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                 lines.clear();
  31                 labels.clear();
  32                 Groups.clear();
  33                 Estimators.clear();
  34
  35                 //allow user to run help
  36                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  37
  38                 else {
  39                         //valid paramters for this command
  40                         string Array[] =  {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
  41                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42
  43                         parser = new OptionParser();
  44                         parser->parse(option, parameters);  delete parser;
  45
  46                         ValidParameters* validParameter = new ValidParameters();
  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                         //required parameters
  54                         phylipfile = validParameter->validFile(parameters, "phylip", true);
  55                         if (phylipfile == "not open") { abort = true; }
  56                         else if (phylipfile == "not found") { phylipfile = ""; }
  57                         else {  globaldata->setPhylipFile(phylipfile);  globaldata->setFormat("phylip");        }
  58
  59                         columnfile = validParameter->validFile(parameters, "column", true);
  60                         if (columnfile == "not open") { abort = true; }
  61                         else if (columnfile == "not found") { columnfile = ""; }
  62                         else {  globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
  63
  64                         namefile = validParameter->validFile(parameters, "name", true);
  65                         if (namefile == "not open") { abort = true; }
  66                         else if (namefile == "not found") { namefile = ""; }
  67                         else {  globaldata->setNameFile(namefile);      }
  68
  69                         format = globaldata->getFormat();
  70
  71                         //error checking on files
  72                         if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; abort = true; }
  73                         else if ((phylipfile != "") && (columnfile != "")) { cout << "When running the tree.shared command with a distance file you may not use both the column and the phylip parameters." << endl; abort = true; }
  74
  75                         if (columnfile != "") {
  76                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
  77                         }
  78
  79                         //check for optional parameter and set defaults
  80                         // ...at some point should added some additional type checking...
  81                         line = validParameter->validFile(parameters, "line", false);
  82                         if (line == "not found") { line = "";  }
  83                         else {
  84                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  85                                 else { allLines = 1;  }
  86                         }
  87
  88                         label = validParameter->validFile(parameters, "label", false);
  89                         if (label == "not found") { label = ""; }
  90                         else {
  91                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  92                                 else { allLines = 1;  }
  93                         }
  94
  95                         //make sure user did not use both the line and label parameters
  96                         if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
  97                         //if the user has not specified any line or labels use the ones from read.otu
  98                         else if((line == "") && (label == "")) {
  99                                 allLines = globaldata->allLines;
 100                                 labels = globaldata->labels;
 101                                 lines = globaldata->lines;
 102                         }
 103
 104                         groups = validParameter->validFile(parameters, "groups", false);
 105                         if (groups == "not found") { groups = ""; }
 106                         else {
 107                                 splitAtDash(groups, Groups);
 108                                 globaldata->Groups = Groups;
 109                         }
 110
 111                         calc = validParameter->validFile(parameters, "calc", false);
 112                         if (calc == "not found") { calc = "jclass-thetayc";  }
 113                         else {
 114                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 115                         }
 116                         splitAtDash(calc, Estimators);
 117
 118                         string temp;
 119                         temp = validParameter->validFile(parameters, "precision", false);                       if (temp == "not found") { temp = "100"; }
 120                         convert(temp, precision);
 121
 122                         temp = validParameter->validFile(parameters, "cutoff", false);                  if (temp == "not found") { temp = "10"; }
 123                         convert(temp, cutoff);
 124                         cutoff += (5 / (precision * 10.0));
 125
 126
 127                         delete validParameter;
 128
 129                         if (abort == false) {
 130
 131                                 validCalculator = new ValidCalculators();
 132
 133                                 if (format == "sharedfile") {
 134                                         int i;
 135                                         for (i=0; i<Estimators.size(); i++) {
 136                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 137                                                         if (Estimators[i] == "jabund") {
 138                                                                 treeCalculators.push_back(new JAbund());
 139                                                         }else if (Estimators[i] == "sorabund") {
 140                                                                 treeCalculators.push_back(new SorAbund());
 141                                                         }else if (Estimators[i] == "jclass") {
 142                                                                 treeCalculators.push_back(new Jclass());
 143                                                         }else if (Estimators[i] == "sorclass") {
 144                                                                 treeCalculators.push_back(new SorClass());
 145                                                         }else if (Estimators[i] == "jest") {
 146                                                                 treeCalculators.push_back(new Jest());
 147                                                         }else if (Estimators[i] == "sorest") {
 148                                                                 treeCalculators.push_back(new SorEst());
 149                                                         }else if (Estimators[i] == "thetayc") {
 150                                                                 treeCalculators.push_back(new ThetaYC());
 151                                                         }else if (Estimators[i] == "thetan") {
 152                                                                 treeCalculators.push_back(new ThetaN());
 153                                                         }else if (Estimators[i] == "morisitahorn") {
 154                                                                 treeCalculators.push_back(new MorHorn());
 155                                                         }else if (Estimators[i] == "braycurtis") {
 156                                                                 treeCalculators.push_back(new BrayCurtis());
 157                                                         }
 158                                                 }
 159                                         }
 160                                 }
 161                         }
 162                 }
 163
 164         }
 165         catch(exception& e) {
 166                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 167                 exit(1);
 168         }
 169         catch(...) {
 170                 cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 171                 exit(1);
 172         }
 173 }
 174
 175 //**********************************************************************************************************************
 176
 177 void TreeGroupCommand::help(){
 178         try {
 179                 cout << "The tree.shared command creates a .tre to represent the similiarity between groups or sequences." << "\n";
 180                 cout << "The tree.shared command can only be executed after a successful read.otu command or by providing a distance file." << "\n";
 181                 cout << "The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, line and label.  You may not use line and label at the same time." << "\n";
 182                 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
 183                 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
 184                 cout << "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";
 185                 cout << "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";
 186                 cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
 187                 cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
 188                 cout << "The default value for groups is all the groups in your groupfile." << "\n";
 189                 cout << "The default value for calc is jclass-thetayc." << "\n";
 190                 cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
 191                 validCalculator->printCalc("treegroup", cout);
 192                 cout << "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile)." << "\n";
 193                 cout << "Example tree.shared(phylip=abrecovery.dist)." << "\n";
 194                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 195         }
 196         catch(exception& e) {
 197                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 198                 exit(1);
 199         }
 200         catch(...) {
 201                 cout << "An unknown error has occurred in the TreeGroupCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 202                 exit(1);
 203         }
 204 }
 205
 206
 207 //**********************************************************************************************************************
 208
 209 TreeGroupCommand::~TreeGroupCommand(){
 210         delete input;
 211         if (format == "sharedfile") {delete read;}
 212         else { delete readMatrix;  delete matrix; delete list; }
 213         delete tmap;
 214         delete validCalculator;
 215
 216 }
 217
 218 //**********************************************************************************************************************
 219
 220 int TreeGroupCommand::execute(){
 221         try {
 222
 223                 if (abort == true) { return 0; }
 224
 225                 if (format == "sharedfile") {
 226                         //if the users entered no valid calculators don't execute command
 227                         if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
 228
 229                         //you have groups
 230                         read = new ReadOTUFile(globaldata->inputFileName);
 231                         read->read(&*globaldata);
 232
 233                         input = globaldata->ginput;
 234                         lookup = input->getSharedRAbundVectors();
 235                         lastLookup = lookup;
 236
 237                         if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
 238
 239                         //create tree file
 240                         makeSimsShared();
 241                 }else{
 242                         //read in dist file
 243                         filename = globaldata->inputFileName;
 244
 245                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 246                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 247
 248                         readMatrix->setCutoff(cutoff);
 249
 250                         if(namefile != ""){
 251                                 nameMap = new NameAssignment(namefile);
 252                                 nameMap->readMap(1,2);
 253                         }
 254                         else{
 255                                 nameMap = NULL;
 256                         }
 257
 258                         readMatrix->read(nameMap);
 259                         list = readMatrix->getListVector();
 260                         matrix = readMatrix->getMatrix();
 261
 262                         //make treemap
 263                         tmap = new TreeMap();
 264                         tmap->makeSim(list);
 265                         globaldata->gTreemap = tmap;
 266
 267                         globaldata->Groups = tmap->namesOfGroups;
 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                         makeSimsDist();
 276
 277                         //create a new filename
 278                         outputFile = getRootName(globaldata->inputFileName) + "tre";
 279
 280                         createTree();
 281                         cout << "Tree complete. " << endl;
 282                 }
 283
 284                 //reset groups parameter
 285                 globaldata->Groups.clear();
 286
 287                 return 0;
 288         }
 289         catch(exception& e) {
 290                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293         catch(...) {
 294                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297 }
 298 //**********************************************************************************************************************
 299
 300 void TreeGroupCommand::createTree(){
 301         try {
 302                 //create tree
 303                 t = new Tree();
 304
 305                 //do merges and create tree structure by setting parents and children
 306                 //there are numGroups - 1 merges to do
 307                 for (int i = 0; i < (numGroups - 1); i++) {
 308                         float largest = -1000.0;
 309
 310                         int row, column;
 311                         //find largest value in sims matrix by searching lower triangle
 312                         for (int j = 1; j < simMatrix.size(); j++) {
 313                                 for (int k = 0; k < j; k++) {
 314                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 315                                 }
 316                         }
 317
 318                         //set non-leaf node info and update leaves to know their parents
 319                         //non-leaf
 320                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 321
 322                         //parents
 323                         t->tree[index[row]].setParent(numGroups + i);
 324                         t->tree[index[column]].setParent(numGroups + i);
 325
 326                         //blength = distance / 2;
 327                         float blength = ((1.0 - largest) / 2);
 328
 329                         //branchlengths
 330                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 331                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 332
 333                         //set your length to leaves to your childs length plus branchlength
 334                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 335
 336
 337                         //update index
 338                         index[row] = numGroups+i;
 339                         index[column] = numGroups+i;
 340
 341                         //remove highest value that caused the merge.
 342                         simMatrix[row][column] = -1000.0;
 343                         simMatrix[column][row] = -1000.0;
 344
 345                         //merge values in simsMatrix
 346                         for (int n = 0; n < simMatrix.size(); n++)      {
 347                                 //row becomes merge of 2 groups
 348                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 349                                 simMatrix[n][row] = simMatrix[row][n];
 350                                 //delete column
 351                                 simMatrix[column][n] = -1000.0;
 352                                 simMatrix[n][column] = -1000.0;
 353                         }
 354                 }
 355
 356                 //adjust tree to make sure root to tip length is .5
 357                 int root = t->findRoot();
 358                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 359
 360                 //assemble tree
 361                 t->assembleTree();
 362
 363                 //print newick file
 364                 t->createNewickFile(outputFile);
 365
 366                 //delete tree
 367                 delete t;
 368
 369         }
 370         catch(exception& e) {
 371                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 372                 exit(1);
 373         }
 374         catch(...) {
 375                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 376                 exit(1);
 377         }
 378 }
 379 /***********************************************************/
 380 void TreeGroupCommand::printSims(ostream& out) {
 381         try {
 382
 383                 //output column headers
 384                 //out << '\t';
 385                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 386                 //out << endl;
 387
 388
 389                 for (int m = 0; m < simMatrix.size(); m++)      {
 390                         //out << lookup[m]->getGroup() << '\t';
 391                         for (int n = 0; n < simMatrix.size(); n++)      {
 392                                 out << simMatrix[m][n] << '\t';
 393                         }
 394                         out << endl;
 395                 }
 396
 397         }
 398         catch(exception& e) {
 399                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 400                 exit(1);
 401         }
 402         catch(...) {
 403                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 404                 exit(1);
 405         }
 406 }
 407 /***********************************************************/
 408 void TreeGroupCommand::makeSimsDist() {
 409         try {
 410                 numGroups = list->size();
 411
 412                 //initialize index
 413                 index.clear();
 414                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 415
 416                 //initialize simMatrix
 417                 simMatrix.clear();
 418                 simMatrix.resize(numGroups);
 419                 for (int m = 0; m < simMatrix.size(); m++)      {
 420                         for (int j = 0; j < simMatrix.size(); j++)      {
 421                                 simMatrix[m].push_back(0.0);
 422                         }
 423                 }
 424
 425                 //go through sparse matrix and fill sims
 426                 //go through each cell in the sparsematrix
 427                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 428                         //similairity = -(distance-1)
 429                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 430                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 431                 }
 432
 433
 434         }
 435         catch(exception& e) {
 436                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 437                 exit(1);
 438         }
 439         catch(...) {
 440                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 441                 exit(1);
 442         }
 443 }
 444
 445 /***********************************************************/
 446 void TreeGroupCommand::makeSimsShared() {
 447         try {
 448                 int count = 1;
 449
 450                 //clear globaldatas old tree names if any
 451                 globaldata->Treenames.clear();
 452
 453                 //fills globaldatas tree names
 454                 globaldata->Treenames = globaldata->Groups;
 455
 456                 //create treemap class from groupmap for tree class to use
 457                 tmap = new TreeMap();
 458                 tmap->makeSim(globaldata->gGroupmap);
 459                 globaldata->gTreemap = tmap;
 460
 461                 set<string> processedLabels;
 462                 set<string> userLabels = labels;
 463                 set<int> userLines = lines;
 464
 465                 //as long as you are not at the end of the file or done wih the lines you want
 466                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 467
 468                         if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 469                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 470                                 process(lookup);
 471
 472                                 processedLabels.insert(lookup[0]->getLabel());
 473                                 userLabels.erase(lookup[0]->getLabel());
 474                                 userLines.erase(count);
 475                         }
 476
 477                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 478                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 479                                 process(lastLookup);
 480
 481                                 processedLabels.insert(lastLookup[0]->getLabel());
 482                                 userLabels.erase(lastLookup[0]->getLabel());
 483                         }
 484
 485                         //prevent memory leak
 486                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 487                         lastLookup = lookup;
 488
 489                         //get next line to process
 490                         lookup = input->getSharedRAbundVectors();
 491                         count++;
 492                 }
 493
 494                 //output error messages about any remaining user labels
 495                 set<string>::iterator it;
 496                 bool needToRun = false;
 497                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 498                         cout << "Your file does not include the label "<< *it;
 499                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 500                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 501                                 needToRun = true;
 502                         }else {
 503                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 504                         }
 505                 }
 506
 507                 //run last line if you need to
 508                 if (needToRun == true)  {
 509                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 510                         process(lastLookup);
 511                 }
 512
 513                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 514                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 515         }
 516         catch(exception& e) {
 517                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 518                 exit(1);
 519         }
 520         catch(...) {
 521                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 522                 exit(1);
 523         }
 524 }
 525
 526 /***********************************************************/
 527 void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 528         try{
 529                                 EstOutput data;
 530                                 vector<SharedRAbundVector*> subset;
 531                                 numGroups = thisLookup.size();
 532
 533                                 //for each calculator
 534                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 535                                         //initialize simMatrix
 536                                         simMatrix.clear();
 537                                         simMatrix.resize(numGroups);
 538                                         for (int m = 0; m < simMatrix.size(); m++)      {
 539                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 540                                                         simMatrix[m].push_back(0.0);
 541                                                 }
 542                                         }
 543
 544                                         //initialize index
 545                                         index.clear();
 546                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 547
 548                                         //create a new filename
 549                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 550
 551                                         for (int k = 0; k < thisLookup.size(); k++) {
 552                                                 for (int l = k; l < thisLookup.size(); l++) {
 553                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 554                                                                 //get estimated similarity between 2 groups
 555
 556                                                                 subset.clear(); //clear out old pair of sharedrabunds
 557                                                                 //add new pair of sharedrabunds
 558                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 559
 560                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 561                                                                 //save values in similarity matrix
 562                                                                 simMatrix[k][l] = data[0];
 563                                                                 simMatrix[l][k] = data[0];
 564                                                         }
 565                                                 }
 566                                         }
 567
 568                                         //creates tree from similarity matrix and write out file
 569                                         createTree();
 570                                 }
 571
 572         }
 573         catch(exception& e) {
 574                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 575                 exit(1);
 576         }
 577         catch(...) {
 578                 cout << "An unknown error has occurred in the TreeGroupCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 579                 exit(1);
 580         }
 581 }
 582 /***********************************************************/
 583
 584
 585