == "braycurtis")          {  pattern =  "[filename],braycurtis";      }
 127         else if (type == "odum")                {  pattern =  "[filename],odum";            }
 128         else if (type == "canberra")            {  pattern =  "[filename],canberra";        }
 129         else if (type == "structeuclidean")     {  pattern =  "[filename],structeuclidean"; }
 130         else if (type == "structchord")         {  pattern =  "[filename],structchord";     }
 131         else if (type == "hellinger")           {  pattern =  "[filename],hellinger";       }
 132         else if (type == "manhattan")           {  pattern =  "[filename],manhattan";       }
 133         else if (type == "structpearson")       {  pattern =  "[filename],structpearson";   }
 134         else if (type == "soergel")             {  pattern =  "[filename],soergel";         }
 135         else if (type == "spearman")            {  pattern =  "[filename],spearman";        }
 136         else if (type == "structkulczynski")    {  pattern =  "[filename],structkulczynski";}
 137         else if (type == "structchi2")          {  pattern =  "[filename],structchi2";      }
 138         else if (type == "speciesprofile")      {  pattern =  "[filename],speciesprofile";  }
 139         else if (type == "hamming")             {  pattern =  "[filename],hamming";         }
 140         else if (type == "gower")               {  pattern =  "[filename],gower";           }
 141         else if (type == "memchi2")             {  pattern =  "[filename],memchi2";         }
 142         else if (type == "memchord")            {  pattern =  "[filename],memchord";        }
 143         else if (type == "memeuclidean")        {  pattern =  "[filename],memeuclidean";    }
 144         else if (type == "mempearson")          {  pattern =  "[filename],mempearson";      }
 145         else if (type == "jsd")                 {  pattern =  "[filename],jsd";             }
 146         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 147
 148         return pattern;
 149     }
 150     catch(exception& e) {
 151         m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
 152         exit(1);
 153     }
 154 }
 155
 156 //**********************************************************************************************************************
 157 CollectSharedCommand::CollectSharedCommand(){
 158         try {
 159                 abort = true; calledHelp = true;
 160                 setParameters();
 161                 vector<string> tempOutNames;
 162                 outputTypes["sharedchao"] = tempOutNames;
 163                 outputTypes["sharedsobs"] = tempOutNames;
 164                 outputTypes["sharedace"] = tempOutNames;
 165                 outputTypes["jabund"] = tempOutNames;
 166                 outputTypes["sorabund"] = tempOutNames;
 167                 outputTypes["jclass"] = tempOutNames;
 168                 outputTypes["sorclass"] = tempOutNames;
 169                 outputTypes["jest"] = tempOutNames;
 170                 outputTypes["sorest"] = tempOutNames;
 171                 outputTypes["thetayc"] = tempOutNames;
 172                 outputTypes["thetan"] = tempOutNames;
 173                 outputTypes["kstest"] = tempOutNames;
 174                 outputTypes["whittaker"] = tempOutNames;
 175                 outputTypes["sharednseqs"] = tempOutNames;
 176                 outputTypes["ochiai"] = tempOutNames;
 177                 outputTypes["anderberg"] = tempOutNames;
 178                 outputTypes["kulczynski"] = tempOutNames;
 179                 outputTypes["kulczynskicody"] = tempOutNames;
 180                 outputTypes["lennon"] = tempOutNames;
 181                 outputTypes["morisitahorn"] = tempOutNames;
 182                 outputTypes["braycurtis"] = tempOutNames;
 183                 outputTypes["odum"] = tempOutNames;
 184                 outputTypes["canberra"] = tempOutNames;
 185                 outputTypes["structeuclidean"] = tempOutNames;
 186                 outputTypes["structchord"] = tempOutNames;
 187                 outputTypes["hellinger"] = tempOutNames;
 188                 outputTypes["manhattan"] = tempOutNames;
 189                 outputTypes["structpearson"] = tempOutNames;
 190                 outputTypes["soergel"] = tempOutNames;
 191                 outputTypes["spearman"] = tempOutNames;
 192                 outputTypes["structkulczynski"] = tempOutNames;
 193                 outputTypes["structchi2"] = tempOutNames;
 194                 outputTypes["speciesprofile"] = tempOutNames;
 195                 outputTypes["hamming"] = tempOutNames;
 196                 outputTypes["gower"] = tempOutNames;
 197                 outputTypes["memchi2"] = tempOutNames;
 198                 outputTypes["memchord"] = tempOutNames;
 199                 outputTypes["memeuclidean"] = tempOutNames;
 200                 outputTypes["mempearson"] = tempOutNames;
 201         outputTypes["jsd"] = tempOutNames;
 202
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 206                 exit(1);
 207         }
 208 }
 209 //**********************************************************************************************************************
 210 CollectSharedCommand::CollectSharedCommand(string option)  {
 211         try {
 212                 abort = false; calledHelp = false;
 213                 allLines = 1;
 214
 215                 //allow user to run help
 216                 if(option == "help") { help(); abort = true; calledHelp = true; }
 217                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 218
 219                 else {
 220                         vector<string> myArray = setParameters();
 221
 222                         OptionParser parser(option);
 223                         map<string,string> parameters=parser.getParameters();
 224                         map<string,string>::iterator it;
 225
 226                         ValidParameters validParameter;
 227
 228                         //check to make sure all parameters are valid for command
 229                         for (it = parameters.begin(); it != parameters.end(); it++) {
 230                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 231                         }
 232
 233                         //initialize outputTypes
 234                         vector<string> tempOutNames;
 235                         outputTypes["sharedchao"] = tempOutNames;
 236                         outputTypes["sharedsobs"] = tempOutNames;
 237                         outputTypes["sharedace"] = tempOutNames;
 238                         outputTypes["jabund"] = tempOutNames;
 239                         outputTypes["sorabund"] = tempOutNames;
 240                         outputTypes["jclass"] = tempOutNames;
 241                         outputTypes["sorclass"] = tempOutNames;
 242                         outputTypes["jest"] = tempOutNames;
 243                         outputTypes["sorest"] = tempOutNames;
 244                         outputTypes["thetayc"] = tempOutNames;
 245                         outputTypes["thetan"] = tempOutNames;
 246                         outputTypes["kstest"] = tempOutNames;
 247                         outputTypes["whittaker"] = tempOutNames;
 248                         outputTypes["sharednseqs"] = tempOutNames;
 249                         outputTypes["ochiai"] = tempOutNames;
 250                         outputTypes["anderberg"] = tempOutNames;
 251                         outputTypes["kulczynski"] = tempOutNames;
 252                         outputTypes["kulczynskicody"] = tempOutNames;
 253                         outputTypes["lennon"] = tempOutNames;
 254                         outputTypes["morisitahorn"] = tempOutNames;
 255                         outputTypes["braycurtis"] = tempOutNames;
 256                         outputTypes["odum"] = tempOutNames;
 257                         outputTypes["canberra"] = tempOutNames;
 258                         outputTypes["structeuclidean"] = tempOutNames;
 259                         outputTypes["structchord"] = tempOutNames;
 260                         outputTypes["hellinger"] = tempOutNames;
 261                         outputTypes["manhattan"] = tempOutNames;
 262                         outputTypes["structpearson"] = tempOutNames;
 263                         outputTypes["soergel"] = tempOutNames;
 264                         outputTypes["spearman"] = tempOutNames;
 265                         outputTypes["structkulczynski"] = tempOutNames;
 266                         outputTypes["speciesprofile"] = tempOutNames;
 267                         outputTypes["structchi2"] = tempOutNames;
 268                         outputTypes["hamming"] = tempOutNames;
 269                         outputTypes["gower"] = tempOutNames;
 270                         outputTypes["memchi2"] = tempOutNames;
 271                         outputTypes["memchord"] = tempOutNames;
 272                         outputTypes["memeuclidean"] = tempOutNames;
 273                         outputTypes["mempearson"] = tempOutNames;
 274             outputTypes["jsd"] = tempOutNames;
 275
 276
 277                         //if the user changes the input directory command factory will send this info to us in the output parameter
 278                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 279                         if (inputDir == "not found"){   inputDir = "";          }
 280                         else {
 281                                 string path;
 282                                 it = parameters.find("shared");
 283                                 //user has given a template file
 284                                 if(it != parameters.end()){
 285                                         path = m->hasPath(it->second);
 286                                         //if the user has not given a path then, add inputdir. else leave path alone.
 287                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 288                                 }
 289                         }
 290
 291                         //get shared file
 292                         sharedfile = validParameter.validFile(parameters, "shared", true);
 293                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 294                         else if (sharedfile == "not found") {
 295                                 //if there is a current shared file, use it
 296                                 sharedfile = m->getSharedFile();
 297                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 298                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 299                         }else { m->setSharedFile(sharedfile); }
 300
 301
 302                         //if the user changes the output directory command factory will send this info to us in the output parameter
 303                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 304
 305                         //check for optional parameter and set defaults
 306                         // ...at some point should added some additional type checking..
 307                         label = validParameter.validFile(parameters, "label", false);
 308                         if (label == "not found") { label = ""; }
 309                         else {
 310                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 311                                 else { allLines = 1;  }
 312                         }
 313
 314                         calc = validParameter.validFile(parameters, "calc", false);
 315                         if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 316                         else {
 317                                  if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 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                         groups = validParameter.validFile(parameters, "groups", false);
 327                         if (groups == "not found") { groups = ""; }
 328                         else {
 329                                 m->splitAtDash(groups, Groups);
 330                         }
 331                         m->setGroups(Groups);
 332
 333                         string temp;
 334                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 335                         m->mothurConvert(temp, freq);
 336
 337                         temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
 338                         all = m->isTrue(temp);
 339
 340                         if (abort == false) {
 341
 342                                 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 343                                 map<string, string> variables;
 344                 variables["[filename]"] = fileNameRoot;
 345
 346                                 ValidCalculators validCalculator;
 347
 348                                 for (int i=0; i<Estimators.size(); i++) {
 349                                         if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
 350                                                 if (Estimators[i] == "sharedchao") {
 351                                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(getOutputFileName("sharedchao", variables))));
 352                                                         outputNames.push_back(getOutputFileName("sharedchao", variables)); outputTypes["sharedchao"].push_back(getOutputFileName("sharedchao", variables));
 353                                                 }else if (Estimators[i] == "sharedsobs") {
 354                                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(getOutputFileName("sharedsobs", variables))));
 355                                                         outputNames.push_back(getOutputFileName("sharedsobs", variables)); outputTypes["sharedsobs"].push_back(getOutputFileName("sharedsobs", variables));
 356                                                 }else if (Estimators[i] == "sharedace") {
 357                                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(getOutputFileName("sharedace", variables))));
 358                                                         outputNames.push_back(getOutputFileName("sharedace", variables)); outputTypes["sharedace"].push_back(getOutputFileName("sharedace", variables));
 359                                                 }else if (Estimators[i] == "jabund") {
 360                                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(getOutputFileName("jabund", variables))));
 361                                                         outputNames.push_back(getOutputFileName("jabund", variables)); outputTypes["jabund"].push_back(getOutputFileName("jabund", variables));
 362                                                 }else if (Estimators[i] == "sorabund") {
 363                                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(getOutputFileName("sorabund", variables))));
 364                                                         outputNames.push_back(getOutputFileName("sorabund", variables)); outputTypes["sorabund"].push_back(getOutputFileName("sorabund", variables));
 365                                                 }else if (Estimators[i] == "jclass") {
 366                                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(getOutputFileName("jclass", variables))));
 367                                                         outputNames.push_back(getOutputFileName("jclass", variables)); outputTypes["jclass"].push_back(getOutputFileName("jclass", variables));
 368                                                 }else if (Estimators[i] == "sorclass") {
 369                                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(getOutputFileName("sorclass", variables))));
 370                                                         outputNames.push_back(getOutputFileName("sorclass", variables)); outputTypes["sorclass"].push_back(getOutputFileName("sorclass", variables));
 371                                                 }else if (Estimators[i] == "jest") {
 372                                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(getOutputFileName("jest", variables))));
 373                                                         outputNames.push_back(getOutputFileName("jest", variables)); outputTypes["jest"].push_back(getOutputFileName("jest", variables));
 374                                                 }else if (Estimators[i] == "sorest") {
 375                                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(getOutputFileName("sorest", variables))));
 376                                                         outputNames.push_back(getOutputFileName("sorest", variables)); outputTypes["sorest"].push_back(getOutputFileName("sorest", variables));
 377                                                 }else if (Estimators[i] == "thetayc") {
 378                                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(getOutputFileName("thetayc", variables))));
 379                                                         outputNames.push_back(getOutputFileName("thetayc", variables)); outputTypes["thetayc"].push_back(getOutputFileName("thetayc", variables));
 380                                                 }else if (Estimators[i] == "thetan") {
 381                                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(getOutputFileName("thetan", variables))));
 382                                                         outputNames.push_back(getOutputFileName("thetan", variables)); outputTypes["thetan"].push_back(getOutputFileName("thetan", variables));
 383                                                 }else if (Estimators[i] == "kstest") {
 384                                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(getOutputFileName("kstest", variables))));
 385                                                         outputNames.push_back(getOutputFileName("kstest", variables)); outputTypes["kstest"].push_back(getOutputFileName("kstest", variables));
 386                                                 }else if (Estimators[i] == "whittaker") {
 387                                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(getOutputFileName("whittaker", variables))));
 388                                                         outputNames.push_back(getOutputFileName("whittaker", variables)); outputTypes["whittaker"].push_back(getOutputFileName("whittaker", variables));
 389                                                 }else if (Estimators[i] == "sharednseqs") {
 390                                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(getOutputFileName("sharednseqs", variables))));
 391                                                         outputNames.push_back(getOutputFileName("sharednseqs", variables)); outputTypes["shared.nseqs"].push_back(getOutputFileName("sharednseqs", variables));
 392                                                 }else if (Estimators[i] == "ochiai") {
 393                                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(getOutputFileName("ochiai", variables))));
 394                                                         outputNames.push_back(getOutputFileName("ochiai", variables)); outputTypes["ochiai"].push_back(getOutputFileName("ochiai", variables));
 395                                                 }else if (Estimators[i] == "anderberg") {
 396                                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(getOutputFileName("anderberg", variables))));
 397                                                         outputNames.push_back(getOutputFileName("anderberg", variables)); outputTypes["anderberg"].push_back(getOutputFileName("anderberg", variables));
 398                                                 }else if (Estimators[i] == "kulczynski") {
 399                                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(getOutputFileName("kulczynski", variables))));
 400                                                         outputNames.push_back(getOutputFileName("kulczynski", variables)); outputTypes["kulczynski"].push_back(getOutputFileName("kulczynski", variables));
 401                                                 }else if (Estimators[i] == "kulczynskicody") {
 402                                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(getOutputFileName("kulczynskicody", variables))));
 403                                                         outputNames.push_back(getOutputFileName("kulczynskicody", variables)); outputTypes["kulczynskicody"].push_back(getOutputFileName("kulczynskicody", variables));
 404                                                 }else if (Estimators[i] == "lennon") {
 405                                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(getOutputFileName("lennon", variables))));
 406                                                         outputNames.push_back(getOutputFileName("lennon", variables)); outputTypes["lennon"].push_back(getOutputFileName("lennon", variables));
 407                                                 }else if (Estimators[i] == "morisitahorn") {
 408                                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(getOutputFileName("morisitahorn", variables))));
 409                                                         outputNames.push_back(getOutputFileName("morisitahorn", variables)); outputTypes["morisitahorn"].push_back(getOutputFileName("morisitahorn", variables));
 410                                                 }else if (Estimators[i] == "braycurtis") {
 411                                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(getOutputFileName("braycurtis", variables))));
 412                                                         outputNames.push_back(getOutputFileName("braycurtis", variables)); outputTypes["braycurtis"].push_back(getOutputFileName("braycurtis", variables));
 413                                                 }else if (Estimators[i] == "odum") {
 414                                                         cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(getOutputFileName("odum", variables))));
 415                                                         outputNames.push_back(getOutputFileName("odum", variables)); outputTypes["odum"].push_back(getOutputFileName("odum", variables));
 416                                                 }else if (Estimators[i] == "canberra") {
 417                                                         cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(getOutputFileName("canberra", variables))));
 418                                                         outputNames.push_back(getOutputFileName("canberra", variables)); outputTypes["canberra"].push_back(getOutputFileName("canberra", variables));
 419                                                 }else if (Estimators[i] == "structeuclidean") {
 420                                                         cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(getOutputFileName("structeuclidean", variables))));
 421                                                         outputNames.push_back(getOutputFileName("structeuclidean", variables)); outputTypes["structeuclidean"].push_back(getOutputFileName("structeuclidean", variables));
 422                                                 }else if (Estimators[i] == "structchord") {
 423                                                         cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(getOutputFileName("structchord", variables))));
 424                                                         outputNames.push_back(getOutputFileName("structchord", variables)); outputTypes["structchord"].push_back(getOutputFileName("structchord", variables));
 425                                                 }else if (Estimators[i] == "hellinger") {
 426                                                         cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(getOutputFileName("hellinger", variables))));
 427                                                         outputNames.push_back(getOutputFileName("hellinger", variables)); outputTypes["hellinger"].push_back(getOutputFileName("hellinger", variables));
 428                                                 }else if (Estimators[i] == "manhattan") {
 429                                                         cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(getOutputFileName("manhattan", variables))));
 430                                                         outputNames.push_back(getOutputFileName("manhattan", variables)); outputTypes["manhattan"].push_back(getOutputFileName("manhattan", variables));
 431                                                 }else if (Estimators[i] == "structpearson") {
 432                                                         cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(getOutputFileName("structpearson", variables))));
 433                                                         outputNames.push_back(getOutputFileName("structpearson", variables)); outputTypes["structpearson"].push_back(getOutputFileName("structpearson", variables));
 434                                                 }else if (Estimators[i] == "soergel") {
 435                                                         cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(getOutputFileName("soergel", variables))));
 436                                                         outputNames.push_back(getOutputFileName("soergel", variables)); outputTypes["soergel"].push_back(getOutputFileName("soergel", variables));
 437                                                 }else if (Estimators[i] == "spearman") {
 438                                                         cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(getOutputFileName("spearman", variables))));
 439                                                         outputNames.push_back(getOutputFileName("spearman", variables)); outputTypes["spearman"].push_back(getOutputFileName("spearman", variables));
 440                                                 }else if (Estimators[i] == "structkulczynski") {
 441                                                         cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(getOutputFileName("structkulczynski", variables))));
 442                                                         outputNames.push_back(getOutputFileName("structkulczynski", variables)); outputTypes["structkulczynski"].push_back(getOutputFileName("structkulczynski", variables));
 443                                                 }else if (Estimators[i] == "speciesprofile") {
 444                                                         cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(getOutputFileName("speciesprofile", variables))));
 445                                                         outputNames.push_back(getOutputFileName("speciesprofile", variables)); outputTypes["speciesprofile"].push_back(getOutputFileName("speciesprofile", variables));
 446                                                 }else if (Estimators[i] == "hamming") {
 447                                                         cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(getOutputFileName("hamming", variables))));
 448                                                         outputNames.push_back(getOutputFileName("hamming", variables)); outputTypes["hamming"].push_back(getOutputFileName("hamming", variables));
 449                                                 }else if (Estimators[i] == "structchi2") {
 450                                                         cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(getOutputFileName("structchi2", variables))));
 451                                                         outputNames.push_back(getOutputFileName("structchi2", variables)); outputTypes["structchi2"].push_back(getOutputFileName("structchi2", variables));
 452                                                 }else if (Estimators[i] == "gower") {
 453                                                         cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(getOutputFileName("gower", variables))));
 454                                                         outputNames.push_back(getOutputFileName("gower", variables)); outputTypes["gower"].push_back(getOutputFileName("gower", variables));
 455                                                 }else if (Estimators[i] == "memchi2") {
 456                                                         cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(getOutputFileName("memchi2", variables))));
 457                                                         outputNames.push_back(getOutputFileName("memchi2", variables)); outputTypes["memchi2"].push_back(getOutputFileName("memchi2", variables));
 458                                                 }else if (Estimators[i] == "memchord") {
 459                                                         cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(getOutputFileName("memchord", variables))));
 460                                                         outputNames.push_back(getOutputFileName("memchord", variables)); outputTypes["memchord"].push_back(getOutputFileName("memchord", variables));
 461                                                 }else if (Estimators[i] == "memeuclidean") {
 462                                                         cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(getOutputFileName("memeuclidean", variables))));
 463                                                         outputNames.push_back(getOutputFileName("memeuclidean", variables)); outputTypes["memeuclidean"].push_back(getOutputFileName("memeuclidean", variables));
 464                                                 }else if (Estimators[i] == "mempearson") {
 465                                                         cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
 466                                                         outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
 467                                                 }else if (Estimators[i] == "jsd") {
 468                                                         cDisplays.push_back(new CollectDisplay(new JSD(), new SharedOneColumnFile(getOutputFileName("jsd", variables))));
 469                                                         outputNames.push_back(getOutputFileName("jsd", variables)); outputTypes["jsd"].push_back(getOutputFileName("jsd", variables));
 470                                                 }
 471
 472                                         }
 473                                 }
 474                         }
 475                 }
 476
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 480                 exit(1);
 481         }
 482 }
 483 //**********************************************************************************************************************
 484 CollectSharedCommand::~CollectSharedCommand(){}
 485 //**********************************************************************************************************************
 486
 487 int CollectSharedCommand::execute(){
 488         try {
 489
 490                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 491
 492                 //if the users entered no valid calculators don't execute command
 493                 if (cDisplays.size() == 0) { return 0; }
 494                 for(int i=0;i<cDisplays.size();i++){    cDisplays[i]->setAll(all);      }
 495
 496                 input = new InputData(sharedfile, "sharedfile");
 497                 order = input->getSharedOrderVector();
 498                 string lastLabel = order->getLabel();
 499
 500                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 501                 set<string> processedLabels;
 502                 set<string> userLabels = labels;
 503
 504                 //set users groups
 505                 SharedUtil* util = new SharedUtil();
 506                 Groups = m->getGroups();
 507                 vector<string> allGroups = m->getAllGroups();
 508                 util->setGroups(Groups, allGroups, "collect");
 509                 m->setGroups(Groups);
 510                 m->setAllGroups(allGroups);
 511                 delete util;
 512
 513                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 514                         if (m->control_pressed) {
 515                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 516                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 517                                         delete order; delete input;
 518                                         m->clearGroups();
 519                                         return 0;
 520                         }
 521
 522                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 523
 524                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 525                                 //create collectors curve
 526                                 cCurve = new Collect(order, cDisplays);
 527                                 cCurve->getSharedCurve(freq);
 528                                 delete cCurve;
 529
 530                                 processedLabels.insert(order->getLabel());
 531                                 userLabels.erase(order->getLabel());
 532                         }
 533
 534                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 535                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 536                                 string saveLabel = order->getLabel();
 537
 538                                 delete order;
 539                                 order = input->getSharedOrderVector(lastLabel);
 540
 541                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 542                                 //create collectors curve
 543                                 cCurve = new Collect(order, cDisplays);
 544                                 cCurve->getSharedCurve(freq);
 545                                 delete cCurve;
 546
 547                                 processedLabels.insert(order->getLabel());
 548                                 userLabels.erase(order->getLabel());
 549
 550                                 //restore real lastlabel to save below
 551                                 order->setLabel(saveLabel);
 552                         }
 553
 554
 555                         lastLabel = order->getLabel();
 556
 557                         //get next line to process
 558                         delete order;
 559                         order = input->getSharedOrderVector();
 560                 }
 561
 562                 if (m->control_pressed) {
 563                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }   outputTypes.clear();
 564                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 565                                         m->clearGroups();
 566                                         delete input;
 567                                         return 0;
 568                 }
 569
 570                 //output error messages about any remaining user labels
 571                 set<string>::iterator it;
 572                 bool needToRun = false;
 573                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 574                         m->mothurOut("Your file does not include the label " + *it);
 575                         if (processedLabels.count(lastLabel) != 1) {
 576                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 577                                 needToRun = true;
 578                         }else {
 579                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 580                         }
 581                 }
 582
 583                 //run last label if you need to
 584                 if (needToRun == true)  {
 585                         if (order != NULL) {  delete order;  }
 586                         order = input->getSharedOrderVector(lastLabel);
 587
 588                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 589                         cCurve = new Collect(order, cDisplays);
 590                         cCurve->getSharedCurve(freq);
 591                         delete cCurve;
 592
 593                         if (m->control_pressed) {
 594                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 595                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 596                                 delete order;
 597                                 delete input;
 598                                 m->clearGroups();
 599                                 return 0;
 600                         }
 601
 602                         delete order;
 603                 }
 604
 605                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 606
 607                 //reset groups parameter
 608                 m->clearGroups();
 609                 delete input;
 610
 611                 m->mothurOutEndLine();
 612                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 613                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 614                 m->mothurOutEndLine();
 615
 616
 617                 return 0;
 618         }
 619         catch(exception& e) {
 620                 m->errorOut(e, "CollectSharedCommand", "execute");
 621                 exit(1);
 622         }
 623 }
 624
 625 /***********************************************************/