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