treegroupscommand.cpp

   1 /*
   2  *  treegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treegroupscommand.h"
  11 #include "subsample.h"
  12 #include "consensus.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> TreeGroupCommand::setParameters(){
  16         try {
  17                 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
  18                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
  19                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
  20                 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
  21         CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  22         CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
  23         CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
  24                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
  25                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  26                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  27                 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  28
  29         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  30 //CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "TreeGroupCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string TreeGroupCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 ValidCalculators validCalculator;
  48                 helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
  49                 helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
  50                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  51                 helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
  52                 helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used.  If you use a column file the name filename is required. \n";
  53                 helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
  54                 helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  55         helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
  56         helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
  57                 helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  58                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  59                 helpString += "The default value for calc is jclass-thetayc.\n";
  60                 helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
  61                 helpString += validCalculator.printCalc("treegroup");
  62                 helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
  63                 helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
  64                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  65                 return helpString;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "TreeGroupCommand", "getHelpString");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
  74         try {
  75         string outputFileName = "";
  76                 map<string, vector<string> >::iterator it;
  77
  78         //is this a type this command creates
  79         it = outputTypes.find(type);
  80         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  81         else {
  82             if (type == "tree")            {   outputFileName =  "tre";   }
  83             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  84         }
  85         return outputFileName;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
  89                 exit(1);
  90         }
  91 }
  92 //**********************************************************************************************************************
  93 TreeGroupCommand::TreeGroupCommand(){
  94         try {
  95                 abort = true; calledHelp = true;
  96                 setParameters();
  97                 //initialize outputTypes
  98                 vector<string> tempOutNames;
  99                 outputTypes["tree"] = tempOutNames;
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108 TreeGroupCommand::TreeGroupCommand(string option)  {
 109         try {
 110                 abort = false; calledHelp = false;
 111                 allLines = 1;
 112
 113                 //allow user to run help
 114                 if(option == "help") { help(); abort = true; calledHelp = true; }
 115                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 116
 117                 else {
 118                         vector<string> myArray = setParameters();
 119
 120                         OptionParser parser(option);
 121                         map<string, string> parameters = parser. getParameters();
 122
 123                         ValidParameters validParameter;
 124                         map<string, string>::iterator it;
 125
 126                         //check to make sure all parameters are valid for command
 127                         for (it = parameters.begin(); it != parameters.end(); it++) {
 128                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 129                         }
 130
 131                         //initialize outputTypes
 132                         vector<string> tempOutNames;
 133                         outputTypes["tree"] = tempOutNames;
 134
 135                         //if the user changes the input directory command factory will send this info to us in the output parameter
 136                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 137                         if (inputDir == "not found"){   inputDir = "";          }
 138                         else {
 139                                 string path;
 140                                 it = parameters.find("phylip");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 146                                 }
 147
 148                                 it = parameters.find("column");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 154                                 }
 155
 156                                 it = parameters.find("name");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 162                                 }
 163                         }
 164
 165                         //check for required parameters
 166                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 167                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 168                         else if (phylipfile == "not found") { phylipfile = ""; }
 169                         else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);       }
 170
 171                         columnfile = validParameter.validFile(parameters, "column", true);
 172                         if (columnfile == "not open") { columnfile = ""; abort = true; }
 173                         else if (columnfile == "not found") { columnfile = ""; }
 174                         else {  inputfile = columnfile; format = "column";      m->setColumnFile(columnfile); }
 175
 176                         sharedfile = validParameter.validFile(parameters, "shared", true);
 177                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 178                         else if (sharedfile == "not found") { sharedfile = ""; }
 179                         else {  inputfile = sharedfile; format = "sharedfile";  m->setSharedFile(sharedfile); }
 180
 181                         namefile = validParameter.validFile(parameters, "name", true);
 182                         if (namefile == "not open") { abort = true; }
 183                         else if (namefile == "not found") { namefile = ""; }
 184                         else { m->setNameFile(namefile); }
 185
 186                         if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
 187                                 //is there are current file available for either of these?
 188                                 //give priority to shared, then column, then phylip
 189                                 sharedfile = m->getSharedFile();
 190                                 if (sharedfile != "") {  inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 191                                 else {
 192                                         columnfile = m->getColumnFile();
 193                                         if (columnfile != "") { inputfile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 194                                         else {
 195                                                 phylipfile = m->getPhylipFile();
 196                                                 if (phylipfile != "") { inputfile = phylipfile;  format = "phylip";  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 197                                                 else {
 198                                                         m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
 199                                                         abort = true;
 200                                                 }
 201                                         }
 202                                 }
 203                         }
 204                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
 205
 206                         if (columnfile != "") {
 207                                 if (namefile == "") {
 208                                         namefile = m->getNameFile();
 209                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 210                                         else {
 211                                                 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
 212                                                 abort = true;
 213                                         }
 214                                 }
 215                         }
 216
 217                         //check for optional parameter and set defaults
 218                         // ...at some point should added some additional type checking...
 219                         label = validParameter.validFile(parameters, "label", false);
 220                         if (label == "not found") { label = ""; }
 221                         else {
 222                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 223                                 else { allLines = 1;  }
 224                         }
 225
 226                         groups = validParameter.validFile(parameters, "groups", false);
 227                         if (groups == "not found") { groups = ""; }
 228                         else {
 229                                 m->splitAtDash(groups, Groups);
 230                                 m->setGroups(Groups);
 231                         }
 232
 233                         calc = validParameter.validFile(parameters, "calc", false);
 234                         if (calc == "not found") { calc = "jclass-thetayc";  }
 235                         else {
 236                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 237                         }
 238                         m->splitAtDash(calc, Estimators);
 239                         if (m->inUsersGroups("citation", Estimators)) {
 240                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 241                                 //remove citation from list of calcs
 242                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 243                         }
 244
 245                         string temp;
 246                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 247                         m->mothurConvert(temp, precision);
 248
 249                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 250                         m->mothurConvert(temp, cutoff);
 251                         cutoff += (5 / (precision * 10.0));
 252
 253             temp = validParameter.validFile(parameters, "processors", false);   if (temp == "not found"){       temp = m->getProcessors();      }
 254                         m->setProcessors(temp);
 255                         m->mothurConvert(temp, processors);
 256
 257             temp = validParameter.validFile(parameters, "iters", false);                        if (temp == "not found") { temp = "1000"; }
 258                         m->mothurConvert(temp, iters);
 259
 260             temp = validParameter.validFile(parameters, "subsample", false);            if (temp == "not found") { temp = "F"; }
 261                         if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
 262             else {
 263                 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; }  //we will set it to smallest group later
 264                 else { subsample = false; }
 265             }
 266
 267             if (subsample == false) { iters = 1; }
 268
 269             if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
 270
 271                         //if the user changes the output directory command factory will send this info to us in the output parameter
 272                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 273                                 outputDir = "";
 274                                 outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
 275                         }
 276                 }
 277
 278         }
 279         catch(exception& e) {
 280                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 281                 exit(1);
 282         }
 283 }
 284 //**********************************************************************************************************************
 285
 286 TreeGroupCommand::~TreeGroupCommand(){
 287         if (abort == false) {
 288                 if (format == "sharedfile") {  delete input; }
 289                 else { delete readMatrix;  delete matrix; delete list; }
 290                 delete tmap;
 291         }
 292
 293 }
 294
 295 //**********************************************************************************************************************
 296
 297 int TreeGroupCommand::execute(){
 298         try {
 299
 300                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 301
 302                 if (format == "sharedfile") {
 303
 304                         ValidCalculators validCalculator;
 305
 306                         for (int i=0; i<Estimators.size(); i++) {
 307                                 if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
 308                                         if (Estimators[i] == "sharedsobs") {
 309                                                 treeCalculators.push_back(new SharedSobsCS());
 310                                         }else if (Estimators[i] == "sharedchao") {
 311                                                 treeCalculators.push_back(new SharedChao1());
 312                                         }else if (Estimators[i] == "sharedace") {
 313                                                 treeCalculators.push_back(new SharedAce());
 314                                         }else if (Estimators[i] == "jabund") {
 315                                                 treeCalculators.push_back(new JAbund());
 316                                         }else if (Estimators[i] == "sorabund") {
 317                                                 treeCalculators.push_back(new SorAbund());
 318                                         }else if (Estimators[i] == "jclass") {
 319                                                 treeCalculators.push_back(new Jclass());
 320                                         }else if (Estimators[i] == "sorclass") {
 321                                                 treeCalculators.push_back(new SorClass());
 322                                         }else if (Estimators[i] == "jest") {
 323                                                 treeCalculators.push_back(new Jest());
 324                                         }else if (Estimators[i] == "sorest") {
 325                                                 treeCalculators.push_back(new SorEst());
 326                                         }else if (Estimators[i] == "thetayc") {
 327                                                 treeCalculators.push_back(new ThetaYC());
 328                                         }else if (Estimators[i] == "thetan") {
 329                                                 treeCalculators.push_back(new ThetaN());
 330                                         }else if (Estimators[i] == "kstest") {
 331                                                 treeCalculators.push_back(new KSTest());
 332                                         }else if (Estimators[i] == "sharednseqs") {
 333                                                 treeCalculators.push_back(new SharedNSeqs());
 334                                         }else if (Estimators[i] == "ochiai") {
 335                                                 treeCalculators.push_back(new Ochiai());
 336                                         }else if (Estimators[i] == "anderberg") {
 337                                                 treeCalculators.push_back(new Anderberg());
 338                                         }else if (Estimators[i] == "kulczynski") {
 339                                                 treeCalculators.push_back(new Kulczynski());
 340                                         }else if (Estimators[i] == "kulczynskicody") {
 341                                                 treeCalculators.push_back(new KulczynskiCody());
 342                                         }else if (Estimators[i] == "lennon") {
 343                                                 treeCalculators.push_back(new Lennon());
 344                                         }else if (Estimators[i] == "morisitahorn") {
 345                                                 treeCalculators.push_back(new MorHorn());
 346                                         }else if (Estimators[i] == "braycurtis") {
 347                                                 treeCalculators.push_back(new BrayCurtis());
 348                                         }else if (Estimators[i] == "whittaker") {
 349                                                 treeCalculators.push_back(new Whittaker());
 350                                         }else if (Estimators[i] == "odum") {
 351                                                 treeCalculators.push_back(new Odum());
 352                                         }else if (Estimators[i] == "canberra") {
 353                                                 treeCalculators.push_back(new Canberra());
 354                                         }else if (Estimators[i] == "structeuclidean") {
 355                                                 treeCalculators.push_back(new StructEuclidean());
 356                                         }else if (Estimators[i] == "structchord") {
 357                                                 treeCalculators.push_back(new StructChord());
 358                                         }else if (Estimators[i] == "hellinger") {
 359                                                 treeCalculators.push_back(new Hellinger());
 360                                         }else if (Estimators[i] == "manhattan") {
 361                                                 treeCalculators.push_back(new Manhattan());
 362                                         }else if (Estimators[i] == "structpearson") {
 363                                                 treeCalculators.push_back(new StructPearson());
 364                                         }else if (Estimators[i] == "soergel") {
 365                                                 treeCalculators.push_back(new Soergel());
 366                                         }else if (Estimators[i] == "spearman") {
 367                                                 treeCalculators.push_back(new Spearman());
 368                                         }else if (Estimators[i] == "structkulczynski") {
 369                                                 treeCalculators.push_back(new StructKulczynski());
 370                                         }else if (Estimators[i] == "speciesprofile") {
 371                                                 treeCalculators.push_back(new SpeciesProfile());
 372                                         }else if (Estimators[i] == "hamming") {
 373                                                 treeCalculators.push_back(new Hamming());
 374                                         }else if (Estimators[i] == "structchi2") {
 375                                                 treeCalculators.push_back(new StructChi2());
 376                                         }else if (Estimators[i] == "gower") {
 377                                                 treeCalculators.push_back(new Gower());
 378                                         }else if (Estimators[i] == "memchi2") {
 379                                                 treeCalculators.push_back(new MemChi2());
 380                                         }else if (Estimators[i] == "memchord") {
 381                                                 treeCalculators.push_back(new MemChord());
 382                                         }else if (Estimators[i] == "memeuclidean") {
 383                                                 treeCalculators.push_back(new MemEuclidean());
 384                                         }else if (Estimators[i] == "mempearson") {
 385                                                 treeCalculators.push_back(new MemPearson());
 386                                         }
 387                                 }
 388                         }
 389
 390                         //if the users entered no valid calculators don't execute command
 391                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 392
 393                         input = new InputData(sharedfile, "sharedfile");
 394                         lookup = input->getSharedRAbundVectors();
 395                         lastLabel = lookup[0]->getLabel();
 396
 397                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 398
 399                         //used in tree constructor
 400                         m->runParse = false;
 401
 402                         //create treemap class from groupmap for tree class to use
 403                         tmap = new TreeMap();
 404                         tmap->makeSim(m->getAllGroups());
 405
 406                         //clear globaldatas old tree names if any
 407                         m->Treenames.clear();
 408
 409                         //fills globaldatas tree names
 410                         m->Treenames = m->getGroups();
 411
 412                         if (m->control_pressed) { return 0; }
 413
 414                         //create tree file
 415                         makeSimsShared();
 416
 417                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 418                 }else{
 419                         //read in dist file
 420                         filename = inputfile;
 421
 422                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 423                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 424
 425                         readMatrix->setCutoff(cutoff);
 426
 427                         if(namefile != ""){
 428                                 nameMap = new NameAssignment(namefile);
 429                                 nameMap->readMap();
 430                         }
 431                         else{
 432                                 nameMap = NULL;
 433                         }
 434
 435                         readMatrix->read(nameMap);
 436                         list = readMatrix->getListVector();
 437                         matrix = readMatrix->getMatrix();
 438
 439                         //make treemap
 440                         tmap = new TreeMap();
 441
 442                         if (m->control_pressed) { return 0; }
 443
 444                         tmap->makeSim(list);
 445
 446                         vector<string> namesGroups = tmap->getNamesOfGroups();
 447                         m->setGroups(namesGroups);
 448
 449                         //clear globaldatas old tree names if any
 450                         m->Treenames.clear();
 451
 452                         //fills globaldatas tree names
 453                         m->Treenames = m->getGroups();
 454
 455                         //used in tree constructor
 456                         m->runParse = false;
 457
 458                         if (m->control_pressed) { return 0; }
 459
 460                         vector< vector<double> > matrix = makeSimsDist();
 461
 462                         if (m->control_pressed) { return 0; }
 463
 464                         //create a new filename
 465                         string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");
 466                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 467
 468                         Tree* newTree = createTree(matrix);
 469
 470             if (newTree != NULL) {  writeTree(outputFile, newTree); delete newTree; }
 471
 472                         if (m->control_pressed) { return 0; }
 473
 474                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 475
 476                 }
 477
 478                 //reset groups parameter
 479                 m->clearGroups();
 480
 481                 //set tree file as new current treefile
 482                 string current = "";
 483                 itTypes = outputTypes.find("tree");
 484                 if (itTypes != outputTypes.end()) {
 485                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 486                 }
 487
 488                 m->mothurOutEndLine();
 489                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 490                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 491                 m->mothurOutEndLine();
 492
 493                 return 0;
 494         }
 495         catch(exception& e) {
 496                 m->errorOut(e, "TreeGroupCommand", "execute");
 497                 exit(1);
 498         }
 499 }
 500 //**********************************************************************************************************************
 501
 502 Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
 503         try {
 504                 //create tree
 505                 t = new Tree(tmap, simMatrix);
 506
 507         if (m->control_pressed) { delete t; t = NULL; return t; }
 508
 509         //assemble tree
 510         map<string, string> empty;
 511                 t->assembleTree(empty);
 512
 513                 return t;
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "TreeGroupCommand", "createTree");
 517                 exit(1);
 518         }
 519 }
 520 /***********************************************************/
 521 int TreeGroupCommand::writeTree(string out, Tree* T) {
 522         try {
 523
 524         //print newick file
 525                 t->createNewickFile(out);
 526
 527         if (m->control_pressed) { m->mothurRemove(out); outputNames.pop_back(); return 1; }
 528
 529         return 0;
 530
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "TreeGroupCommand", "printSims");
 534                 exit(1);
 535         }
 536 }
 537
 538 /***********************************************************/
 539 void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
 540         try {
 541
 542         for (int m = 0; m < simMatrix.size(); m++)      {
 543                         //out << lookup[m]->getGroup() << '\t';
 544                         for (int n = 0; n < simMatrix.size(); n++)      {
 545                                 out << simMatrix[m][n] << '\t';
 546                         }
 547                         out << endl;
 548                 }
 549
 550         }
 551         catch(exception& e) {
 552                 m->errorOut(e, "TreeGroupCommand", "printSims");
 553                 exit(1);
 554         }
 555 }
 556 /***********************************************************/
 557 vector< vector<double> > TreeGroupCommand::makeSimsDist() {
 558         try {
 559                 numGroups = list->size();
 560
 561                 //initialize simMatrix
 562                 vector< vector<double> > simMatrix;
 563                 simMatrix.resize(numGroups);
 564                 for (int k = 0; k < simMatrix.size(); k++)      {
 565                         for (int j = 0; j < simMatrix.size(); j++)      {
 566                                 simMatrix[k].push_back(0.0);
 567                         }
 568                 }
 569
 570                 //go through sparse matrix and fill sims
 571                 //go through each cell in the sparsematrix
 572                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 573                         //similairity = -(distance-1)
 574                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 575                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 576
 577                         if (m->control_pressed) { return simMatrix; }
 578
 579                 }
 580
 581                 return simMatrix;
 582         }
 583         catch(exception& e) {
 584                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 585                 exit(1);
 586         }
 587 }
 588
 589 /***********************************************************/
 590 int TreeGroupCommand::makeSimsShared() {
 591         try {
 592
 593         if (subsample) {
 594             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
 595                 subsampleSize = lookup[0]->getNumSeqs();
 596                 for (int i = 1; i < lookup.size(); i++) {
 597                     int thisSize = lookup[i]->getNumSeqs();
 598
 599                     if (thisSize < subsampleSize) {     subsampleSize = thisSize;       }
 600                 }
 601             }else {
 602                 m->clearGroups();
 603                 Groups.clear();
 604                 vector<SharedRAbundVector*> temp;
 605                 for (int i = 0; i < lookup.size(); i++) {
 606                     if (lookup[i]->getNumSeqs() < subsampleSize) {
 607                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 608                         delete lookup[i];
 609                     }else {
 610                         Groups.push_back(lookup[i]->getGroup());
 611                         temp.push_back(lookup[i]);
 612                     }
 613                 }
 614                 lookup = temp;
 615                 m->setGroups(Groups);
 616             }
 617
 618             if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
 619         }
 620
 621         numGroups = lookup.size();
 622                 lines.resize(processors);
 623                 for (int i = 0; i < processors; i++) {
 624                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 625                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 626                 }
 627
 628                 set<string> processedLabels;
 629                 set<string> userLabels = labels;
 630
 631                 //as long as you are not at the end of the file or done wih the lines you want
 632                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 633                         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
 634
 635                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 636                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 637                                 process(lookup);
 638
 639                                 processedLabels.insert(lookup[0]->getLabel());
 640                                 userLabels.erase(lookup[0]->getLabel());
 641                         }
 642
 643                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 644                                 string saveLabel = lookup[0]->getLabel();
 645
 646                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 647                                 lookup = input->getSharedRAbundVectors(lastLabel);
 648
 649                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 650                                 process(lookup);
 651
 652                                 processedLabels.insert(lookup[0]->getLabel());
 653                                 userLabels.erase(lookup[0]->getLabel());
 654
 655                                 //restore real lastlabel to save below
 656                                 lookup[0]->setLabel(saveLabel);
 657                         }
 658
 659                         lastLabel = lookup[0]->getLabel();
 660
 661                         //get next line to process
 662                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 663                         lookup = input->getSharedRAbundVectors();
 664                 }
 665
 666                 if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
 667
 668                 //output error messages about any remaining user labels
 669                 set<string>::iterator it;
 670                 bool needToRun = false;
 671                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 672                         m->mothurOut("Your file does not include the label " + *it);
 673                         if (processedLabels.count(lastLabel) != 1) {
 674                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 675                                 needToRun = true;
 676                         }else {
 677                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 678                         }
 679                 }
 680
 681                 //run last label if you need to
 682                 if (needToRun == true)  {
 683                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 684                         lookup = input->getSharedRAbundVectors(lastLabel);
 685
 686                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 687                         process(lookup);
 688                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 689                 }
 690
 691                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 692
 693                 return 0;
 694         }
 695         catch(exception& e) {
 696                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 697                 exit(1);
 698         }
 699 }
 700
 701 /***********************************************************/
 702 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 703         try{
 704                 vector< vector< vector<seqDist> > > calcDistsTotals;  //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
 705         vector< vector<seqDist>  > calcDists; calcDists.resize(treeCalculators.size());
 706
 707         for (int thisIter = 0; thisIter < iters; thisIter++) {
 708
 709             vector<SharedRAbundVector*> thisItersLookup = thisLookup;
 710
 711             if (subsample) {
 712                 SubSample sample;
 713                 vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
 714
 715                 //make copy of lookup so we don't get access violations
 716                 vector<SharedRAbundVector*> newLookup;
 717                 for (int k = 0; k < thisItersLookup.size(); k++) {
 718                     SharedRAbundVector* temp = new SharedRAbundVector();
 719                     temp->setLabel(thisItersLookup[k]->getLabel());
 720                     temp->setGroup(thisItersLookup[k]->getGroup());
 721                     newLookup.push_back(temp);
 722                 }
 723
 724                 //for each bin
 725                 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 726                     if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 727                     for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 728                 }
 729
 730                 tempLabels = sample.getSample(newLookup, subsampleSize);
 731                 thisItersLookup = newLookup;
 732             }
 733
 734             if(processors == 1){
 735                 driver(thisItersLookup, 0, numGroups, calcDists);
 736             }else{
 737                 int process = 1;
 738                 vector<int> processIDS;
 739
 740 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 741                 //loop through and create all the processes you want
 742                 while (process != processors) {
 743                     int pid = fork();
 744
 745                     if (pid > 0) {
 746                         processIDS.push_back(pid);
 747                         process++;
 748                     }else if (pid == 0){
 749
 750                         driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
 751
 752                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
 753                         ofstream outtemp;
 754                         m->openOutputFile(tempdistFileName, outtemp);
 755
 756                         for (int i = 0; i < calcDists.size(); i++) {
 757                             outtemp << calcDists[i].size() << endl;
 758
 759                             for (int j = 0; j < calcDists[i].size(); j++) {
 760                                 outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 761                             }
 762                         }
 763                         outtemp.close();
 764
 765                         exit(0);
 766                     }else {
 767                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 768                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 769                         exit(0);
 770                     }
 771                 }
 772
 773                 //parent do your part
 774                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 775
 776                 //force parent to wait until all the processes are done
 777                 for (int i = 0; i < processIDS.size(); i++) {
 778                     int temp = processIDS[i];
 779                     wait(&temp);
 780                 }
 781
 782                 for (int i = 0; i < processIDS.size(); i++) {
 783                     string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 784                     ifstream intemp;
 785                     m->openInputFile(tempdistFileName, intemp);
 786
 787                     for (int k = 0; k < calcDists.size(); k++) {
 788                         int size = 0;
 789                         intemp >> size; m->gobble(intemp);
 790
 791                         for (int j = 0; j < size; j++) {
 792                             int seq1 = 0;
 793                             int seq2 = 0;
 794                             float dist = 1.0;
 795
 796                             intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 797
 798                             seqDist tempDist(seq1, seq2, dist);
 799                             calcDists[k].push_back(tempDist);
 800                         }
 801                     }
 802                     intemp.close();
 803                     m->mothurRemove(tempdistFileName);
 804                 }
 805 #else
 806                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 807                 //Windows version shared memory, so be careful when passing variables through the treeSharedData struct.
 808                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 809                 //Taking advantage of shared memory to pass results vectors.
 810                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 811
 812                 vector<treeSharedData*> pDataArray;
 813                 DWORD   dwThreadIdArray[processors-1];
 814                 HANDLE  hThreadArray[processors-1];
 815
 816                 //Create processor worker threads.
 817                 for( int i=1; i<processors; i++ ){
 818
 819                     //make copy of lookup so we don't get access violations
 820                     vector<SharedRAbundVector*> newLookup;
 821                     for (int k = 0; k < thisItersLookup.size(); k++) {
 822                         SharedRAbundVector* temp = new SharedRAbundVector();
 823                         temp->setLabel(thisItersLookup[k]->getLabel());
 824                         temp->setGroup(thisItersLookup[k]->getGroup());
 825                         newLookup.push_back(temp);
 826                     }
 827
 828                     //for each bin
 829                     for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 830                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 831                         for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 832                     }
 833
 834                     // Allocate memory for thread data.
 835                     treeSharedData* tempSum = new treeSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
 836                     pDataArray.push_back(tempSum);
 837                     processIDS.push_back(i);
 838
 839                     hThreadArray[i-1] = CreateThread(NULL, 0, MyTreeSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 840                 }
 841
 842                 //parent do your part
 843                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 844
 845                 //Wait until all threads have terminated.
 846                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 847
 848                 //Close all thread handles and free memory allocations.
 849                 for(int i=0; i < pDataArray.size(); i++){
 850                     for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  }
 851
 852                     for (int k = 0; k < calcDists.size(); k++) {
 853                         int size = pDataArray[i]->calcDists[k].size();
 854                         for (int j = 0; j < size; j++) {    calcDists[k].push_back(pDataArray[i]->calcDists[k][j]);    }
 855                     }
 856
 857                     CloseHandle(hThreadArray[i]);
 858                     delete pDataArray[i];
 859                 }
 860
 861 #endif
 862             }
 863
 864             calcDistsTotals.push_back(calcDists);
 865
 866             if (subsample) {
 867
 868                 //clean up memory
 869                 for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
 870                 thisItersLookup.clear();
 871                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
 872             }
 873                 }
 874
 875         if (iters != 1) {
 876             //we need to find the average distance and standard deviation for each groups distance
 877
 878             vector< vector<seqDist>  > calcAverages; calcAverages.resize(treeCalculators.size());
 879             for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
 880                 calcAverages[i].resize(calcDistsTotals[0][i].size());
 881
 882                 for (int j = 0; j < calcAverages[i].size(); j++) {
 883                     calcAverages[i][j].seq1 = calcDists[i][j].seq1;
 884                     calcAverages[i][j].seq2 = calcDists[i][j].seq2;
 885                     calcAverages[i][j].dist = 0.0;
 886                 }
 887             }
 888
 889             for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
 890                 for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
 891                     for (int j = 0; j < calcAverages[i].size(); j++) {
 892                         calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
 893                     }
 894                 }
 895             }
 896
 897             for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
 898                 for (int j = 0; j < calcAverages[i].size(); j++) {
 899                     calcAverages[i][j].dist /= (float) iters;
 900                 }
 901             }
 902
 903             //create average tree for each calc
 904             for (int i = 0; i < calcDists.size(); i++) {
 905                 vector< vector<double> > matrix; //square matrix to represent the distance
 906                 matrix.resize(thisLookup.size());
 907                 for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 908
 909                 for (int j = 0; j < calcAverages[i].size(); j++) {
 910                     int row = calcAverages[i][j].seq1;
 911                     int column = calcAverages[i][j].seq2;
 912                     float dist = calcAverages[i][j].dist;
 913
 914                     matrix[row][column] = dist;
 915                     matrix[column][row] = dist;
 916                 }
 917
 918                 //create a new filename
 919                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");
 920                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 921
 922                 //creates tree from similarity matrix and write out file
 923                 Tree* newTree = createTree(matrix);
 924                 if (newTree != NULL) { writeTree(outputFile, newTree); }
 925             }
 926
 927             //create all trees for each calc and find their consensus tree
 928             for (int i = 0; i < calcDists.size(); i++) {
 929                 if (m->control_pressed) { break; }
 930
 931                 //create a new filename
 932                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");
 933                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 934
 935                 ofstream outAll;
 936                 m->openOutputFile(outputFile, outAll);
 937
 938                 vector<Tree*> trees;
 939                 for (int myIter = 0; myIter < iters; myIter++) {
 940
 941                     if(m->control_pressed) { break; }
 942
 943                     //initialize matrix
 944                     vector< vector<double> > matrix; //square matrix to represent the distance
 945                     matrix.resize(thisLookup.size());
 946                     for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 947
 948                     for (int j = 0; j < calcDistsTotals[myIter][i].size(); j++) {
 949                         int row = calcDistsTotals[myIter][i][j].seq1;
 950                         int column = calcDistsTotals[myIter][i][j].seq2;
 951                         double dist = calcDistsTotals[myIter][i][j].dist;
 952
 953                         matrix[row][column] = dist;
 954                         matrix[column][row] = dist;
 955                     }
 956
 957                     //creates tree from similarity matrix and write out file
 958                     Tree* newTree = createTree(matrix);
 959                     if (newTree != NULL) {
 960                         newTree->print(outAll);
 961                         trees.push_back(newTree);
 962                     }
 963                 }
 964                 outAll.close();
 965                 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
 966
 967                 Consensus consensus;
 968                 //clear old tree names if any
 969                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
 970                 Tree* conTree = consensus.getTree(trees);
 971
 972                 //create a new filename
 973                 string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");
 974                 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
 975                 ofstream outTree;
 976                 m->openOutputFile(conFile, outTree);
 977
 978                 if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
 979             }
 980
 981         }else {
 982
 983             for (int i = 0; i < calcDists.size(); i++) {
 984                 if (m->control_pressed) { break; }
 985
 986                 //initialize matrix
 987                 vector< vector<double> > matrix; //square matrix to represent the distance
 988                 matrix.resize(thisLookup.size());
 989                 for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 990
 991                 for (int j = 0; j < calcDists[i].size(); j++) {
 992                     int row = calcDists[i][j].seq1;
 993                     int column = calcDists[i][j].seq2;
 994                     double dist = calcDists[i][j].dist;
 995
 996                     matrix[row][column] = dist;
 997                     matrix[column][row] = dist;
 998                 }
 999
1000                 //create a new filename
1001                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");
1002                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
1003
1004                 //creates tree from similarity matrix and write out file
1005                 Tree* newTree = createTree(matrix);
1006                 if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
1007             }
1008         }
1009
1010                 return 0;
1011         }
1012         catch(exception& e) {
1013                 m->errorOut(e, "TreeGroupCommand", "process");
1014                 exit(1);
1015         }
1016 }
1017 /**************************************************************************************************/
1018 int TreeGroupCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
1019         try {
1020                 vector<SharedRAbundVector*> subset;
1021                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
1022
1023                         for (int l = 0; l < k; l++) {
1024
1025                                 if (k != l) { //we dont need to similiarity of a groups to itself
1026                                         subset.clear(); //clear out old pair of sharedrabunds
1027                                         //add new pair of sharedrabunds
1028                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
1029
1030                                         for(int i=0;i<treeCalculators.size();i++) {
1031
1032                                                 //if this calc needs all groups to calculate the pair load all groups
1033                                                 if (treeCalculators[i]->getNeedsAll()) {
1034                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
1035                                                         for (int w = 0; w < thisLookup.size(); w++) {
1036                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
1037                                                         }
1038                                                 }
1039
1040                                                 vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
1041
1042                                                 if (m->control_pressed) { return 1; }
1043
1044                                                 seqDist temp(l, k, -(tempdata[0]-1.0));
1045                                                 calcDists[i].push_back(temp);
1046                                         }
1047                                 }
1048                         }
1049                 }
1050
1051                 return 0;
1052         }
1053         catch(exception& e) {
1054                 m->errorOut(e, "TreeGroupCommand", "driver");
1055                 exit(1);
1056         }
1057 }
1058 /***********************************************************/
1059
1060
1061