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
  53
  54 //**********************************************************************************************************************
  55 vector<string> CollectSharedCommand::setParameters(){
  56         try {
  57                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
  58                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  59                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
  60                 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", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
  61                 CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
  62                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  63                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  64                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  65
  66                 vector<string> myArray;
  67                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  68                 return myArray;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "CollectSharedCommand", "setParameters");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 string CollectSharedCommand::getHelpString(){
  77         try {
  78                 string helpString = "";
  79                 ValidCalculators validCalculator;
  80                 helpString += "The collect.shared command parameters are shared, label, freq, calc and groups.  shared is required if there is no current sharedfile. \n";
  81                 helpString += "The collect.shared command should be in the following format: \n";
  82                 helpString += "collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n";
  83                 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";
  84                 helpString += "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n";
  85                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  86                 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";
  87                 helpString += validCalculator.printCalc("shared");
  88                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  89                 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";
  90                 helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
  91                 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";
  92                 helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
  93                 return helpString;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "CollectSharedCommand", "getHelpString");
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************
 101 string CollectSharedCommand::getOutputPattern(string type) {
 102     try {
 103         string pattern = "";
 104
 105         if (type == "sharedchao")               {  pattern =  "[filename],shared.chao";     }
 106         else if (type == "sharedsobs")          {  pattern =  "[filename],shared.sobs";     }
 107         else if (type == "sharedace")           {  pattern =  "[filename],shared.ace";      }
 108         else if (type == "jabund")              {  pattern =  "[filename],jabund";          }
 109         else if (type == "sorabund")            {  pattern =  "[filename],sorabund";        }
 110         else if (type == "jclass")              {  pattern =  "[filename],jclass";          }
 111         else if (type == "sorclass")            {  pattern =  "[filename],sorclass";        }
 112         else if (type == "jest")                {  pattern =  "[filename],jest";            }
 113         else if (type == "sorest")              {  pattern =  "[filename],sorest";          }
 114         else if (type == "thetayc")             {  pattern =  "[filename],thetayc";         }
 115         else if (type == "thetan")              {  pattern =  "[filename],thetan";          }
 116         else if (type == "kstest")              {  pattern =  "[filename],kstest";          }
 117         else if (type == "whittaker")           {  pattern =  "[filename],whittaker";       }
 118         else if (type == "sharednseqs")         {  pattern =  "[filename],shared.nseqs";    }
 119         else if (type == "ochiai")              {  pattern =  "[filename],ochiai";          }
 120         else if (type == "anderberg")           {  pattern =  "[filename],anderberg";       }
 121         else if (type == "kulczynski")          {  pattern =  "[filename],kulczynski";      }
 122         else if (type == "kulczynskicody")      {  pattern =  "[filename],kulczynskicody";  }
 123         else if (type == "lennon")              {  pattern =  "[filename],lennon";          }
 124         else if (type == "morisitahorn")        {  pattern =  "[filename],morisitahorn";    }
 125         else if (type == "braycurtis")          {  pattern =  "[filename],braycurtis";      }
 126         else if (type == "odum")                {  pattern =  "[filename],odum";            }
 127         else if (type == "canberra")            {  pattern =  "[filename],canberra";        }
 128         else if (type == "structeuclidean")     {  pattern =  "[filename],structeuclidean"; }
 129         else if (type == "structchord")         {  pattern =  "[filename],structchord";     }
 130         else if (type == "hellinger")           {  pattern =  "[filename],hellinger";       }
 131         else if (type == "manhattan")           {  pattern =  "[filename],manhattan";       }
 132         else if (type == "structpearson")       {  pattern =  "[filename],structpearson";   }
 133         else if (type == "soergel")             {  pattern =  "[filename],soergel";         }
 134         else if (type == "spearman")            {  pattern =  "[filename],spearman";        }
 135         else if (type == "structkulczynski")    {  pattern =  "[filename],structkulczynski";}
 136         else if (type == "structchi2")          {  pattern =  "[filename],structchi2";      }
 137         else if (type == "speciesprofile")      {  pattern =  "[filename],speciesprofile";  }
 138         else if (type == "hamming")             {  pattern =  "[filename],hamming";         }
 139         else if (type == "gower")               {  pattern =  "[filename],gower";           }
 140         else if (type == "memchi2")             {  pattern =  "[filename],memchi2";         }
 141         else if (type == "memchord")            {  pattern =  "[filename],memchord";        }
 142         else if (type == "memeuclidean")        {  pattern =  "[filename],memeuclidean";    }
 143         else if (type == "mempearson")          {  pattern =  "[filename],mempearson";      }
 144         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 145
 146         return pattern;
 147     }
 148     catch(exception& e) {
 149         m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
 150         exit(1);
 151     }
 152 }
 153
 154 //**********************************************************************************************************************
 155 CollectSharedCommand::CollectSharedCommand(){
 156         try {
 157                 abort = true; calledHelp = true;
 158                 setParameters();
 159                 vector<string> tempOutNames;
 160                 outputTypes["sharedchao"] = tempOutNames;
 161                 outputTypes["sharedsobs"] = tempOutNames;
 162                 outputTypes["sharedace"] = tempOutNames;
 163                 outputTypes["jabund"] = tempOutNames;
 164                 outputTypes["sorabund"] = tempOutNames;
 165                 outputTypes["jclass"] = tempOutNames;
 166                 outputTypes["sorclass"] = tempOutNames;
 167                 outputTypes["jest"] = tempOutNames;
 168                 outputTypes["sorest"] = tempOutNames;
 169                 outputTypes["thetayc"] = tempOutNames;
 170                 outputTypes["thetan"] = tempOutNames;
 171                 outputTypes["kstest"] = tempOutNames;
 172                 outputTypes["whittaker"] = tempOutNames;
 173                 outputTypes["sharednseqs"] = tempOutNames;
 174                 outputTypes["ochiai"] = tempOutNames;
 175                 outputTypes["anderberg"] = tempOutNames;
 176                 outputTypes["kulczynski"] = tempOutNames;
 177                 outputTypes["kulczynskicody"] = tempOutNames;
 178                 outputTypes["lennon"] = tempOutNames;
 179                 outputTypes["morisitahorn"] = tempOutNames;
 180                 outputTypes["braycurtis"] = tempOutNames;
 181                 outputTypes["odum"] = tempOutNames;
 182                 outputTypes["canberra"] = tempOutNames;
 183                 outputTypes["structeuclidean"] = tempOutNames;
 184                 outputTypes["structchord"] = tempOutNames;
 185                 outputTypes["hellinger"] = tempOutNames;
 186                 outputTypes["manhattan"] = tempOutNames;
 187                 outputTypes["structpearson"] = tempOutNames;
 188                 outputTypes["soergel"] = tempOutNames;
 189                 outputTypes["spearman"] = tempOutNames;
 190                 outputTypes["structkulczynski"] = tempOutNames;
 191                 outputTypes["structchi2"] = tempOutNames;
 192                 outputTypes["speciesprofile"] = tempOutNames;
 193                 outputTypes["hamming"] = tempOutNames;
 194                 outputTypes["gower"] = tempOutNames;
 195                 outputTypes["memchi2"] = tempOutNames;
 196                 outputTypes["memchord"] = tempOutNames;
 197                 outputTypes["memeuclidean"] = tempOutNames;
 198                 outputTypes["mempearson"] = tempOutNames;
 199
 200         }
 201         catch(exception& e) {
 202                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 203                 exit(1);
 204         }
 205 }
 206 //**********************************************************************************************************************
 207 CollectSharedCommand::CollectSharedCommand(string option)  {
 208         try {
 209                 abort = false; calledHelp = false;
 210                 allLines = 1;
 211
 212                 //allow user to run help
 213                 if(option == "help") { help(); abort = true; calledHelp = true; }
 214                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 215
 216                 else {
 217                         vector<string> myArray = setParameters();
 218
 219                         OptionParser parser(option);
 220                         map<string,string> parameters=parser.getParameters();
 221                         map<string,string>::iterator it;
 222
 223                         ValidParameters validParameter;
 224
 225                         //check to make sure all parameters are valid for command
 226                         for (it = parameters.begin(); it != parameters.end(); it++) {
 227                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 228                         }
 229
 230                         //initialize outputTypes
 231                         vector<string> tempOutNames;
 232                         outputTypes["sharedchao"] = tempOutNames;
 233                         outputTypes["sharedsobs"] = tempOutNames;
 234                         outputTypes["sharedace"] = tempOutNames;
 235                         outputTypes["jabund"] = tempOutNames;
 236                         outputTypes["sorabund"] = tempOutNames;
 237                         outputTypes["jclass"] = tempOutNames;
 238                         outputTypes["sorclass"] = tempOutNames;
 239                         outputTypes["jest"] = tempOutNames;
 240                         outputTypes["sorest"] = tempOutNames;
 241                         outputTypes["thetayc"] = tempOutNames;
 242                         outputTypes["thetan"] = tempOutNames;
 243                         outputTypes["kstest"] = tempOutNames;
 244                         outputTypes["whittaker"] = tempOutNames;
 245                         outputTypes["sharednseqs"] = tempOutNames;
 246                         outputTypes["ochiai"] = tempOutNames;
 247                         outputTypes["anderberg"] = tempOutNames;
 248                         outputTypes["kulczynski"] = tempOutNames;
 249                         outputTypes["kulczynskicody"] = tempOutNames;
 250                         outputTypes["lennon"] = tempOutNames;
 251                         outputTypes["morisitahorn"] = tempOutNames;
 252                         outputTypes["braycurtis"] = tempOutNames;
 253                         outputTypes["odum"] = tempOutNames;
 254                         outputTypes["canberra"] = tempOutNames;
 255                         outputTypes["structeuclidean"] = tempOutNames;
 256                         outputTypes["structchord"] = tempOutNames;
 257                         outputTypes["hellinger"] = tempOutNames;
 258                         outputTypes["manhattan"] = tempOutNames;
 259                         outputTypes["structpearson"] = tempOutNames;
 260                         outputTypes["soergel"] = tempOutNames;
 261                         outputTypes["spearman"] = tempOutNames;
 262                         outputTypes["structkulczynski"] = tempOutNames;
 263                         outputTypes["speciesprofile"] = tempOutNames;
 264                         outputTypes["structchi2"] = tempOutNames;
 265                         outputTypes["hamming"] = tempOutNames;
 266                         outputTypes["gower"] = tempOutNames;
 267                         outputTypes["memchi2"] = tempOutNames;
 268                         outputTypes["memchord"] = tempOutNames;
 269                         outputTypes["memeuclidean"] = tempOutNames;
 270                         outputTypes["mempearson"] = tempOutNames;
 271
 272
 273                         //if the user changes the input directory command factory will send this info to us in the output parameter
 274                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 275                         if (inputDir == "not found"){   inputDir = "";          }
 276                         else {
 277                                 string path;
 278                                 it = parameters.find("shared");
 279                                 //user has given a template file
 280                                 if(it != parameters.end()){
 281                                         path = m->hasPath(it->second);
 282                                         //if the user has not given a path then, add inputdir. else leave path alone.
 283                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 284                                 }
 285                         }
 286
 287                         //get shared file
 288                         sharedfile = validParameter.validFile(parameters, "shared", true);
 289                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 290                         else if (sharedfile == "not found") {
 291                                 //if there is a current shared file, use it
 292                                 sharedfile = m->getSharedFile();
 293                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 294                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 295                         }else { m->setSharedFile(sharedfile); }
 296
 297
 298                         //if the user changes the output directory command factory will send this info to us in the output parameter
 299                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 300
 301                         //check for optional parameter and set defaults
 302                         // ...at some point should added some additional type checking..
 303                         label = validParameter.validFile(parameters, "label", false);
 304                         if (label == "not found") { label = ""; }
 305                         else {
 306                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 307                                 else { allLines = 1;  }
 308                         }
 309
 310                         calc = validParameter.validFile(parameters, "calc", false);
 311                         if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 312                         else {
 313                                  if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 314                         }
 315                         m->splitAtDash(calc, Estimators);
 316                         if (m->inUsersGroups("citation", Estimators)) {
 317                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 318                                 //remove citation from list of calcs
 319                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 320                         }
 321
 322                         groups = validParameter.validFile(parameters, "groups", false);
 323                         if (groups == "not found") { groups = ""; }
 324                         else {
 325                                 m->splitAtDash(groups, Groups);
 326                         }
 327                         m->setGroups(Groups);
 328
 329                         string temp;
 330                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 331                         m->mothurConvert(temp, freq);
 332
 333                         temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
 334                         all = m->isTrue(temp);
 335
 336                         if (abort == false) {
 337
 338                                 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 339                                 map<string, string> variables;
 340                 variables["[filename]"] = fileNameRoot;
 341
 342                                 ValidCalculators validCalculator;
 343
 344                                 for (int i=0; i<Estimators.size(); i++) {
 345                                         if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
 346                                                 if (Estimators[i] == "sharedchao") {
 347                                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(getOutputFileName("sharedchao", variables))));
 348                                                         outputNames.push_back(getOutputFileName("sharedchao", variables)); outputTypes["sharedchao"].push_back(getOutputFileName("sharedchao", variables));
 349                                                 }else if (Estimators[i] == "sharedsobs") {
 350                                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(getOutputFileName("sharedsobs", variables))));
 351                                                         outputNames.push_back(getOutputFileName("sharedsobs", variables)); outputTypes["sharedsobs"].push_back(getOutputFileName("sharedsobs", variables));
 352                                                 }else if (Estimators[i] == "sharedace") {
 353                                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(getOutputFileName("sharedace", variables))));
 354                                                         outputNames.push_back(getOutputFileName("sharedace", variables)); outputTypes["sharedace"].push_back(getOutputFileName("sharedace", variables));
 355                                                 }else if (Estimators[i] == "jabund") {
 356                                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(getOutputFileName("jabund", variables))));
 357                                                         outputNames.push_back(getOutputFileName("jabund", variables)); outputTypes["jabund"].push_back(getOutputFileName("jabund", variables));
 358                                                 }else if (Estimators[i] == "sorabund") {
 359                                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(getOutputFileName("sorabund", variables))));
 360                                                         outputNames.push_back(getOutputFileName("sorabund", variables)); outputTypes["sorabund"].push_back(getOutputFileName("sorabund", variables));
 361                                                 }else if (Estimators[i] == "jclass") {
 362                                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(getOutputFileName("jclass", variables))));
 363                                                         outputNames.push_back(getOutputFileName("jclass", variables)); outputTypes["jclass"].push_back(getOutputFileName("jclass", variables));
 364                                                 }else if (Estimators[i] == "sorclass") {
 365                                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(getOutputFileName("sorclass", variables))));
 366                                                         outputNames.push_back(getOutputFileName("sorclass", variables)); outputTypes["sorclass"].push_back(getOutputFileName("sorclass", variables));
 367                                                 }else if (Estimators[i] == "jest") {
 368                                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(getOutputFileName("jest", variables))));
 369                                                         outputNames.push_back(getOutputFileName("jest", variables)); outputTypes["jest"].push_back(getOutputFileName("jest", variables));
 370                                                 }else if (Estimators[i] == "sorest") {
 371                                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(getOutputFileName("sorest", variables))));
 372                                                         outputNames.push_back(getOutputFileName("sorest", variables)); outputTypes["sorest"].push_back(getOutputFileName("sorest", variables));
 373                                                 }else if (Estimators[i] == "thetayc") {
 374                                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(getOutputFileName("thetayc", variables))));
 375                                                         outputNames.push_back(getOutputFileName("thetayc", variables)); outputTypes["thetayc"].push_back(getOutputFileName("thetayc", variables));
 376                                                 }else if (Estimators[i] == "thetan") {
 377                                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(getOutputFileName("thetan", variables))));
 378                                                         outputNames.push_back(getOutputFileName("thetan", variables)); outputTypes["thetan"].push_back(getOutputFileName("thetan", variables));
 379                                                 }else if (Estimators[i] == "kstest") {
 380                                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(getOutputFileName("kstest", variables))));
 381                                                         outputNames.push_back(getOutputFileName("kstest", variables)); outputTypes["kstest"].push_back(getOutputFileName("kstest", variables));
 382                                                 }else if (Estimators[i] == "whittaker") {
 383                                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(getOutputFileName("whittaker", variables))));
 384                                                         outputNames.push_back(getOutputFileName("whittaker", variables)); outputTypes["whittaker"].push_back(getOutputFileName("whittaker", variables));
 385                                                 }else if (Estimators[i] == "sharednseqs") {
 386                                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(getOutputFileName("sharednseqs", variables))));
 387                                                         outputNames.push_back(getOutputFileName("sharednseqs", variables)); outputTypes["shared.nseqs"].push_back(getOutputFileName("sharednseqs", variables));
 388                                                 }else if (Estimators[i] == "ochiai") {
 389                                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(getOutputFileName("ochiai", variables))));
 390                                                         outputNames.push_back(getOutputFileName("ochiai", variables)); outputTypes["ochiai"].push_back(getOutputFileName("ochiai", variables));
 391                                                 }else if (Estimators[i] == "anderberg") {
 392                                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(getOutputFileName("anderberg", variables))));
 393                                                         outputNames.push_back(getOutputFileName("anderberg", variables)); outputTypes["anderberg"].push_back(getOutputFileName("anderberg", variables));
 394                                                 }else if (Estimators[i] == "kulczynski") {
 395                                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(getOutputFileName("kulczynski", variables))));
 396                                                         outputNames.push_back(getOutputFileName("kulczynski", variables)); outputTypes["kulczynski"].push_back(getOutputFileName("kulczynski", variables));
 397                                                 }else if (Estimators[i] == "kulczynskicody") {
 398                                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(getOutputFileName("kulczynskicody", variables))));
 399                                                         outputNames.push_back(getOutputFileName("kulczynskicody", variables)); outputTypes["kulczynskicody"].push_back(getOutputFileName("kulczynskicody", variables));
 400                                                 }else if (Estimators[i] == "lennon") {
 401                                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(getOutputFileName("lennon", variables))));
 402                                                         outputNames.push_back(getOutputFileName("lennon", variables)); outputTypes["lennon"].push_back(getOutputFileName("lennon", variables));
 403                                                 }else if (Estimators[i] == "morisitahorn") {
 404                                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(getOutputFileName("morisitahorn", variables))));
 405                                                         outputNames.push_back(getOutputFileName("morisitahorn", variables)); outputTypes["morisitahorn"].push_back(getOutputFileName("morisitahorn", variables));
 406                                                 }else if (Estimators[i] == "braycurtis") {
 407                                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(getOutputFileName("braycurtis", variables))));
 408                                                         outputNames.push_back(getOutputFileName("braycurtis", variables)); outputTypes["braycurtis"].push_back(getOutputFileName("braycurtis", variables));
 409                                                 }else if (Estimators[i] == "odum") {
 410                                                         cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(getOutputFileName("odum", variables))));
 411                                                         outputNames.push_back(getOutputFileName("odum", variables)); outputTypes["odum"].push_back(getOutputFileName("odum", variables));
 412                                                 }else if (Estimators[i] == "canberra") {
 413                                                         cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(getOutputFileName("canberra", variables))));
 414                                                         outputNames.push_back(getOutputFileName("canberra", variables)); outputTypes["canberra"].push_back(getOutputFileName("canberra", variables));
 415                                                 }else if (Estimators[i] == "structeuclidean") {
 416                                                         cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(getOutputFileName("structeuclidean", variables))));
 417                                                         outputNames.push_back(getOutputFileName("structeuclidean", variables)); outputTypes["structeuclidean"].push_back(getOutputFileName("structeuclidean", variables));
 418                                                 }else if (Estimators[i] == "structchord") {
 419                                                         cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(getOutputFileName("structchord", variables))));
 420                                                         outputNames.push_back(getOutputFileName("structchord", variables)); outputTypes["structchord"].push_back(getOutputFileName("structchord", variables));
 421                                                 }else if (Estimators[i] == "hellinger") {
 422                                                         cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(getOutputFileName("hellinger", variables))));
 423                                                         outputNames.push_back(getOutputFileName("hellinger", variables)); outputTypes["hellinger"].push_back(getOutputFileName("hellinger", variables));
 424                                                 }else if (Estimators[i] == "manhattan") {
 425                                                         cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(getOutputFileName("manhattan", variables))));
 426                                                         outputNames.push_back(getOutputFileName("manhattan", variables)); outputTypes["manhattan"].push_back(getOutputFileName("manhattan", variables));
 427                                                 }else if (Estimators[i] == "structpearson") {
 428                                                         cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(getOutputFileName("structpearson", variables))));
 429                                                         outputNames.push_back(getOutputFileName("structpearson", variables)); outputTypes["structpearson"].push_back(getOutputFileName("structpearson", variables));
 430                                                 }else if (Estimators[i] == "soergel") {
 431                                                         cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(getOutputFileName("soergel", variables))));
 432                                                         outputNames.push_back(getOutputFileName("soergel", variables)); outputTypes["soergel"].push_back(getOutputFileName("soergel", variables));
 433                                                 }else if (Estimators[i] == "spearman") {
 434                                                         cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(getOutputFileName("spearman", variables))));
 435                                                         outputNames.push_back(getOutputFileName("spearman", variables)); outputTypes["spearman"].push_back(getOutputFileName("spearman", variables));
 436                                                 }else if (Estimators[i] == "structkulczynski") {
 437                                                         cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(getOutputFileName("structkulczynski", variables))));
 438                                                         outputNames.push_back(getOutputFileName("structkulczynski", variables)); outputTypes["structkulczynski"].push_back(getOutputFileName("structkulczynski", variables));
 439                                                 }else if (Estimators[i] == "speciesprofile") {
 440                                                         cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(getOutputFileName("speciesprofile", variables))));
 441                                                         outputNames.push_back(getOutputFileName("speciesprofile", variables)); outputTypes["speciesprofile"].push_back(getOutputFileName("speciesprofile", variables));
 442                                                 }else if (Estimators[i] == "hamming") {
 443                                                         cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(getOutputFileName("hamming", variables))));
 444                                                         outputNames.push_back(getOutputFileName("hamming", variables)); outputTypes["hamming"].push_back(getOutputFileName("hamming", variables));
 445                                                 }else if (Estimators[i] == "structchi2") {
 446                                                         cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(getOutputFileName("structchi2", variables))));
 447                                                         outputNames.push_back(getOutputFileName("structchi2", variables)); outputTypes["structchi2"].push_back(getOutputFileName("structchi2", variables));
 448                                                 }else if (Estimators[i] == "gower") {
 449                                                         cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(getOutputFileName("gower", variables))));
 450                                                         outputNames.push_back(getOutputFileName("gower", variables)); outputTypes["gower"].push_back(getOutputFileName("gower", variables));
 451                                                 }else if (Estimators[i] == "memchi2") {
 452                                                         cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(getOutputFileName("memchi2", variables))));
 453                                                         outputNames.push_back(getOutputFileName("memchi2", variables)); outputTypes["memchi2"].push_back(getOutputFileName("memchi2", variables));
 454                                                 }else if (Estimators[i] == "memchord") {
 455                                                         cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(getOutputFileName("memchord", variables))));
 456                                                         outputNames.push_back(getOutputFileName("memchord", variables)); outputTypes["memchord"].push_back(getOutputFileName("memchord", variables));
 457                                                 }else if (Estimators[i] == "memeuclidean") {
 458                                                         cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(getOutputFileName("memeuclidean", variables))));
 459                                                         outputNames.push_back(getOutputFileName("memeuclidean", variables)); outputTypes["memeuclidean"].push_back(getOutputFileName("memeuclidean", variables));
 460                                                 }else if (Estimators[i] == "mempearson") {
 461                                                         cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
 462                                                         outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
 463                                                 }
 464
 465                                         }
 466                                 }
 467                         }
 468                 }
 469
 470         }
 471         catch(exception& e) {
 472                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 473                 exit(1);
 474         }
 475 }
 476 //**********************************************************************************************************************
 477 CollectSharedCommand::~CollectSharedCommand(){}
 478 //**********************************************************************************************************************
 479
 480 int CollectSharedCommand::execute(){
 481         try {
 482
 483                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 484
 485                 //if the users entered no valid calculators don't execute command
 486                 if (cDisplays.size() == 0) { return 0; }
 487                 for(int i=0;i<cDisplays.size();i++){    cDisplays[i]->setAll(all);      }
 488
 489                 input = new InputData(sharedfile, "sharedfile");
 490                 order = input->getSharedOrderVector();
 491                 string lastLabel = order->getLabel();
 492
 493                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 494                 set<string> processedLabels;
 495                 set<string> userLabels = labels;
 496
 497                 //set users groups
 498                 SharedUtil* util = new SharedUtil();
 499                 Groups = m->getGroups();
 500                 vector<string> allGroups = m->getAllGroups();
 501                 util->setGroups(Groups, allGroups, "collect");
 502                 m->setGroups(Groups);
 503                 m->setAllGroups(allGroups);
 504                 delete util;
 505
 506                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 507                         if (m->control_pressed) {
 508                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 509                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 510                                         delete order; delete input;
 511                                         m->clearGroups();
 512                                         return 0;
 513                         }
 514
 515                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 516
 517                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 518                                 //create collectors curve
 519                                 cCurve = new Collect(order, cDisplays);
 520                                 cCurve->getSharedCurve(freq);
 521                                 delete cCurve;
 522
 523                                 processedLabels.insert(order->getLabel());
 524                                 userLabels.erase(order->getLabel());
 525                         }
 526
 527                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 528                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 529                                 string saveLabel = order->getLabel();
 530
 531                                 delete order;
 532                                 order = input->getSharedOrderVector(lastLabel);
 533
 534                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 535                                 //create collectors curve
 536                                 cCurve = new Collect(order, cDisplays);
 537                                 cCurve->getSharedCurve(freq);
 538                                 delete cCurve;
 539
 540                                 processedLabels.insert(order->getLabel());
 541                                 userLabels.erase(order->getLabel());
 542
 543                                 //restore real lastlabel to save below
 544                                 order->setLabel(saveLabel);
 545                         }
 546
 547
 548                         lastLabel = order->getLabel();
 549
 550                         //get next line to process
 551                         delete order;
 552                         order = input->getSharedOrderVector();
 553                 }
 554
 555                 if (m->control_pressed) {
 556                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }   outputTypes.clear();
 557                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 558                                         m->clearGroups();
 559                                         delete input;
 560                                         return 0;
 561                 }
 562
 563                 //output error messages about any remaining user labels
 564                 set<string>::iterator it;
 565                 bool needToRun = false;
 566                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 567                         m->mothurOut("Your file does not include the label " + *it);
 568                         if (processedLabels.count(lastLabel) != 1) {
 569                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 570                                 needToRun = true;
 571                         }else {
 572                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 573                         }
 574                 }
 575
 576                 //run last label if you need to
 577                 if (needToRun == true)  {
 578                         if (order != NULL) {  delete order;  }
 579                         order = input->getSharedOrderVector(lastLabel);
 580
 581                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 582                         cCurve = new Collect(order, cDisplays);
 583                         cCurve->getSharedCurve(freq);
 584                         delete cCurve;
 585
 586                         if (m->control_pressed) {
 587                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 588                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 589                                 delete order;
 590                                 delete input;
 591                                 m->clearGroups();
 592                                 return 0;
 593                         }
 594
 595                         delete order;
 596                 }
 597
 598                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 599
 600                 //reset groups parameter
 601                 m->clearGroups();
 602                 delete input;
 603
 604                 m->mothurOutEndLine();
 605                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 606                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 607                 m->mothurOutEndLine();
 608
 609
 610                 return 0;
 611         }
 612         catch(exception& e) {
 613                 m->errorOut(e, "CollectSharedCommand", "execute");
 614                 exit(1);
 615         }
 616 }
 617
 618 /***********************************************************/