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 "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24
  25 TreeGroupCommand::TreeGroupCommand(string option)  {
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 abort = false;
  29                 allLines = 1;
  30                 labels.clear();
  31                 Groups.clear();
  32                 Estimators.clear();
  33
  34                 //allow user to run help
  35                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  36
  37                 else {
  38                         //valid paramters for this command
  39                         string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
  40                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  41
  42                         OptionParser parser(option);
  43                         map<string, string> parameters = parser. getParameters();
  44
  45                         ValidParameters validParameter;
  46                         map<string, string>::iterator it;
  47
  48                         //check to make sure all parameters are valid for command
  49                         for (it = parameters.begin(); it != parameters.end(); it++) {
  50                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  51                         }
  52
  53                         globaldata->newRead();
  54
  55                         //if the user changes the input directory command factory will send this info to us in the output parameter
  56                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  57                         if (inputDir == "not found"){   inputDir = "";          }
  58                         else {
  59                                 string path;
  60                                 it = parameters.find("phylip");
  61                                 //user has given a template file
  62                                 if(it != parameters.end()){
  63                                         path = m->hasPath(it->second);
  64                                         //if the user has not given a path then, add inputdir. else leave path alone.
  65                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  66                                 }
  67
  68                                 it = parameters.find("column");
  69                                 //user has given a template file
  70                                 if(it != parameters.end()){
  71                                         path = m->hasPath(it->second);
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.
  73                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
  74                                 }
  75
  76                                 it = parameters.find("name");
  77                                 //user has given a template file
  78                                 if(it != parameters.end()){
  79                                         path = m->hasPath(it->second);
  80                                         //if the user has not given a path then, add inputdir. else leave path alone.
  81                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  82                                 }
  83                         }
  84
  85                         format = globaldata->getFormat();
  86
  87                         //required parameters
  88                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  89                         if (phylipfile == "not open") { abort = true; }
  90                         else if (phylipfile == "not found") { phylipfile = ""; }
  91                         else {  format = "phylip";  globaldata->setPhylipFile(phylipfile);      }
  92
  93                         columnfile = validParameter.validFile(parameters, "column", true);
  94                         if (columnfile == "not open") { abort = true; }
  95                         else if (columnfile == "not found") { columnfile = ""; }
  96                         else {  format = "column"; globaldata->setColumnFile(columnfile);       }
  97
  98                         namefile = validParameter.validFile(parameters, "name", true);
  99                         if (namefile == "not open") { abort = true; }
 100                         else if (namefile == "not found") { namefile = ""; }
 101                         else {  globaldata->setNameFile(namefile);      }
 102
 103                         //error checking on files
 104                         if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { m->mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); m->mothurOutEndLine(); abort = true; }
 105                         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; }
 106
 107                         if (columnfile != "") {
 108                                 if (namefile == "") {  m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
 109                         }
 110
 111                         //check for optional parameter and set defaults
 112                         // ...at some point should added some additional type checking...
 113                         label = validParameter.validFile(parameters, "label", false);
 114                         if (label == "not found") { label = ""; }
 115                         else {
 116                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 117                                 else { allLines = 1;  }
 118                         }
 119
 120                         //if the user has not specified any labels use the ones from read.otu
 121                         if(label == "") {
 122                                 allLines = globaldata->allLines;
 123                                 labels = globaldata->labels;
 124                         }
 125
 126                         groups = validParameter.validFile(parameters, "groups", false);
 127                         if (groups == "not found") { groups = ""; }
 128                         else {
 129                                 m->splitAtDash(groups, Groups);
 130                                 globaldata->Groups = Groups;
 131                         }
 132
 133                         calc = validParameter.validFile(parameters, "calc", false);
 134                         if (calc == "not found") { calc = "jclass-thetayc";  }
 135                         else {
 136                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 137                         }
 138                         m->splitAtDash(calc, Estimators);
 139
 140                         string temp;
 141                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 142                         convert(temp, precision);
 143
 144                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 145                         convert(temp, cutoff);
 146                         cutoff += (5 / (precision * 10.0));
 147
 148                         //if the user changes the output directory command factory will send this info to us in the output parameter
 149                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 150                                 outputDir = "";
 151                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 152                         }
 153
 154
 155                         if (abort == false) {
 156
 157                                 validCalculator = new ValidCalculators();
 158
 159                                 if (format == "sharedfile") {
 160                                         int i;
 161                                         for (i=0; i<Estimators.size(); i++) {
 162                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 163                                                         if (Estimators[i] == "jabund") {
 164                                                                 treeCalculators.push_back(new JAbund());
 165                                                         }else if (Estimators[i] == "sorabund") {
 166                                                                 treeCalculators.push_back(new SorAbund());
 167                                                         }else if (Estimators[i] == "jclass") {
 168                                                                 treeCalculators.push_back(new Jclass());
 169                                                         }else if (Estimators[i] == "sorclass") {
 170                                                                 treeCalculators.push_back(new SorClass());
 171                                                         }else if (Estimators[i] == "jest") {
 172                                                                 treeCalculators.push_back(new Jest());
 173                                                         }else if (Estimators[i] == "sorest") {
 174                                                                 treeCalculators.push_back(new SorEst());
 175                                                         }else if (Estimators[i] == "thetayc") {
 176                                                                 treeCalculators.push_back(new ThetaYC());
 177                                                         }else if (Estimators[i] == "thetan") {
 178                                                                 treeCalculators.push_back(new ThetaN());
 179                                                         }else if (Estimators[i] == "morisitahorn") {
 180                                                                 treeCalculators.push_back(new MorHorn());
 181                                                         }else if (Estimators[i] == "braycurtis") {
 182                                                                 treeCalculators.push_back(new BrayCurtis());
 183                                                         }
 184                                                 }
 185                                         }
 186                                 }
 187                         }
 188                 }
 189
 190         }
 191         catch(exception& e) {
 192                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 193                 exit(1);
 194         }
 195 }
 196
 197 //**********************************************************************************************************************
 198
 199 void TreeGroupCommand::help(){
 200         try {
 201                 m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
 202                 m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
 203                 m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
 204                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 205                 m->mothurOut("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");
 206                 m->mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used.  If you use a column file the name filename is required. \n");
 207                 m->mothurOut("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");
 208                 m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
 209                 m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
 210                 m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
 211                 m->mothurOut("The default value for calc is jclass-thetayc.\n");
 212                 m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
 213                 validCalculator->printCalc("treegroup", cout);
 214                 m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
 215                 m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
 216                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 217         }
 218         catch(exception& e) {
 219                 m->errorOut(e, "TreeGroupCommand", "help");
 220                 exit(1);
 221         }
 222 }
 223
 224
 225 //**********************************************************************************************************************
 226
 227 TreeGroupCommand::~TreeGroupCommand(){
 228         globaldata->Groups.clear();
 229         if (abort == false) {
 230
 231                 if (format == "sharedfile") { delete read;  delete input; globaldata->ginput = NULL; }
 232                 else { delete readMatrix;  delete matrix; delete list; }
 233                 delete tmap;  globaldata->gTreemap = NULL;
 234                 delete validCalculator;
 235         }
 236
 237 }
 238
 239 //**********************************************************************************************************************
 240
 241 int TreeGroupCommand::execute(){
 242         try {
 243
 244                 if (abort == true) { return 0; }
 245
 246                 if (format == "sharedfile") {
 247                         //if the users entered no valid calculators don't execute command
 248                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 249
 250                         if (globaldata->gGroupmap != NULL) {  delete globaldata->gGroupmap;   globaldata->gGroupmap = NULL;  }
 251                         //you have groups
 252                         read = new ReadOTUFile(globaldata->inputFileName);
 253                         read->read(&*globaldata);
 254
 255                         input = globaldata->ginput;
 256                         lookup = input->getSharedRAbundVectors();
 257                         lastLabel = lookup[0]->getLabel();
 258
 259                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 260
 261                         //used in tree constructor
 262                         globaldata->runParse = false;
 263
 264                         //create treemap class from groupmap for tree class to use
 265                         tmap = new TreeMap();
 266                         tmap->makeSim(globaldata->gGroupmap);
 267                         globaldata->gTreemap = tmap;
 268
 269                         //clear globaldatas old tree names if any
 270                         globaldata->Treenames.clear();
 271
 272                         //fills globaldatas tree names
 273                         globaldata->Treenames = globaldata->Groups;
 274
 275                         if (m->control_pressed) { return 0; }
 276
 277                         //create tree file
 278                         makeSimsShared();
 279
 280                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 281                 }else{
 282                         //read in dist file
 283                         filename = globaldata->inputFileName;
 284
 285                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 286                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 287
 288                         readMatrix->setCutoff(cutoff);
 289
 290                         if(namefile != ""){
 291                                 nameMap = new NameAssignment(namefile);
 292                                 nameMap->readMap();
 293                         }
 294                         else{
 295                                 nameMap = NULL;
 296                         }
 297
 298                         readMatrix->read(nameMap);
 299                         list = readMatrix->getListVector();
 300                         matrix = readMatrix->getMatrix();
 301
 302                         //make treemap
 303                         tmap = new TreeMap();
 304
 305                         if (m->control_pressed) { return 0; }
 306
 307                         tmap->makeSim(list);
 308                         globaldata->gTreemap = tmap;
 309
 310                         globaldata->Groups = tmap->namesOfGroups;
 311
 312                         //clear globaldatas old tree names if any
 313                         globaldata->Treenames.clear();
 314
 315                         //fills globaldatas tree names
 316                         globaldata->Treenames = globaldata->Groups;
 317
 318                         //used in tree constructor
 319                         globaldata->runParse = false;
 320
 321                         if (m->control_pressed) { return 0; }
 322
 323                         makeSimsDist();
 324
 325                         if (m->control_pressed) { return 0; }
 326
 327                         //create a new filename
 328                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";
 329                         outputNames.push_back(outputFile);
 330
 331                         createTree();
 332
 333                         if (m->control_pressed) { return 0; }
 334
 335                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 336
 337                 }
 338
 339                 //reset groups parameter
 340                 globaldata->Groups.clear();
 341
 342                 m->mothurOutEndLine();
 343                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 344                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 345                 m->mothurOutEndLine();
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "TreeGroupCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 //**********************************************************************************************************************
 355
 356 int TreeGroupCommand::createTree(){
 357         try {
 358                 //create tree
 359                 t = new Tree();
 360
 361                 //do merges and create tree structure by setting parents and children
 362                 //there are numGroups - 1 merges to do
 363                 for (int i = 0; i < (numGroups - 1); i++) {
 364                         float largest = -1000.0;
 365
 366                         if (m->control_pressed) { delete t; return 1; }
 367
 368                         int row, column;
 369                         //find largest value in sims matrix by searching lower triangle
 370                         for (int j = 1; j < simMatrix.size(); j++) {
 371                                 for (int k = 0; k < j; k++) {
 372                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 373                                 }
 374                         }
 375
 376                         //set non-leaf node info and update leaves to know their parents
 377                         //non-leaf
 378                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 379
 380                         //parents
 381                         t->tree[index[row]].setParent(numGroups + i);
 382                         t->tree[index[column]].setParent(numGroups + i);
 383
 384                         //blength = distance / 2;
 385                         float blength = ((1.0 - largest) / 2);
 386
 387                         //branchlengths
 388                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 389                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 390
 391                         //set your length to leaves to your childs length plus branchlength
 392                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 393
 394
 395                         //update index
 396                         index[row] = numGroups+i;
 397                         index[column] = numGroups+i;
 398
 399                         //remove highest value that caused the merge.
 400                         simMatrix[row][column] = -1000.0;
 401                         simMatrix[column][row] = -1000.0;
 402
 403                         //merge values in simsMatrix
 404                         for (int n = 0; n < simMatrix.size(); n++)      {
 405                                 //row becomes merge of 2 groups
 406                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 407                                 simMatrix[n][row] = simMatrix[row][n];
 408                                 //delete column
 409                                 simMatrix[column][n] = -1000.0;
 410                                 simMatrix[n][column] = -1000.0;
 411                         }
 412                 }
 413
 414                 //adjust tree to make sure root to tip length is .5
 415                 int root = t->findRoot();
 416                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 417
 418                 //assemble tree
 419                 t->assembleTree();
 420
 421                 if (m->control_pressed) { delete t; return 1; }
 422
 423                 //print newick file
 424                 t->createNewickFile(outputFile);
 425
 426                 //delete tree
 427                 delete t;
 428
 429                 if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
 430
 431                 return 0;
 432
 433         }
 434         catch(exception& e) {
 435                 m->errorOut(e, "TreeGroupCommand", "createTree");
 436                 exit(1);
 437         }
 438 }
 439 /***********************************************************/
 440 void TreeGroupCommand::printSims(ostream& out) {
 441         try {
 442
 443                 //output column headers
 444                 //out << '\t';
 445                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 446                 //out << endl;
 447
 448
 449                 for (int m = 0; m < simMatrix.size(); m++)      {
 450                         //out << lookup[m]->getGroup() << '\t';
 451                         for (int n = 0; n < simMatrix.size(); n++)      {
 452                                 out << simMatrix[m][n] << '\t';
 453                         }
 454                         out << endl;
 455                 }
 456
 457         }
 458         catch(exception& e) {
 459                 m->errorOut(e, "TreeGroupCommand", "printSims");
 460                 exit(1);
 461         }
 462 }
 463 /***********************************************************/
 464 int TreeGroupCommand::makeSimsDist() {
 465         try {
 466                 numGroups = list->size();
 467
 468                 //initialize index
 469                 index.clear();
 470                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 471
 472                 //initialize simMatrix
 473                 simMatrix.clear();
 474                 simMatrix.resize(numGroups);
 475                 for (int k = 0; k < simMatrix.size(); k++)      {
 476                         for (int j = 0; j < simMatrix.size(); j++)      {
 477                                 simMatrix[k].push_back(0.0);
 478                         }
 479                 }
 480
 481                 //go through sparse matrix and fill sims
 482                 //go through each cell in the sparsematrix
 483                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 484                         //similairity = -(distance-1)
 485                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 486                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 487
 488                         if (m->control_pressed) { return 1; }
 489
 490                 }
 491
 492                 return 0;
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 496                 exit(1);
 497         }
 498 }
 499
 500 /***********************************************************/
 501 int TreeGroupCommand::makeSimsShared() {
 502         try {
 503                 set<string> processedLabels;
 504                 set<string> userLabels = labels;
 505
 506                 //as long as you are not at the end of the file or done wih the lines you want
 507                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 508                         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; }
 509
 510                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 511                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 512                                 process(lookup);
 513
 514                                 processedLabels.insert(lookup[0]->getLabel());
 515                                 userLabels.erase(lookup[0]->getLabel());
 516                         }
 517
 518                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 519                                 string saveLabel = lookup[0]->getLabel();
 520
 521                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 522                                 lookup = input->getSharedRAbundVectors(lastLabel);
 523
 524                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 525                                 process(lookup);
 526
 527                                 processedLabels.insert(lookup[0]->getLabel());
 528                                 userLabels.erase(lookup[0]->getLabel());
 529
 530                                 //restore real lastlabel to save below
 531                                 lookup[0]->setLabel(saveLabel);
 532                         }
 533
 534                         lastLabel = lookup[0]->getLabel();
 535
 536                         //get next line to process
 537                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 538                         lookup = input->getSharedRAbundVectors();
 539                 }
 540
 541                 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; }
 542
 543                 //output error messages about any remaining user labels
 544                 set<string>::iterator it;
 545                 bool needToRun = false;
 546                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 547                         m->mothurOut("Your file does not include the label " + *it);
 548                         if (processedLabels.count(lastLabel) != 1) {
 549                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 550                                 needToRun = true;
 551                         }else {
 552                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 553                         }
 554                 }
 555
 556                 //run last label if you need to
 557                 if (needToRun == true)  {
 558                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 559                         lookup = input->getSharedRAbundVectors(lastLabel);
 560
 561                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 562                         process(lookup);
 563                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 564                 }
 565
 566                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 567
 568                 return 0;
 569         }
 570         catch(exception& e) {
 571                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 572                 exit(1);
 573         }
 574 }
 575
 576 /***********************************************************/
 577 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 578         try{
 579                                 EstOutput data;
 580                                 vector<SharedRAbundVector*> subset;
 581                                 numGroups = thisLookup.size();
 582
 583                                 //for each calculator
 584                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 585                                         //initialize simMatrix
 586                                         simMatrix.clear();
 587                                         simMatrix.resize(numGroups);
 588                                         for (int k = 0; k < simMatrix.size(); k++)      {
 589                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 590                                                         simMatrix[k].push_back(0.0);
 591                                                 }
 592                                         }
 593
 594                                         //initialize index
 595                                         index.clear();
 596                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 597
 598                                         //create a new filename
 599                                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 600                                         outputNames.push_back(outputFile);
 601
 602                                         for (int k = 0; k < thisLookup.size(); k++) {
 603                                                 for (int l = k; l < thisLookup.size(); l++) {
 604                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 605                                                                 //get estimated similarity between 2 groups
 606
 607                                                                 subset.clear(); //clear out old pair of sharedrabunds
 608                                                                 //add new pair of sharedrabunds
 609                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 610
 611                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 612                                                 //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
 613                                                                 if (m->control_pressed) { return 1; }
 614
 615                                                                 //save values in similarity matrix
 616                                                                 simMatrix[k][l] = data[0];
 617                                                                 simMatrix[l][k] = data[0];
 618                                                         }
 619                                                 }
 620                                         }
 621
 622                                         if (m->control_pressed) { return 1; }
 623                                         //creates tree from similarity matrix and write out file
 624                                         createTree();
 625
 626                                         if (m->control_pressed) { return 1; }
 627                                 }
 628
 629                                 return 0;
 630
 631         }
 632         catch(exception& e) {
 633                 m->errorOut(e, "TreeGroupCommand", "process");
 634                 exit(1);
 635         }
 636 }
 637 /***********************************************************/
 638
 639
 640