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); 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); 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::getOutputFileNameTag(string type, string inputName=""){
 102         try {
 103         string outputFileName = "";
 104                 map<string, vector<string> >::iterator it;
 105
 106         //is this a type this command creates
 107         it = outputTypes.find(type);
 108         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
 109         else {
 110             if (type == "sharedchao")               {  outputFileName =  "shared.chao";     }
 111             else if (type == "sharedsobs")          {  outputFileName =  "shared.sobs";     }
 112             else if (type == "sharedace")           {  outputFileName =  "shared.ace";      }
 113             else if (type == "jabund")              {  outputFileName =  "jabund";          }
 114             else if (type == "sorabund")            {  outputFileName =  "sorabund";        }
 115             else if (type == "jclass")              {  outputFileName =  "jclass";          }
 116             else if (type == "sorclass")            {  outputFileName =  "sorclass";        }
 117             else if (type == "jest")                {  outputFileName =  "jest";            }
 118             else if (type == "sorest")              {  outputFileName =  "sorest";          }
 119             else if (type == "thetayc")             {  outputFileName =  "thetayc";         }
 120             else if (type == "thetan")              {  outputFileName =  "thetan";          }
 121             else if (type == "kstest")              {  outputFileName =  "kstest";          }
 122             else if (type == "whittaker")           {  outputFileName =  "whittaker";       }
 123             else if (type == "sharednseqs")         {  outputFileName =  "shared.nseqs";    }
 124             else if (type == "ochiai")              {  outputFileName =  "ochiai";          }
 125             else if (type == "anderberg")           {  outputFileName =  "anderberg";       }
 126             else if (type == "kulczynski")          {  outputFileName =  "kulczynski";      }
 127             else if (type == "kulczynskicody")      {  outputFileName =  "kulczynskicody";  }
 128             else if (type == "lennon")              {  outputFileName =  "lennon";          }
 129             else if (type == "morisitahorn")        {  outputFileName =  "morisitahorn";    }
 130             else if (type == "braycurtis")          {  outputFileName =  "braycurtis";      }
 131             else if (type == "odum")                {  outputFileName =  "odum";            }
 132             else if (type == "canberra")            {  outputFileName =  "canberra";        }
 133             else if (type == "structeuclidean")     {  outputFileName =  "structeuclidean"; }
 134             else if (type == "structchord")         {  outputFileName =  "structchord";     }
 135             else if (type == "hellinger")           {  outputFileName =  "hellinger";       }
 136             else if (type == "manhattan")           {  outputFileName =  "manhattan";       }
 137             else if (type == "structpearson")       {  outputFileName =  "structpearson";   }
 138             else if (type == "soergel")             {  outputFileName =  "soergel";         }
 139             else if (type == "spearman")            {  outputFileName =  "spearman";        }
 140             else if (type == "structkulczynski")    {  outputFileName =  "structkulczynski";}
 141             else if (type == "structchi2")          {  outputFileName =  "structchi2";      }
 142             else if (type == "speciesprofile")      {  outputFileName =  "speciesprofile";  }
 143             else if (type == "hamming")             {  outputFileName =  "hamming";         }
 144             else if (type == "gower")               {  outputFileName =  "gower";           }
 145             else if (type == "memchi2")             {  outputFileName =  "memchi2";         }
 146             else if (type == "memchord")            {  outputFileName =  "memchord";        }
 147             else if (type == "memeuclidean")        {  outputFileName =  "memeuclidean";    }
 148             else if (type == "mempearson")          {  outputFileName =  "mempearson";      }
 149             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 150         }
 151         return outputFileName;
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "CollectSharedCommand", "getOutputFileNameTag");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159 CollectSharedCommand::CollectSharedCommand(){
 160         try {
 161                 abort = true; calledHelp = true;
 162                 setParameters();
 163                 vector<string> tempOutNames;
 164                 outputTypes["sharedchao"] = tempOutNames;
 165                 outputTypes["sharedsobs"] = tempOutNames;
 166                 outputTypes["sharedace"] = tempOutNames;
 167                 outputTypes["jabund"] = tempOutNames;
 168                 outputTypes["sorabund"] = tempOutNames;
 169                 outputTypes["jclass"] = tempOutNames;
 170                 outputTypes["sorclass"] = tempOutNames;
 171                 outputTypes["jest"] = tempOutNames;
 172                 outputTypes["sorest"] = tempOutNames;
 173                 outputTypes["thetayc"] = tempOutNames;
 174                 outputTypes["thetan"] = tempOutNames;
 175                 outputTypes["kstest"] = tempOutNames;
 176                 outputTypes["whittaker"] = tempOutNames;
 177                 outputTypes["sharednseqs"] = tempOutNames;
 178                 outputTypes["ochiai"] = tempOutNames;
 179                 outputTypes["anderberg"] = tempOutNames;
 180                 outputTypes["kulczynski"] = tempOutNames;
 181                 outputTypes["kulczynskicody"] = tempOutNames;
 182                 outputTypes["lennon"] = tempOutNames;
 183                 outputTypes["morisitahorn"] = tempOutNames;
 184                 outputTypes["braycurtis"] = tempOutNames;
 185                 outputTypes["odum"] = tempOutNames;
 186                 outputTypes["canberra"] = tempOutNames;
 187                 outputTypes["structeuclidean"] = tempOutNames;
 188                 outputTypes["structchord"] = tempOutNames;
 189                 outputTypes["hellinger"] = tempOutNames;
 190                 outputTypes["manhattan"] = tempOutNames;
 191                 outputTypes["structpearson"] = tempOutNames;
 192                 outputTypes["soergel"] = tempOutNames;
 193                 outputTypes["spearman"] = tempOutNames;
 194                 outputTypes["structkulczynski"] = tempOutNames;
 195                 outputTypes["structchi2"] = tempOutNames;
 196                 outputTypes["speciesprofile"] = tempOutNames;
 197                 outputTypes["hamming"] = tempOutNames;
 198                 outputTypes["gower"] = tempOutNames;
 199                 outputTypes["memchi2"] = tempOutNames;
 200                 outputTypes["memchord"] = tempOutNames;
 201                 outputTypes["memeuclidean"] = tempOutNames;
 202                 outputTypes["mempearson"] = tempOutNames;
 203
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 207                 exit(1);
 208         }
 209 }
 210 //**********************************************************************************************************************
 211 CollectSharedCommand::CollectSharedCommand(string option)  {
 212         try {
 213                 abort = false; calledHelp = false;
 214                 allLines = 1;
 215
 216                 //allow user to run help
 217                 if(option == "help") { help(); abort = true; calledHelp = true; }
 218                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 219
 220                 else {
 221                         vector<string> myArray = setParameters();
 222
 223                         OptionParser parser(option);
 224                         map<string,string> parameters=parser.getParameters();
 225                         map<string,string>::iterator it;
 226
 227                         ValidParameters validParameter;
 228
 229                         //check to make sure all parameters are valid for command
 230                         for (it = parameters.begin(); it != parameters.end(); it++) {
 231                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 232                         }
 233
 234                         //initialize outputTypes
 235                         vector<string> tempOutNames;
 236                         outputTypes["sharedchao"] = tempOutNames;
 237                         outputTypes["sharedsobs"] = tempOutNames;
 238                         outputTypes["sharedace"] = tempOutNames;
 239                         outputTypes["jabund"] = tempOutNames;
 240                         outputTypes["sorabund"] = tempOutNames;
 241                         outputTypes["jclass"] = tempOutNames;
 242                         outputTypes["sorclass"] = tempOutNames;
 243                         outputTypes["jest"] = tempOutNames;
 244                         outputTypes["sorest"] = tempOutNames;
 245                         outputTypes["thetayc"] = tempOutNames;
 246                         outputTypes["thetan"] = tempOutNames;
 247                         outputTypes["kstest"] = tempOutNames;
 248                         outputTypes["whittaker"] = tempOutNames;
 249                         outputTypes["sharednseqs"] = tempOutNames;
 250                         outputTypes["ochiai"] = tempOutNames;
 251                         outputTypes["anderberg"] = tempOutNames;
 252                         outputTypes["kulczynski"] = tempOutNames;
 253                         outputTypes["kulczynskicody"] = tempOutNames;
 254                         outputTypes["lennon"] = tempOutNames;
 255                         outputTypes["morisitahorn"] = tempOutNames;
 256                         outputTypes["braycurtis"] = tempOutNames;
 257                         outputTypes["odum"] = tempOutNames;
 258                         outputTypes["canberra"] = tempOutNames;
 259                         outputTypes["structeuclidean"] = tempOutNames;
 260                         outputTypes["structchord"] = tempOutNames;
 261                         outputTypes["hellinger"] = tempOutNames;
 262                         outputTypes["manhattan"] = tempOutNames;
 263                         outputTypes["structpearson"] = tempOutNames;
 264                         outputTypes["soergel"] = tempOutNames;
 265                         outputTypes["spearman"] = tempOutNames;
 266                         outputTypes["structkulczynski"] = tempOutNames;
 267                         outputTypes["speciesprofile"] = tempOutNames;
 268                         outputTypes["structchi2"] = tempOutNames;
 269                         outputTypes["hamming"] = tempOutNames;
 270                         outputTypes["gower"] = tempOutNames;
 271                         outputTypes["memchi2"] = tempOutNames;
 272                         outputTypes["memchord"] = tempOutNames;
 273                         outputTypes["memeuclidean"] = tempOutNames;
 274                         outputTypes["mempearson"] = 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
 344                                 ValidCalculators validCalculator;
 345
 346                                 for (int i=0; i<Estimators.size(); i++) {
 347                                         if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
 348                                                 if (Estimators[i] == "sharedchao") {
 349                                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedchao"))));
 350                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedchao")); outputTypes["sharedchao"].push_back(fileNameRoot+getOutputFileNameTag("sharedchao"));
 351                                                 }else if (Estimators[i] == "sharedsobs") {
 352                                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedsobs"))));
 353                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedsobs")); outputTypes["sharedsobs"].push_back(fileNameRoot+getOutputFileNameTag("sharedsobs"));
 354                                                 }else if (Estimators[i] == "sharedace") {
 355                                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedace"))));
 356                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedace")); outputTypes["sharedace"].push_back(fileNameRoot+getOutputFileNameTag("sharedace"));
 357                                                 }else if (Estimators[i] == "jabund") {
 358                                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jabund"))));
 359                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("jabund")); outputTypes["jabund"].push_back(fileNameRoot+getOutputFileNameTag("jabund"));
 360                                                 }else if (Estimators[i] == "sorabund") {
 361                                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorabund"))));
 362                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorabund")); outputTypes["sorabund"].push_back(fileNameRoot+getOutputFileNameTag("sorabund"));
 363                                                 }else if (Estimators[i] == "jclass") {
 364                                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jclass"))));
 365                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("jclass")); outputTypes["jclass"].push_back(fileNameRoot+getOutputFileNameTag("jclass"));
 366                                                 }else if (Estimators[i] == "sorclass") {
 367                                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorclass"))));
 368                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorclass")); outputTypes["sorclass"].push_back(fileNameRoot+getOutputFileNameTag("sorclass"));
 369                                                 }else if (Estimators[i] == "jest") {
 370                                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jest"))));
 371                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("jest")); outputTypes["jest"].push_back(fileNameRoot+getOutputFileNameTag("jest"));
 372                                                 }else if (Estimators[i] == "sorest") {
 373                                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorest"))));
 374                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorest")); outputTypes["sorest"].push_back(fileNameRoot+getOutputFileNameTag("sorest"));
 375                                                 }else if (Estimators[i] == "thetayc") {
 376                                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("thetayc"))));
 377                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("thetayc")); outputTypes["thetayc"].push_back(fileNameRoot+getOutputFileNameTag("thetayc"));
 378                                                 }else if (Estimators[i] == "thetan") {
 379                                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("thetan"))));
 380                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("thetan")); outputTypes["thetan"].push_back(fileNameRoot+getOutputFileNameTag("thetan"));
 381                                                 }else if (Estimators[i] == "kstest") {
 382                                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kstest"))));
 383                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("kstest")); outputTypes["kstest"].push_back(fileNameRoot+getOutputFileNameTag("kstest"));
 384                                                 }else if (Estimators[i] == "whittaker") {
 385                                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("whittaker"))));
 386                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("whittaker")); outputTypes["whittaker"].push_back(fileNameRoot+getOutputFileNameTag("whittaker"));
 387                                                 }else if (Estimators[i] == "sharednseqs") {
 388                                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharednseqs"))));
 389                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharednseqs")); outputTypes["shared.nseqs"].push_back(fileNameRoot+getOutputFileNameTag("sharednseqs"));
 390                                                 }else if (Estimators[i] == "ochiai") {
 391                                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("ochiai"))));
 392                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("ochiai")); outputTypes["ochiai"].push_back(fileNameRoot+getOutputFileNameTag("ochiai"));
 393                                                 }else if (Estimators[i] == "anderberg") {
 394                                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("anderberg"))));
 395                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("anderberg")); outputTypes["anderberg"].push_back(fileNameRoot+getOutputFileNameTag("anderberg"));
 396                                                 }else if (Estimators[i] == "kulczynski") {
 397                                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kulczynski"))));
 398                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("kulczynski")); outputTypes["kulczynski"].push_back(fileNameRoot+getOutputFileNameTag("kulczynski"));
 399                                                 }else if (Estimators[i] == "kulczynskicody") {
 400                                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kulczynskicody"))));
 401                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("kulczynskicody")); outputTypes["kulczynskicody"].push_back(fileNameRoot+getOutputFileNameTag("kulczynskicody"));
 402                                                 }else if (Estimators[i] == "lennon") {
 403                                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("lennon"))));
 404                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("lennon")); outputTypes["lennon"].push_back(fileNameRoot+getOutputFileNameTag("lennon"));
 405                                                 }else if (Estimators[i] == "morisitahorn") {
 406                                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("morisitahorn"))));
 407                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("morisitahorn")); outputTypes["morisitahorn"].push_back(fileNameRoot+getOutputFileNameTag("morisitahorn"));
 408                                                 }else if (Estimators[i] == "braycurtis") {
 409                                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("braycurtis"))));
 410                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("braycurtis")); outputTypes["braycurtis"].push_back(fileNameRoot+getOutputFileNameTag("braycurtis"));
 411                                                 }else if (Estimators[i] == "odum") {
 412                                                         cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("odum"))));
 413                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("odum")); outputTypes["odum"].push_back(fileNameRoot+getOutputFileNameTag("odum"));
 414                                                 }else if (Estimators[i] == "canberra") {
 415                                                         cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("canberra"))));
 416                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("canberra")); outputTypes["canberra"].push_back(fileNameRoot+getOutputFileNameTag("canberra"));
 417                                                 }else if (Estimators[i] == "structeuclidean") {
 418                                                         cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structeuclidean"))));
 419                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("structeuclidean")); outputTypes["structeuclidean"].push_back(fileNameRoot+getOutputFileNameTag("structeuclidean"));
 420                                                 }else if (Estimators[i] == "structchord") {
 421                                                         cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structchord"))));
 422                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("structchord")); outputTypes["structchord"].push_back(fileNameRoot+getOutputFileNameTag("structchord"));
 423                                                 }else if (Estimators[i] == "hellinger") {
 424                                                         cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("hellinger"))));
 425                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("hellinger")); outputTypes["hellinger"].push_back(fileNameRoot+getOutputFileNameTag("hellinger"));
 426                                                 }else if (Estimators[i] == "manhattan") {
 427                                                         cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("manhattan"))));
 428                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("manhattan")); outputTypes["manhattan"].push_back(fileNameRoot+getOutputFileNameTag("manhattan"));
 429                                                 }else if (Estimators[i] == "structpearson") {
 430                                                         cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structpearson"))));
 431                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("structpearson")); outputTypes["structpearson"].push_back(fileNameRoot+getOutputFileNameTag("structpearson"));
 432                                                 }else if (Estimators[i] == "soergel") {
 433                                                         cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("soergel"))));
 434                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("soergel")); outputTypes["soergel"].push_back(fileNameRoot+getOutputFileNameTag("soergel"));
 435                                                 }else if (Estimators[i] == "spearman") {
 436                                                         cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("spearman"))));
 437                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("spearman")); outputTypes["spearman"].push_back(fileNameRoot+getOutputFileNameTag("spearman"));
 438                                                 }else if (Estimators[i] == "structkulczynski") {
 439                                                         cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structkulczynski"))));
 440                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("structkulczynski")); outputTypes["structkulczynski"].push_back(fileNameRoot+getOutputFileNameTag("structkulczynski"));
 441                                                 }else if (Estimators[i] == "speciesprofile") {
 442                                                         cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("speciesprofile"))));
 443                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("speciesprofile")); outputTypes["speciesprofile"].push_back(fileNameRoot+getOutputFileNameTag("speciesprofile"));
 444                                                 }else if (Estimators[i] == "hamming") {
 445                                                         cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("hamming"))));
 446                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("hamming")); outputTypes["hamming"].push_back(fileNameRoot+getOutputFileNameTag("hamming"));
 447                                                 }else if (Estimators[i] == "structchi2") {
 448                                                         cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structchi2"))));
 449                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("structchi2")); outputTypes["structchi2"].push_back(fileNameRoot+getOutputFileNameTag("structchi2"));
 450                                                 }else if (Estimators[i] == "gower") {
 451                                                         cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("gower"))));
 452                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("gower")); outputTypes["gower"].push_back(fileNameRoot+getOutputFileNameTag("gower"));
 453                                                 }else if (Estimators[i] == "memchi2") {
 454                                                         cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memchi2"))));
 455                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("memchi2")); outputTypes["memchi2"].push_back(fileNameRoot+getOutputFileNameTag("memchi2"));
 456                                                 }else if (Estimators[i] == "memchord") {
 457                                                         cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memchord"))));
 458                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("memchord")); outputTypes["memchord"].push_back(fileNameRoot+getOutputFileNameTag("memchord"));
 459                                                 }else if (Estimators[i] == "memeuclidean") {
 460                                                         cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memeuclidean"))));
 461                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("memeuclidean")); outputTypes["memeuclidean"].push_back(fileNameRoot+getOutputFileNameTag("memeuclidean"));
 462                                                 }else if (Estimators[i] == "mempearson") {
 463                                                         cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("mempearson"))));
 464                                                         outputNames.push_back(fileNameRoot+getOutputFileNameTag("mempearson")); outputTypes["mempearson"].push_back(fileNameRoot+getOutputFileNameTag("mempearson"));
 465                                                 }
 466
 467                                         }
 468                                 }
 469                         }
 470                 }
 471
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 475                 exit(1);
 476         }
 477 }
 478 //**********************************************************************************************************************
 479 CollectSharedCommand::~CollectSharedCommand(){}
 480 //**********************************************************************************************************************
 481
 482 int CollectSharedCommand::execute(){
 483         try {
 484
 485                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 486
 487                 //if the users entered no valid calculators don't execute command
 488                 if (cDisplays.size() == 0) { return 0; }
 489                 for(int i=0;i<cDisplays.size();i++){    cDisplays[i]->setAll(all);      }
 490
 491                 input = new InputData(sharedfile, "sharedfile");
 492                 order = input->getSharedOrderVector();
 493                 string lastLabel = order->getLabel();
 494
 495                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 496                 set<string> processedLabels;
 497                 set<string> userLabels = labels;
 498
 499                 //set users groups
 500                 SharedUtil* util = new SharedUtil();
 501                 Groups = m->getGroups();
 502                 vector<string> allGroups = m->getAllGroups();
 503                 util->setGroups(Groups, allGroups, "collect");
 504                 m->setGroups(Groups);
 505                 m->setAllGroups(allGroups);
 506                 delete util;
 507
 508                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 509                         if (m->control_pressed) {
 510                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 511                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 512                                         delete order; delete input;
 513                                         m->clearGroups();
 514                                         return 0;
 515                         }
 516
 517                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 518
 519                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 520                                 //create collectors curve
 521                                 cCurve = new Collect(order, cDisplays);
 522                                 cCurve->getSharedCurve(freq);
 523                                 delete cCurve;
 524
 525                                 processedLabels.insert(order->getLabel());
 526                                 userLabels.erase(order->getLabel());
 527                         }
 528
 529                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 530                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 531                                 string saveLabel = order->getLabel();
 532
 533                                 delete order;
 534                                 order = input->getSharedOrderVector(lastLabel);
 535
 536                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 537                                 //create collectors curve
 538                                 cCurve = new Collect(order, cDisplays);
 539                                 cCurve->getSharedCurve(freq);
 540                                 delete cCurve;
 541
 542                                 processedLabels.insert(order->getLabel());
 543                                 userLabels.erase(order->getLabel());
 544
 545                                 //restore real lastlabel to save below
 546                                 order->setLabel(saveLabel);
 547                         }
 548
 549
 550                         lastLabel = order->getLabel();
 551
 552                         //get next line to process
 553                         delete order;
 554                         order = input->getSharedOrderVector();
 555                 }
 556
 557                 if (m->control_pressed) {
 558                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }   outputTypes.clear();
 559                                         for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 560                                         m->clearGroups();
 561                                         delete input;
 562                                         return 0;
 563                 }
 564
 565                 //output error messages about any remaining user labels
 566                 set<string>::iterator it;
 567                 bool needToRun = false;
 568                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 569                         m->mothurOut("Your file does not include the label " + *it);
 570                         if (processedLabels.count(lastLabel) != 1) {
 571                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 572                                 needToRun = true;
 573                         }else {
 574                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 575                         }
 576                 }
 577
 578                 //run last label if you need to
 579                 if (needToRun == true)  {
 580                         if (order != NULL) {  delete order;  }
 581                         order = input->getSharedOrderVector(lastLabel);
 582
 583                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 584                         cCurve = new Collect(order, cDisplays);
 585                         cCurve->getSharedCurve(freq);
 586                         delete cCurve;
 587
 588                         if (m->control_pressed) {
 589                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
 590                                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 591                                 delete order;
 592                                 delete input;
 593                                 m->clearGroups();
 594                                 return 0;
 595                         }
 596
 597                         delete order;
 598                 }
 599
 600                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 601
 602                 //reset groups parameter
 603                 m->clearGroups();
 604                 delete input;
 605
 606                 m->mothurOutEndLine();
 607                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 608                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 609                 m->mothurOutEndLine();
 610
 611
 612                 return 0;
 613         }
 614         catch(exception& e) {
 615                 m->errorOut(e, "CollectSharedCommand", "execute");
 616                 exit(1);
 617         }
 618 }
 619
 620 /***********************************************************/