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                 abort = true;
  38                 globaldata = GlobalData::getInstance();
  39                 //initialize outputTypes
  40                 vector<string> tempOutNames;
  41                 outputTypes["tree"] = tempOutNames;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> TreeGroupCommand::getRequiredParameters(){
  50         try {
  51                 vector<string> myArray;
  52                 return myArray;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "TreeGroupCommand", "getRequiredParameters");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 vector<string> TreeGroupCommand::getRequiredFiles(){
  61         try {
  62                 string Array[] =  {"phylip","column","shared","or"};
  63                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  64                 return myArray;
  65         }
  66         catch(exception& e) {
  67                 m->errorOut(e, "TreeGroupCommand", "getRequiredFiles");
  68                 exit(1);
  69         }
  70 }
  71 //**********************************************************************************************************************
  72
  73 TreeGroupCommand::TreeGroupCommand(string option)  {
  74         try {
  75                 globaldata = GlobalData::getInstance();
  76                 abort = false;
  77                 allLines = 1;
  78                 labels.clear();
  79                 Groups.clear();
  80                 Estimators.clear();
  81
  82                 //allow user to run help
  83                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  84
  85                 else {
  86                         //valid paramters for this command
  87                         string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
  88                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  89
  90                         OptionParser parser(option);
  91                         map<string, string> parameters = parser. getParameters();
  92
  93                         ValidParameters validParameter;
  94                         map<string, string>::iterator it;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["tree"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("phylip");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 116                                 }
 117
 118                                 it = parameters.find("column");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 124                                 }
 125
 126                                 it = parameters.find("name");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 132                                 }
 133                         }
 134
 135                         format = globaldata->getFormat();
 136
 137                         //required parameters
 138                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 139                         if (phylipfile == "not open") { abort = true; }
 140                         else if (phylipfile == "not found") { phylipfile = ""; }
 141                         else {  globaldata->newRead(); format = "phylip";  globaldata->setPhylipFile(phylipfile);       }
 142
 143                         columnfile = validParameter.validFile(parameters, "column", true);
 144                         if (columnfile == "not open") { abort = true; }
 145                         else if (columnfile == "not found") { columnfile = ""; }
 146                         else {  globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile);        }
 147
 148                         namefile = validParameter.validFile(parameters, "name", true);
 149                         if (namefile == "not open") { abort = true; }
 150                         else if (namefile == "not found") { namefile = ""; }
 151                         else {  globaldata->setNameFile(namefile);      }
 152
 153                         //error checking on files
 154                         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; }
 155                         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; }
 156
 157                         if (columnfile != "") {
 158                                 if (namefile == "") {  m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
 159                         }
 160
 161                         //check for optional parameter and set defaults
 162                         // ...at some point should added some additional type checking...
 163                         label = validParameter.validFile(parameters, "label", false);
 164                         if (label == "not found") { label = ""; }
 165                         else {
 166                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 167                                 else { allLines = 1;  }
 168                         }
 169
 170                         //if the user has not specified any labels use the ones from read.otu
 171                         if(label == "") {
 172                                 allLines = globaldata->allLines;
 173                                 labels = globaldata->labels;
 174                         }
 175
 176                         groups = validParameter.validFile(parameters, "groups", false);
 177                         if (groups == "not found") { groups = ""; }
 178                         else {
 179                                 m->splitAtDash(groups, Groups);
 180                                 globaldata->Groups = Groups;
 181                         }
 182
 183                         calc = validParameter.validFile(parameters, "calc", false);
 184                         if (calc == "not found") { calc = "jclass-thetayc";  }
 185                         else {
 186                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 187                         }
 188                         m->splitAtDash(calc, Estimators);
 189
 190                         string temp;
 191                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 192                         convert(temp, precision);
 193
 194                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 195                         convert(temp, cutoff);
 196                         cutoff += (5 / (precision * 10.0));
 197
 198                         //if the user changes the output directory command factory will send this info to us in the output parameter
 199                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 200                                 outputDir = "";
 201                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 202                         }
 203
 204
 205                         if (abort == false) {
 206
 207                                 validCalculator = new ValidCalculators();
 208
 209                                 if (format == "sharedfile") {
 210                                         int i;
 211                                         for (i=0; i<Estimators.size(); i++) {
 212                                                 if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
 213                                                         if (Estimators[i] == "jabund") {
 214                                                                 treeCalculators.push_back(new JAbund());
 215                                                         }else if (Estimators[i] == "sorabund") {
 216                                                                 treeCalculators.push_back(new SorAbund());
 217                                                         }else if (Estimators[i] == "jclass") {
 218                                                                 treeCalculators.push_back(new Jclass());
 219                                                         }else if (Estimators[i] == "sorclass") {
 220                                                                 treeCalculators.push_back(new SorClass());
 221                                                         }else if (Estimators[i] == "jest") {
 222                                                                 treeCalculators.push_back(new Jest());
 223                                                         }else if (Estimators[i] == "sorest") {
 224                                                                 treeCalculators.push_back(new SorEst());
 225                                                         }else if (Estimators[i] == "thetayc") {
 226                                                                 treeCalculators.push_back(new ThetaYC());
 227                                                         }else if (Estimators[i] == "thetan") {
 228                                                                 treeCalculators.push_back(new ThetaN());
 229                                                         }else if (Estimators[i] == "morisitahorn") {
 230                                                                 treeCalculators.push_back(new MorHorn());
 231                                                         }else if (Estimators[i] == "braycurtis") {
 232                                                                 treeCalculators.push_back(new BrayCurtis());
 233                                                         }
 234                                                 }
 235                                         }
 236                                 }
 237                         }
 238                 }
 239
 240         }
 241         catch(exception& e) {
 242                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 243                 exit(1);
 244         }
 245 }
 246
 247 //**********************************************************************************************************************
 248
 249 void TreeGroupCommand::help(){
 250         try {
 251                 m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
 252                 m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
 253                 m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
 254                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 255                 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");
 256                 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");
 257                 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");
 258                 m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
 259                 m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
 260                 m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
 261                 m->mothurOut("The default value for calc is jclass-thetayc.\n");
 262                 m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
 263                 validCalculator->printCalc("treegroup", cout);
 264                 m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
 265                 m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
 266                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 267         }
 268         catch(exception& e) {
 269                 m->errorOut(e, "TreeGroupCommand", "help");
 270                 exit(1);
 271         }
 272 }
 273
 274
 275 //**********************************************************************************************************************
 276
 277 TreeGroupCommand::~TreeGroupCommand(){
 278         globaldata->Groups.clear();
 279         if (abort == false) {
 280
 281                 if (format == "sharedfile") { delete read;  delete input; globaldata->ginput = NULL; }
 282                 else { delete readMatrix;  delete matrix; delete list; }
 283                 delete tmap;  globaldata->gTreemap = NULL;
 284                 delete validCalculator;
 285         }
 286
 287 }
 288
 289 //**********************************************************************************************************************
 290
 291 int TreeGroupCommand::execute(){
 292         try {
 293
 294                 if (abort == true) { return 0; }
 295
 296                 if (format == "sharedfile") {
 297                         //if the users entered no valid calculators don't execute command
 298                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 299
 300                         if (globaldata->gGroupmap != NULL) {  delete globaldata->gGroupmap;   globaldata->gGroupmap = NULL;  }
 301                         //you have groups
 302                         read = new ReadOTUFile(globaldata->inputFileName);
 303                         read->read(&*globaldata);
 304
 305                         input = globaldata->ginput;
 306                         lookup = input->getSharedRAbundVectors();
 307                         lastLabel = lookup[0]->getLabel();
 308
 309                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 310
 311                         //used in tree constructor
 312                         globaldata->runParse = false;
 313
 314                         //create treemap class from groupmap for tree class to use
 315                         tmap = new TreeMap();
 316                         tmap->makeSim(globaldata->gGroupmap);
 317                         globaldata->gTreemap = tmap;
 318
 319                         //clear globaldatas old tree names if any
 320                         globaldata->Treenames.clear();
 321
 322                         //fills globaldatas tree names
 323                         globaldata->Treenames = globaldata->Groups;
 324
 325                         if (m->control_pressed) { return 0; }
 326
 327                         //create tree file
 328                         makeSimsShared();
 329
 330                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 331                 }else{
 332                         //read in dist file
 333                         filename = globaldata->inputFileName;
 334
 335                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 336                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 337
 338                         readMatrix->setCutoff(cutoff);
 339
 340                         if(namefile != ""){
 341                                 nameMap = new NameAssignment(namefile);
 342                                 nameMap->readMap();
 343                         }
 344                         else{
 345                                 nameMap = NULL;
 346                         }
 347
 348                         readMatrix->read(nameMap);
 349                         list = readMatrix->getListVector();
 350                         matrix = readMatrix->getMatrix();
 351
 352                         //make treemap
 353                         tmap = new TreeMap();
 354
 355                         if (m->control_pressed) { return 0; }
 356
 357                         tmap->makeSim(list);
 358                         globaldata->gTreemap = tmap;
 359
 360                         globaldata->Groups = tmap->namesOfGroups;
 361
 362                         //clear globaldatas old tree names if any
 363                         globaldata->Treenames.clear();
 364
 365                         //fills globaldatas tree names
 366                         globaldata->Treenames = globaldata->Groups;
 367
 368                         //used in tree constructor
 369                         globaldata->runParse = false;
 370
 371                         if (m->control_pressed) { return 0; }
 372
 373                         makeSimsDist();
 374
 375                         if (m->control_pressed) { return 0; }
 376
 377                         //create a new filename
 378                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";
 379                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 380
 381                         createTree();
 382
 383                         if (m->control_pressed) { return 0; }
 384
 385                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 386
 387                 }
 388
 389                 //reset groups parameter
 390                 globaldata->Groups.clear();
 391
 392                 m->mothurOutEndLine();
 393                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 394                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 395                 m->mothurOutEndLine();
 396
 397                 return 0;
 398         }
 399         catch(exception& e) {
 400                 m->errorOut(e, "TreeGroupCommand", "execute");
 401                 exit(1);
 402         }
 403 }
 404 //**********************************************************************************************************************
 405
 406 int TreeGroupCommand::createTree(){
 407         try {
 408                 //create tree
 409                 t = new Tree();
 410
 411                 //do merges and create tree structure by setting parents and children
 412                 //there are numGroups - 1 merges to do
 413                 for (int i = 0; i < (numGroups - 1); i++) {
 414                         float largest = -1000.0;
 415
 416                         if (m->control_pressed) { delete t; return 1; }
 417
 418                         int row, column;
 419                         //find largest value in sims matrix by searching lower triangle
 420                         for (int j = 1; j < simMatrix.size(); j++) {
 421                                 for (int k = 0; k < j; k++) {
 422                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 423                                 }
 424                         }
 425
 426                         //set non-leaf node info and update leaves to know their parents
 427                         //non-leaf
 428                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 429
 430                         //parents
 431                         t->tree[index[row]].setParent(numGroups + i);
 432                         t->tree[index[column]].setParent(numGroups + i);
 433
 434                         //blength = distance / 2;
 435                         float blength = ((1.0 - largest) / 2);
 436
 437                         //branchlengths
 438                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 439                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 440
 441                         //set your length to leaves to your childs length plus branchlength
 442                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 443
 444
 445                         //update index
 446                         index[row] = numGroups+i;
 447                         index[column] = numGroups+i;
 448
 449                         //remove highest value that caused the merge.
 450                         simMatrix[row][column] = -1000.0;
 451                         simMatrix[column][row] = -1000.0;
 452
 453                         //merge values in simsMatrix
 454                         for (int n = 0; n < simMatrix.size(); n++)      {
 455                                 //row becomes merge of 2 groups
 456                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 457                                 simMatrix[n][row] = simMatrix[row][n];
 458                                 //delete column
 459                                 simMatrix[column][n] = -1000.0;
 460                                 simMatrix[n][column] = -1000.0;
 461                         }
 462                 }
 463
 464                 //adjust tree to make sure root to tip length is .5
 465                 int root = t->findRoot();
 466                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 467
 468                 //assemble tree
 469                 t->assembleTree();
 470
 471                 if (m->control_pressed) { delete t; return 1; }
 472
 473                 //print newick file
 474                 t->createNewickFile(outputFile);
 475
 476                 //delete tree
 477                 delete t;
 478
 479                 if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
 480
 481                 return 0;
 482
 483         }
 484         catch(exception& e) {
 485                 m->errorOut(e, "TreeGroupCommand", "createTree");
 486                 exit(1);
 487         }
 488 }
 489 /***********************************************************/
 490 void TreeGroupCommand::printSims(ostream& out) {
 491         try {
 492
 493                 //output column headers
 494                 //out << '\t';
 495                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 496                 //out << endl;
 497
 498
 499                 for (int m = 0; m < simMatrix.size(); m++)      {
 500                         //out << lookup[m]->getGroup() << '\t';
 501                         for (int n = 0; n < simMatrix.size(); n++)      {
 502                                 out << simMatrix[m][n] << '\t';
 503                         }
 504                         out << endl;
 505                 }
 506
 507         }
 508         catch(exception& e) {
 509                 m->errorOut(e, "TreeGroupCommand", "printSims");
 510                 exit(1);
 511         }
 512 }
 513 /***********************************************************/
 514 int TreeGroupCommand::makeSimsDist() {
 515         try {
 516                 numGroups = list->size();
 517
 518                 //initialize index
 519                 index.clear();
 520                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 521
 522                 //initialize simMatrix
 523                 simMatrix.clear();
 524                 simMatrix.resize(numGroups);
 525                 for (int k = 0; k < simMatrix.size(); k++)      {
 526                         for (int j = 0; j < simMatrix.size(); j++)      {
 527                                 simMatrix[k].push_back(0.0);
 528                         }
 529                 }
 530
 531                 //go through sparse matrix and fill sims
 532                 //go through each cell in the sparsematrix
 533                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 534                         //similairity = -(distance-1)
 535                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 536                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 537
 538                         if (m->control_pressed) { return 1; }
 539
 540                 }
 541
 542                 return 0;
 543         }
 544         catch(exception& e) {
 545                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 546                 exit(1);
 547         }
 548 }
 549
 550 /***********************************************************/
 551 int TreeGroupCommand::makeSimsShared() {
 552         try {
 553                 set<string> processedLabels;
 554                 set<string> userLabels = labels;
 555
 556                 //as long as you are not at the end of the file or done wih the lines you want
 557                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 558                         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; }
 559
 560                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 561                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 562                                 process(lookup);
 563
 564                                 processedLabels.insert(lookup[0]->getLabel());
 565                                 userLabels.erase(lookup[0]->getLabel());
 566                         }
 567
 568                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 569                                 string saveLabel = lookup[0]->getLabel();
 570
 571                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 572                                 lookup = input->getSharedRAbundVectors(lastLabel);
 573
 574                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 575                                 process(lookup);
 576
 577                                 processedLabels.insert(lookup[0]->getLabel());
 578                                 userLabels.erase(lookup[0]->getLabel());
 579
 580                                 //restore real lastlabel to save below
 581                                 lookup[0]->setLabel(saveLabel);
 582                         }
 583
 584                         lastLabel = lookup[0]->getLabel();
 585
 586                         //get next line to process
 587                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 588                         lookup = input->getSharedRAbundVectors();
 589                 }
 590
 591                 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; }
 592
 593                 //output error messages about any remaining user labels
 594                 set<string>::iterator it;
 595                 bool needToRun = false;
 596                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 597                         m->mothurOut("Your file does not include the label " + *it);
 598                         if (processedLabels.count(lastLabel) != 1) {
 599                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 600                                 needToRun = true;
 601                         }else {
 602                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 603                         }
 604                 }
 605
 606                 //run last label if you need to
 607                 if (needToRun == true)  {
 608                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 609                         lookup = input->getSharedRAbundVectors(lastLabel);
 610
 611                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 612                         process(lookup);
 613                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 614                 }
 615
 616                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 617
 618                 return 0;
 619         }
 620         catch(exception& e) {
 621                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 622                 exit(1);
 623         }
 624 }
 625
 626 /***********************************************************/
 627 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 628         try{
 629                                 EstOutput data;
 630                                 vector<SharedRAbundVector*> subset;
 631                                 numGroups = thisLookup.size();
 632
 633                                 //for each calculator
 634                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 635                                         //initialize simMatrix
 636                                         simMatrix.clear();
 637                                         simMatrix.resize(numGroups);
 638                                         for (int k = 0; k < simMatrix.size(); k++)      {
 639                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 640                                                         simMatrix[k].push_back(0.0);
 641                                                 }
 642                                         }
 643
 644                                         //initialize index
 645                                         index.clear();
 646                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 647
 648                                         //create a new filename
 649                                         outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 650                                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 651
 652                                         for (int k = 0; k < thisLookup.size(); k++) {
 653                                                 for (int l = k; l < thisLookup.size(); l++) {
 654                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 655                                                                 //get estimated similarity between 2 groups
 656
 657                                                                 subset.clear(); //clear out old pair of sharedrabunds
 658                                                                 //add new pair of sharedrabunds
 659                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 660
 661                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 662                                                 //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
 663                                                                 if (m->control_pressed) { return 1; }
 664
 665                                                                 //save values in similarity matrix
 666                                                                 simMatrix[k][l] = data[0];
 667                                                                 simMatrix[l][k] = data[0];
 668                                                         }
 669                                                 }
 670                                         }
 671
 672                                         //createdistance file from simMatrix
 673                                         /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
 674                                         ofstream outDist;
 675                                         m->openOutputFile(o, outDist);
 676                                         outDist << simMatrix.size() << endl;
 677                                         for (int k = 0; k < simMatrix.size(); k++) {
 678                                                 outDist << thisLookup[k]->getGroup() << '\t';
 679                                                 for (int l = 0; l < k; l++) {
 680                                                         outDist << (1.0-simMatrix[k][l]) << '\t';
 681                                                 }
 682                                                 outDist << endl;
 683                                         }
 684                                         outDist.close();*/
 685
 686
 687                                         if (m->control_pressed) { return 1; }
 688                                         //creates tree from similarity matrix and write out file
 689                                         createTree();
 690
 691                                         if (m->control_pressed) { return 1; }
 692                                 }
 693
 694                                 return 0;
 695
 696         }
 697         catch(exception& e) {
 698                 m->errorOut(e, "TreeGroupCommand", "process");
 699                 exit(1);
 700         }
 701 }
 702 /***********************************************************/
 703
 704
 705