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 vector<string> TreeGroupCommand::getValidParameters(){
  24         try {
  25                 string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
  26                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "TreeGroupCommand", "getValidParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 TreeGroupCommand::TreeGroupCommand(){
  36         try {
  37                 //initialize outputTypes
  38                 vector<string> tempOutNames;
  39                 outputTypes["tree"] = tempOutNames;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 vector<string> TreeGroupCommand::getRequiredParameters(){
  48         try {
  49                 vector<string> myArray;
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "TreeGroupCommand", "getRequiredParameters");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 vector<string> TreeGroupCommand::getRequiredFiles(){
  59         try {
  60                 string Array[] =  {"phylip","column","shared","or"};
  61                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  62                 return myArray;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "TreeGroupCommand", "getRequiredFiles");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 TreeGroupCommand::TreeGroupCommand(string option)  {
  72         try {
  73                 globaldata = GlobalData::getInstance();
  74                 abort = false;
  75                 allLines = 1;
  76                 labels.clear();
  77                 Groups.clear();
  78                 Estimators.clear();
  79
  80                 //allow user to run help
  81                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  82
  83                 else {
  84                         //valid paramters for this command
  85                         string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
  86                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  87
  88                         OptionParser parser(option);
  89                         map<string, string> parameters = parser. getParameters();
  90
  91                         ValidParameters validParameter;
  92                         map<string, string>::iterator it;
  93
  94                         //check to make sure all parameters are valid for command
  95                         for (it = parameters.begin(); it != parameters.end(); it++) {
  96                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["tree"] = tempOutNames;
 102
 103                         //if the user changes the input directory command factory will send this info to us in the output parameter
 104                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 105                         if (inputDir == "not found"){   inputDir = "";          }
 106                         else {
 107                                 string path;
 108                                 it = parameters.find("phylip");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 114                                 }
 115
 116                                 it = parameters.find("column");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 122                                 }
 123
 124                                 it = parameters.find("name");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 130                                 }
 131                         }
 132
 133                         format = globaldata->getFormat();
 134
 135                         //required parameters
 136                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 137                         if (phylipfile == "not open") { abort = true; }
 138                         else if (phylipfile == "not found") { phylipfile = ""; }
 139                         else {  globaldata->newRead(); format = "phylip";  globaldata->setPhylipFile(phylipfile);       }
 140
 141                         columnfile = validParameter.validFile(parameters, "column", true);
 142                         if (columnfile == "not open") { abort = true; }
 143                         else if (columnfile == "not found") { columnfile = ""; }
 144                         else {  globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile);        }
 145
 146                         namefile = validParameter.validFile(parameters, "name", true);
 147                         if (namefile == "not open") { abort = true; }
 148                         else if (namefile == "not found") { namefile = ""; }
 149                         else {  globaldata->setNameFile(namefile);      }
 150
 151                         //error checking on files
 152                         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; }
 153                         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; }
 154
 155                         if (columnfile != "") {
 156                                 if (namefile == "") {  m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
 157                         }
 158
 159                         //check for optional parameter and set defaults
 160                         // ...at some point should added some additional type checking...
 161                         label = validParameter.validFile(parameters, "label", false);
 162                         if (label == "not found") { label = ""; }
 163                         else {
 164                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 165                                 else { allLines = 1;  }
 166                         }
 167
 168                         //if the user has not specified any labels use the ones from read.otu
 169                         if(label == "") {
 170                                 allLines = globaldata->allLines;
 171                                 labels = globaldata->labels;
 172                         }
 173
 174                         groups = validParameter.validFile(parameters, "groups", false);
 175                         if (groups == "not found") { groups = ""; }
 176                         else {
 177                                 m->splitAtDash(groups, Groups);
 178                                 globaldata->Groups = Groups;
 179                         }
 180
 181                         calc = validParameter.validFile(parameters, "calc", false);
 182                         if (calc == "not found") { calc = "jclass-thetayc";  }
 183                         else {
 184                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 185                         }
 186                         m->splitAtDash(calc, Estimators);
 187
 188                         string temp;
 189                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 190                         convert(temp, precision);
 191
 192                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 193                         convert(temp, cutoff);
 194                         cutoff += (5 / (precision * 10.0));
 195
 196                         //if the user changes the output directory command factory will send this info to us in the output parameter
 197                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 198                                 outputDir = "";
 199                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 200                         }
 201
 202
 203                         if (abort == false) {
 204
 205                                 validCalculator = new ValidCalculators();
 206
 207                                 if (format == "sharedfile") {
 208                                         int i;
 209                                         for (i=0; i<Estimators.size(); i++) {
 210                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 211                                                         if (Estimators[i] == "jabund") {
 212                                                                 treeCalculators.push_back(new JAbund());
 213                                                         }else if (Estimators[i] == "sorabund") {
 214                                                                 treeCalculators.push_back(new SorAbund());
 215                                                         }else if (Estimators[i] == "jclass") {
 216                                                                 treeCalculators.push_back(new Jclass());
 217                                                         }else if (Estimators[i] == "sorclass") {
 218                                                                 treeCalculators.push_back(new SorClass());
 219                                                         }else if (Estimators[i] == "jest") {
 220                                                                 treeCalculators.push_back(new Jest());
 221                                                         }else if (Estimators[i] == "sorest") {
 222                                                                 treeCalculators.push_back(new SorEst());
 223                                                         }else if (Estimators[i] == "thetayc") {
 224                                                                 treeCalculators.push_back(new ThetaYC());
 225                                                         }else if (Estimators[i] == "thetan") {
 226                                                                 treeCalculators.push_back(new ThetaN());
 227                                                         }else if (Estimators[i] == "morisitahorn") {
 228                                                                 treeCalculators.push_back(new MorHorn());
 229                                                         }else if (Estimators[i] == "braycurtis") {
 230                                                                 treeCalculators.push_back(new BrayCurtis());
 231                                                         }
 232                                                 }
 233                                         }
 234                                 }
 235                         }
 236                 }
 237
 238         }
 239         catch(exception& e) {
 240                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 241                 exit(1);
 242         }
 243 }
 244
 245 //**********************************************************************************************************************
 246
 247 void TreeGroupCommand::help(){
 248         try {
 249                 m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
 250                 m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
 251                 m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
 252                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 253                 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");
 254                 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");
 255                 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");
 256                 m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
 257                 m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
 258                 m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
 259                 m->mothurOut("The default value for calc is jclass-thetayc.\n");
 260                 m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
 261                 validCalculator->printCalc("treegroup", cout);
 262                 m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
 263                 m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
 264                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 265         }
 266         catch(exception& e) {
 267                 m->errorOut(e, "TreeGroupCommand", "help");
 268                 exit(1);
 269         }
 270 }
 271
 272
 273 //**********************************************************************************************************************
 274
 275 TreeGroupCommand::~TreeGroupCommand(){
 276         globaldata->Groups.clear();
 277         if (abort == false) {
 278
 279                 if (format == "sharedfile") { delete read;  delete input; globaldata->ginput = NULL; }
 280                 else { delete readMatrix;  delete matrix; delete list; }
 281                 delete tmap;  globaldata->gTreemap = NULL;
 282                 delete validCalculator;
 283         }
 284
 285 }
 286
 287 //**********************************************************************************************************************
 288
 289 int TreeGroupCommand::execute(){
 290         try {
 291
 292                 if (abort == true) { return 0; }
 293
 294                 if (format == "sharedfile") {
 295                         //if the users entered no valid calculators don't execute command
 296                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 297
 298                         if (globaldata->gGroupmap != NULL) {  delete globaldata->gGroupmap;   globaldata->gGroupmap = NULL;  }
 299                         //you have groups
 300                         read = new ReadOTUFile(globaldata->inputFileName);
 301                         read->read(&*globaldata);
 302
 303                         input = globaldata->ginput;
 304                         lookup = input->getSharedRAbundVectors();
 305                         lastLabel = lookup[0]->getLabel();
 306
 307                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 308
 309                         //used in tree constructor
 310                         globaldata->runParse = false;
 311
 312                         //create treemap class from groupmap for tree class to use
 313                         tmap = new TreeMap();
 314                         tmap->makeSim(globaldata->gGroupmap);
 315                         globaldata->gTreemap = tmap;
 316
 317                         //clear globaldatas old tree names if any
 318                         globaldata->Treenames.clear();
 319
 320                         //fills globaldatas tree names
 321                         globaldata->Treenames = globaldata->Groups;
 322
 323                         if (m->control_pressed) { return 0; }
 324
 325                         //create tree file
 326                         makeSimsShared();
 327
 328                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 329                 }else{
 330                         //read in dist file
 331                         filename = globaldata->inputFileName;
 332
 333                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 334                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 335
 336                         readMatrix->setCutoff(cutoff);
 337
 338                         if(namefile != ""){
 339                                 nameMap = new NameAssignment(namefile);
 340                                 nameMap->readMap();
 341                         }
 342                         else{
 343                                 nameMap = NULL;
 344                         }
 345
 346                         readMatrix->read(nameMap);
 347                         list = readMatrix->getListVector();
 348                         matrix = readMatrix->getMatrix();
 349
 350                         //make treemap
 351                         tmap = new TreeMap();
 352
 353                         if (m->control_pressed) { return 0; }
 354
 355                         tmap->makeSim(list);
 356                         globaldata->gTreemap = tmap;
 357
 358                         globaldata->Groups = tmap->namesOfGroups;
 359
 360                         //clear globaldatas old tree names if any
 361                         globaldata->Treenames.clear();
 362
 363                         //fills globaldatas tree names
 364                         globaldata->Treenames = globaldata->Groups;
 365
 366                         //used in tree constructor
 367                         globaldata->runParse = false;
 368
 369                         if (m->control_pressed) { return 0; }
 370
 371                         makeSimsDist();
 372
 373                         if (m->control_pressed) { return 0; }
 374
 375                         //create a new filename
 376                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";
 377                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 378
 379                         createTree();
 380
 381                         if (m->control_pressed) { return 0; }
 382
 383                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 384
 385                 }
 386
 387                 //reset groups parameter
 388                 globaldata->Groups.clear();
 389
 390                 m->mothurOutEndLine();
 391                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 392                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 393                 m->mothurOutEndLine();
 394
 395                 return 0;
 396         }
 397         catch(exception& e) {
 398                 m->errorOut(e, "TreeGroupCommand", "execute");
 399                 exit(1);
 400         }
 401 }
 402 //**********************************************************************************************************************
 403
 404 int TreeGroupCommand::createTree(){
 405         try {
 406                 //create tree
 407                 t = new Tree();
 408
 409                 //do merges and create tree structure by setting parents and children
 410                 //there are numGroups - 1 merges to do
 411                 for (int i = 0; i < (numGroups - 1); i++) {
 412                         float largest = -1000.0;
 413
 414                         if (m->control_pressed) { delete t; return 1; }
 415
 416                         int row, column;
 417                         //find largest value in sims matrix by searching lower triangle
 418                         for (int j = 1; j < simMatrix.size(); j++) {
 419                                 for (int k = 0; k < j; k++) {
 420                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 421                                 }
 422                         }
 423
 424                         //set non-leaf node info and update leaves to know their parents
 425                         //non-leaf
 426                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 427
 428                         //parents
 429                         t->tree[index[row]].setParent(numGroups + i);
 430                         t->tree[index[column]].setParent(numGroups + i);
 431
 432                         //blength = distance / 2;
 433                         float blength = ((1.0 - largest) / 2);
 434
 435                         //branchlengths
 436                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 437                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 438
 439                         //set your length to leaves to your childs length plus branchlength
 440                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 441
 442
 443                         //update index
 444                         index[row] = numGroups+i;
 445                         index[column] = numGroups+i;
 446
 447                         //remove highest value that caused the merge.
 448                         simMatrix[row][column] = -1000.0;
 449                         simMatrix[column][row] = -1000.0;
 450
 451                         //merge values in simsMatrix
 452                         for (int n = 0; n < simMatrix.size(); n++)      {
 453                                 //row becomes merge of 2 groups
 454                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 455                                 simMatrix[n][row] = simMatrix[row][n];
 456                                 //delete column
 457                                 simMatrix[column][n] = -1000.0;
 458                                 simMatrix[n][column] = -1000.0;
 459                         }
 460                 }
 461
 462                 //adjust tree to make sure root to tip length is .5
 463                 int root = t->findRoot();
 464                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 465
 466                 //assemble tree
 467                 t->assembleTree();
 468
 469                 if (m->control_pressed) { delete t; return 1; }
 470
 471                 //print newick file
 472                 t->createNewickFile(outputFile);
 473
 474                 //delete tree
 475                 delete t;
 476
 477                 if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
 478
 479                 return 0;
 480
 481         }
 482         catch(exception& e) {
 483                 m->errorOut(e, "TreeGroupCommand", "createTree");
 484                 exit(1);
 485         }
 486 }
 487 /***********************************************************/
 488 void TreeGroupCommand::printSims(ostream& out) {
 489         try {
 490
 491                 //output column headers
 492                 //out << '\t';
 493                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 494                 //out << endl;
 495
 496
 497                 for (int m = 0; m < simMatrix.size(); m++)      {
 498                         //out << lookup[m]->getGroup() << '\t';
 499                         for (int n = 0; n < simMatrix.size(); n++)      {
 500                                 out << simMatrix[m][n] << '\t';
 501                         }
 502                         out << endl;
 503                 }
 504
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "TreeGroupCommand", "printSims");
 508                 exit(1);
 509         }
 510 }
 511 /***********************************************************/
 512 int TreeGroupCommand::makeSimsDist() {
 513         try {
 514                 numGroups = list->size();
 515
 516                 //initialize index
 517                 index.clear();
 518                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 519
 520                 //initialize simMatrix
 521                 simMatrix.clear();
 522                 simMatrix.resize(numGroups);
 523                 for (int k = 0; k < simMatrix.size(); k++)      {
 524                         for (int j = 0; j < simMatrix.size(); j++)      {
 525                                 simMatrix[k].push_back(0.0);
 526                         }
 527                 }
 528
 529                 //go through sparse matrix and fill sims
 530                 //go through each cell in the sparsematrix
 531                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 532                         //similairity = -(distance-1)
 533                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 534                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 535
 536                         if (m->control_pressed) { return 1; }
 537
 538                 }
 539
 540                 return 0;
 541         }
 542         catch(exception& e) {
 543                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 544                 exit(1);
 545         }
 546 }
 547
 548 /***********************************************************/
 549 int TreeGroupCommand::makeSimsShared() {
 550         try {
 551                 set<string> processedLabels;
 552                 set<string> userLabels = labels;
 553
 554                 //as long as you are not at the end of the file or done wih the lines you want
 555                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 556                         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; }
 557
 558                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 559                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 560                                 process(lookup);
 561
 562                                 processedLabels.insert(lookup[0]->getLabel());
 563                                 userLabels.erase(lookup[0]->getLabel());
 564                         }
 565
 566                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 567                                 string saveLabel = lookup[0]->getLabel();
 568
 569                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 570                                 lookup = input->getSharedRAbundVectors(lastLabel);
 571
 572                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 573                                 process(lookup);
 574
 575                                 processedLabels.insert(lookup[0]->getLabel());
 576                                 userLabels.erase(lookup[0]->getLabel());
 577
 578                                 //restore real lastlabel to save below
 579                                 lookup[0]->setLabel(saveLabel);
 580                         }
 581
 582                         lastLabel = lookup[0]->getLabel();
 583
 584                         //get next line to process
 585                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 586                         lookup = input->getSharedRAbundVectors();
 587                 }
 588
 589                 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; }
 590
 591                 //output error messages about any remaining user labels
 592                 set<string>::iterator it;
 593                 bool needToRun = false;
 594                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 595                         m->mothurOut("Your file does not include the label " + *it);
 596                         if (processedLabels.count(lastLabel) != 1) {
 597                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 598                                 needToRun = true;
 599                         }else {
 600                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 601                         }
 602                 }
 603
 604                 //run last label if you need to
 605                 if (needToRun == true)  {
 606                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 607                         lookup = input->getSharedRAbundVectors(lastLabel);
 608
 609                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 610                         process(lookup);
 611                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 612                 }
 613
 614                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 615
 616                 return 0;
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 620                 exit(1);
 621         }
 622 }
 623
 624 /***********************************************************/
 625 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 626         try{
 627                                 EstOutput data;
 628                                 vector<SharedRAbundVector*> subset;
 629                                 numGroups = thisLookup.size();
 630
 631                                 //for each calculator
 632                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 633                                         //initialize simMatrix
 634                                         simMatrix.clear();
 635                                         simMatrix.resize(numGroups);
 636                                         for (int k = 0; k < simMatrix.size(); k++)      {
 637                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 638                                                         simMatrix[k].push_back(0.0);
 639                                                 }
 640                                         }
 641
 642                                         //initialize index
 643                                         index.clear();
 644                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 645
 646                                         //create a new filename
 647                                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 648                                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 649
 650                                         for (int k = 0; k < thisLookup.size(); k++) {
 651                                                 for (int l = k; l < thisLookup.size(); l++) {
 652                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 653                                                                 //get estimated similarity between 2 groups
 654
 655                                                                 subset.clear(); //clear out old pair of sharedrabunds
 656                                                                 //add new pair of sharedrabunds
 657                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 658
 659                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 660                                                 //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
 661                                                                 if (m->control_pressed) { return 1; }
 662
 663                                                                 //save values in similarity matrix
 664                                                                 simMatrix[k][l] = data[0];
 665                                                                 simMatrix[l][k] = data[0];
 666                                                         }
 667                                                 }
 668                                         }
 669
 670                                         if (m->control_pressed) { return 1; }
 671                                         //creates tree from similarity matrix and write out file
 672                                         createTree();
 673
 674                                         if (m->control_pressed) { return 1; }
 675                                 }
 676
 677                                 return 0;
 678
 679         }
 680         catch(exception& e) {
 681                 m->errorOut(e, "TreeGroupCommand", "process");
 682                 exit(1);
 683         }
 684 }
 685 /***********************************************************/
 686
 687
 688