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