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                         OptionParser parser(option);
  44                         map<string, string> parameters = parser. getParameters();
  45
  46                         ValidParameters validParameter;
  47
  48                         //check to make sure all parameters are valid for command
  49                         for (map<string, string>::iterator 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 {  format = "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 {  format = "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                         if (abort == false) {
 128
 129                                 validCalculator = new ValidCalculators();
 130
 131                                 if (format == "sharedfile") {
 132                                         int i;
 133                                         for (i=0; i<Estimators.size(); i++) {
 134                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 135                                                         if (Estimators[i] == "jabund") {
 136                                                                 treeCalculators.push_back(new JAbund());
 137                                                         }else if (Estimators[i] == "sorabund") {
 138                                                                 treeCalculators.push_back(new SorAbund());
 139                                                         }else if (Estimators[i] == "jclass") {
 140                                                                 treeCalculators.push_back(new Jclass());
 141                                                         }else if (Estimators[i] == "sorclass") {
 142                                                                 treeCalculators.push_back(new SorClass());
 143                                                         }else if (Estimators[i] == "jest") {
 144                                                                 treeCalculators.push_back(new Jest());
 145                                                         }else if (Estimators[i] == "sorest") {
 146                                                                 treeCalculators.push_back(new SorEst());
 147                                                         }else if (Estimators[i] == "thetayc") {
 148                                                                 treeCalculators.push_back(new ThetaYC());
 149                                                         }else if (Estimators[i] == "thetan") {
 150                                                                 treeCalculators.push_back(new ThetaN());
 151                                                         }else if (Estimators[i] == "morisitahorn") {
 152                                                                 treeCalculators.push_back(new MorHorn());
 153                                                         }else if (Estimators[i] == "braycurtis") {
 154                                                                 treeCalculators.push_back(new BrayCurtis());
 155                                                         }
 156                                                 }
 157                                         }
 158                                 }
 159                         }
 160                 }
 161
 162         }
 163         catch(exception& e) {
 164                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167         catch(...) {
 168                 cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171 }
 172
 173 //**********************************************************************************************************************
 174
 175 void TreeGroupCommand::help(){
 176         try {
 177                 cout << "The tree.shared command creates a .tre to represent the similiarity between groups or sequences." << "\n";
 178                 cout << "The tree.shared command can only be executed after a successful read.otu command or by providing a distance file." << "\n";
 179                 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";
 180                 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
 181                 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";
 182                 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";
 183                 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";
 184                 cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
 185                 cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
 186                 cout << "The default value for groups is all the groups in your groupfile." << "\n";
 187                 cout << "The default value for calc is jclass-thetayc." << "\n";
 188                 cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
 189                 validCalculator->printCalc("treegroup", cout);
 190                 cout << "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile)." << "\n";
 191                 cout << "Example tree.shared(phylip=abrecovery.dist)." << "\n";
 192                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the TreeGroupCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203
 204
 205 //**********************************************************************************************************************
 206
 207 TreeGroupCommand::~TreeGroupCommand(){
 208         delete input;
 209         if (format == "sharedfile") {delete read;}
 210         else { delete readMatrix;  delete matrix; delete list; }
 211         delete tmap;
 212         delete validCalculator;
 213
 214 }
 215
 216 //**********************************************************************************************************************
 217
 218 int TreeGroupCommand::execute(){
 219         try {
 220
 221                 if (abort == true) { return 0; }
 222
 223                 if (format == "sharedfile") {
 224                         //if the users entered no valid calculators don't execute command
 225                         if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
 226
 227                         //you have groups
 228                         read = new ReadOTUFile(globaldata->inputFileName);
 229                         read->read(&*globaldata);
 230
 231                         input = globaldata->ginput;
 232                         lookup = input->getSharedRAbundVectors();
 233                         lastLookup = lookup;
 234
 235                         if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
 236
 237                         //create tree file
 238                         makeSimsShared();
 239                 }else{
 240                         //read in dist file
 241                         filename = globaldata->inputFileName;
 242
 243                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 244                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 245
 246                         readMatrix->setCutoff(cutoff);
 247
 248                         if(namefile != ""){
 249                                 nameMap = new NameAssignment(namefile);
 250                                 nameMap->readMap(1,2);
 251                         }
 252                         else{
 253                                 nameMap = NULL;
 254                         }
 255
 256                         readMatrix->read(nameMap);
 257                         list = readMatrix->getListVector();
 258                         matrix = readMatrix->getMatrix();
 259
 260                         //make treemap
 261                         tmap = new TreeMap();
 262                         tmap->makeSim(list);
 263                         globaldata->gTreemap = tmap;
 264
 265                         globaldata->Groups = tmap->namesOfGroups;
 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                         makeSimsDist();
 274
 275                         //create a new filename
 276                         outputFile = getRootName(globaldata->inputFileName) + "tre";
 277
 278                         createTree();
 279                         cout << "Tree complete. " << endl;
 280                 }
 281
 282                 //reset groups parameter
 283                 globaldata->Groups.clear();
 284
 285                 return 0;
 286         }
 287         catch(exception& e) {
 288                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 289                 exit(1);
 290         }
 291         catch(...) {
 292                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 293                 exit(1);
 294         }
 295 }
 296 //**********************************************************************************************************************
 297
 298 void TreeGroupCommand::createTree(){
 299         try {
 300                 //create tree
 301                 t = new Tree();
 302
 303                 //do merges and create tree structure by setting parents and children
 304                 //there are numGroups - 1 merges to do
 305                 for (int i = 0; i < (numGroups - 1); i++) {
 306                         float largest = -1000.0;
 307
 308                         int row, column;
 309                         //find largest value in sims matrix by searching lower triangle
 310                         for (int j = 1; j < simMatrix.size(); j++) {
 311                                 for (int k = 0; k < j; k++) {
 312                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 313                                 }
 314                         }
 315
 316                         //set non-leaf node info and update leaves to know their parents
 317                         //non-leaf
 318                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 319
 320                         //parents
 321                         t->tree[index[row]].setParent(numGroups + i);
 322                         t->tree[index[column]].setParent(numGroups + i);
 323
 324                         //blength = distance / 2;
 325                         float blength = ((1.0 - largest) / 2);
 326
 327                         //branchlengths
 328                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 329                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 330
 331                         //set your length to leaves to your childs length plus branchlength
 332                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 333
 334
 335                         //update index
 336                         index[row] = numGroups+i;
 337                         index[column] = numGroups+i;
 338
 339                         //remove highest value that caused the merge.
 340                         simMatrix[row][column] = -1000.0;
 341                         simMatrix[column][row] = -1000.0;
 342
 343                         //merge values in simsMatrix
 344                         for (int n = 0; n < simMatrix.size(); n++)      {
 345                                 //row becomes merge of 2 groups
 346                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 347                                 simMatrix[n][row] = simMatrix[row][n];
 348                                 //delete column
 349                                 simMatrix[column][n] = -1000.0;
 350                                 simMatrix[n][column] = -1000.0;
 351                         }
 352                 }
 353
 354                 //adjust tree to make sure root to tip length is .5
 355                 int root = t->findRoot();
 356                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 357
 358                 //assemble tree
 359                 t->assembleTree();
 360
 361                 //print newick file
 362                 t->createNewickFile(outputFile);
 363
 364                 //delete tree
 365                 delete t;
 366
 367         }
 368         catch(exception& e) {
 369                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 370                 exit(1);
 371         }
 372         catch(...) {
 373                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 374                 exit(1);
 375         }
 376 }
 377 /***********************************************************/
 378 void TreeGroupCommand::printSims(ostream& out) {
 379         try {
 380
 381                 //output column headers
 382                 //out << '\t';
 383                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 384                 //out << endl;
 385
 386
 387                 for (int m = 0; m < simMatrix.size(); m++)      {
 388                         //out << lookup[m]->getGroup() << '\t';
 389                         for (int n = 0; n < simMatrix.size(); n++)      {
 390                                 out << simMatrix[m][n] << '\t';
 391                         }
 392                         out << endl;
 393                 }
 394
 395         }
 396         catch(exception& e) {
 397                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 398                 exit(1);
 399         }
 400         catch(...) {
 401                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 402                 exit(1);
 403         }
 404 }
 405 /***********************************************************/
 406 void TreeGroupCommand::makeSimsDist() {
 407         try {
 408                 numGroups = list->size();
 409
 410                 //initialize index
 411                 index.clear();
 412                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 413
 414                 //initialize simMatrix
 415                 simMatrix.clear();
 416                 simMatrix.resize(numGroups);
 417                 for (int m = 0; m < simMatrix.size(); m++)      {
 418                         for (int j = 0; j < simMatrix.size(); j++)      {
 419                                 simMatrix[m].push_back(0.0);
 420                         }
 421                 }
 422
 423                 //go through sparse matrix and fill sims
 424                 //go through each cell in the sparsematrix
 425                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 426                         //similairity = -(distance-1)
 427                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 428                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 429                 }
 430
 431
 432         }
 433         catch(exception& e) {
 434                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 435                 exit(1);
 436         }
 437         catch(...) {
 438                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 439                 exit(1);
 440         }
 441 }
 442
 443 /***********************************************************/
 444 void TreeGroupCommand::makeSimsShared() {
 445         try {
 446                 int count = 1;
 447
 448                 //clear globaldatas old tree names if any
 449                 globaldata->Treenames.clear();
 450
 451                 //fills globaldatas tree names
 452                 globaldata->Treenames = globaldata->Groups;
 453
 454                 //create treemap class from groupmap for tree class to use
 455                 tmap = new TreeMap();
 456                 tmap->makeSim(globaldata->gGroupmap);
 457                 globaldata->gTreemap = tmap;
 458
 459                 set<string> processedLabels;
 460                 set<string> userLabels = labels;
 461                 set<int> userLines = lines;
 462
 463                 //as long as you are not at the end of the file or done wih the lines you want
 464                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 465
 466                         if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 467                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 468                                 process(lookup);
 469
 470                                 processedLabels.insert(lookup[0]->getLabel());
 471                                 userLabels.erase(lookup[0]->getLabel());
 472                                 userLines.erase(count);
 473                         }
 474
 475                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 476                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 477                                 process(lastLookup);
 478
 479                                 processedLabels.insert(lastLookup[0]->getLabel());
 480                                 userLabels.erase(lastLookup[0]->getLabel());
 481                         }
 482
 483                         //prevent memory leak
 484                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 485                         lastLookup = lookup;
 486
 487                         //get next line to process
 488                         lookup = input->getSharedRAbundVectors();
 489                         count++;
 490                 }
 491
 492                 //output error messages about any remaining user labels
 493                 set<string>::iterator it;
 494                 bool needToRun = false;
 495                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 496                         cout << "Your file does not include the label "<< *it;
 497                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 498                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 499                                 needToRun = true;
 500                         }else {
 501                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 502                         }
 503                 }
 504
 505                 //run last line if you need to
 506                 if (needToRun == true)  {
 507                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 508                         process(lastLookup);
 509                 }
 510
 511                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 512                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 513         }
 514         catch(exception& e) {
 515                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 516                 exit(1);
 517         }
 518         catch(...) {
 519                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 520                 exit(1);
 521         }
 522 }
 523
 524 /***********************************************************/
 525 void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 526         try{
 527                                 EstOutput data;
 528                                 vector<SharedRAbundVector*> subset;
 529                                 numGroups = thisLookup.size();
 530
 531                                 //for each calculator
 532                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 533                                         //initialize simMatrix
 534                                         simMatrix.clear();
 535                                         simMatrix.resize(numGroups);
 536                                         for (int m = 0; m < simMatrix.size(); m++)      {
 537                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 538                                                         simMatrix[m].push_back(0.0);
 539                                                 }
 540                                         }
 541
 542                                         //initialize index
 543                                         index.clear();
 544                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 545
 546                                         //create a new filename
 547                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 548
 549                                         for (int k = 0; k < thisLookup.size(); k++) {
 550                                                 for (int l = k; l < thisLookup.size(); l++) {
 551                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 552                                                                 //get estimated similarity between 2 groups
 553
 554                                                                 subset.clear(); //clear out old pair of sharedrabunds
 555                                                                 //add new pair of sharedrabunds
 556                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 557
 558                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 559                                                                 //save values in similarity matrix
 560                                                                 simMatrix[k][l] = data[0];
 561                                                                 simMatrix[l][k] = data[0];
 562                                                         }
 563                                                 }
 564                                         }
 565
 566                                         //creates tree from similarity matrix and write out file
 567                                         createTree();
 568                                 }
 569
 570         }
 571         catch(exception& e) {
 572                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 573                 exit(1);
 574         }
 575         catch(...) {
 576                 cout << "An unknown error has occurred in the TreeGroupCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 577                 exit(1);
 578         }
 579 }
 580 /***********************************************************/
 581
 582
 583