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(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 format = globaldata->getFormat();
  29                 validCalculator = new ValidCalculators();
  30
  31                 if (format == "sharedfile") {
  32                         int i;
  33                         for (i=0; i<globaldata->Estimators.size(); i++) {
  34                                 if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
  35                                         if (globaldata->Estimators[i] == "jabund") {
  36                                                 treeCalculators.push_back(new JAbund());
  37                                         }else if (globaldata->Estimators[i] == "sorabund") {
  38                                                 treeCalculators.push_back(new SorAbund());
  39                                         }else if (globaldata->Estimators[i] == "jclass") {
  40                                                 treeCalculators.push_back(new Jclass());
  41                                         }else if (globaldata->Estimators[i] == "sorclass") {
  42                                                 treeCalculators.push_back(new SorClass());
  43                                         }else if (globaldata->Estimators[i] == "jest") {
  44                                                 treeCalculators.push_back(new Jest());
  45                                         }else if (globaldata->Estimators[i] == "sorest") {
  46                                                 treeCalculators.push_back(new SorEst());
  47                                         }else if (globaldata->Estimators[i] == "thetayc") {
  48                                                 treeCalculators.push_back(new ThetaYC());
  49                                         }else if (globaldata->Estimators[i] == "thetan") {
  50                                                 treeCalculators.push_back(new ThetaN());
  51                                         }else if (globaldata->Estimators[i] == "morisitahorn") {
  52                                                 treeCalculators.push_back(new MorHorn());
  53                                         }else if (globaldata->Estimators[i] == "braycurtis") {
  54                                                 treeCalculators.push_back(new BrayCurtis());
  55                                         }
  56                                 }
  57                         }
  58                 }
  59
  60                 //reset calc for next command
  61                 globaldata->setCalc("");
  62
  63         }
  64         catch(exception& e) {
  65                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68         catch(...) {
  69                 cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74
  75 TreeGroupCommand::~TreeGroupCommand(){
  76         delete input;
  77         if (format == "sharedfile") {delete read;}
  78         else { delete readMatrix;  delete matrix; delete list; }
  79         delete tmap;
  80
  81 }
  82
  83 //**********************************************************************************************************************
  84
  85 int TreeGroupCommand::execute(){
  86         try {
  87                 if (format == "sharedfile") {
  88                         //if the users entered no valid calculators don't execute command
  89                         if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
  90
  91                         //you have groups
  92                         read = new ReadOTUFile(globaldata->inputFileName);
  93                         read->read(&*globaldata);
  94
  95                         input = globaldata->ginput;
  96                         lookup = input->getSharedRAbundVectors();
  97                         lastLookup = lookup;
  98
  99                         if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
 100
 101                         //create tree file
 102                         makeSimsShared();
 103                 }else{
 104                         //read in dist file
 105                         filename = globaldata->inputFileName;
 106
 107                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 108                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 109
 110                         if(globaldata->getPrecision() != ""){
 111                                 convert(globaldata->getPrecision(), precision);
 112                         }
 113
 114                         if(globaldata->getCutOff() != ""){
 115                                 convert(globaldata->getCutOff(), cutoff);
 116                                 cutoff += (5 / (precision * 10.0));
 117                         }
 118                         readMatrix->setCutoff(cutoff);
 119
 120                         if(globaldata->getNameFile() != ""){
 121                                 nameMap = new NameAssignment(globaldata->getNameFile());
 122                                 nameMap->readMap(1,2);
 123                         }
 124                         else{
 125                                 nameMap = NULL;
 126                         }
 127
 128                         readMatrix->read(nameMap);
 129                         list = readMatrix->getListVector();
 130                         matrix = readMatrix->getMatrix();
 131
 132                         //make treemap
 133                         tmap = new TreeMap();
 134                         tmap->makeSim(list);
 135                         globaldata->gTreemap = tmap;
 136
 137                         globaldata->Groups = tmap->namesOfGroups;
 138
 139                         //clear globaldatas old tree names if any
 140                         globaldata->Treenames.clear();
 141
 142                         //fills globaldatas tree names
 143                         globaldata->Treenames = globaldata->Groups;
 144
 145                         makeSimsDist();
 146
 147                         //create a new filename
 148                         outputFile = getRootName(globaldata->inputFileName) + "tre";
 149
 150                         createTree();
 151                 }
 152
 153                 //reset groups parameter
 154                 globaldata->Groups.clear();  globaldata->setGroups("");
 155
 156                 return 0;
 157         }
 158         catch(exception& e) {
 159                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 160                 exit(1);
 161         }
 162         catch(...) {
 163                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 164                 exit(1);
 165         }
 166 }
 167 //**********************************************************************************************************************
 168
 169 void TreeGroupCommand::createTree(){
 170         try {
 171                 //create tree
 172                 t = new Tree();
 173
 174                 //do merges and create tree structure by setting parents and children
 175                 //there are numGroups - 1 merges to do
 176                 for (int i = 0; i < (numGroups - 1); i++) {
 177                         float largest = -1000.0;
 178
 179                         int row, column;
 180                         //find largest value in sims matrix by searching lower triangle
 181                         for (int j = 1; j < simMatrix.size(); j++) {
 182                                 for (int k = 0; k < j; k++) {
 183                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 184                                 }
 185                         }
 186
 187                         //set non-leaf node info and update leaves to know their parents
 188                         //non-leaf
 189                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 190
 191                         //parents
 192                         t->tree[index[row]].setParent(numGroups + i);
 193                         t->tree[index[column]].setParent(numGroups + i);
 194
 195                         //blength = distance / 2;
 196                         float blength = ((1.0 - largest) / 2);
 197
 198                         //branchlengths
 199                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 200                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 201
 202                         //set your length to leaves to your childs length plus branchlength
 203                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 204
 205
 206                         //update index
 207                         index[row] = numGroups+i;
 208                         index[column] = numGroups+i;
 209
 210                         //remove highest value that caused the merge.
 211                         simMatrix[row][column] = -1000.0;
 212                         simMatrix[column][row] = -1000.0;
 213
 214                         //merge values in simsMatrix
 215                         for (int n = 0; n < simMatrix.size(); n++)      {
 216                                 //row becomes merge of 2 groups
 217                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 218                                 simMatrix[n][row] = simMatrix[row][n];
 219                                 //delete column
 220                                 simMatrix[column][n] = -1000.0;
 221                                 simMatrix[n][column] = -1000.0;
 222                         }
 223                 }
 224
 225                 //adjust tree to make sure root to tip length is .5
 226                 int root = t->findRoot();
 227                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 228
 229                 //assemble tree
 230                 t->assembleTree();
 231
 232                 //print newick file
 233                 t->createNewickFile(outputFile);
 234
 235                 //delete tree
 236                 delete t;
 237
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247 }
 248 /***********************************************************/
 249 void TreeGroupCommand::printSims(ostream& out) {
 250         try {
 251
 252                 //output column headers
 253                 //out << '\t';
 254                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 255                 //out << endl;
 256
 257
 258                 for (int m = 0; m < simMatrix.size(); m++)      {
 259                         //out << lookup[m]->getGroup() << '\t';
 260                         for (int n = 0; n < simMatrix.size(); n++)      {
 261                                 out << simMatrix[m][n] << '\t';
 262                         }
 263                         out << endl;
 264                 }
 265
 266         }
 267         catch(exception& e) {
 268                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 269                 exit(1);
 270         }
 271         catch(...) {
 272                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 273                 exit(1);
 274         }
 275 }
 276 /***********************************************************/
 277 void TreeGroupCommand::makeSimsDist() {
 278         try {
 279                 numGroups = list->size();
 280
 281                 //initialize index
 282                 index.clear();
 283                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 284
 285                 //initialize simMatrix
 286                 simMatrix.clear();
 287                 simMatrix.resize(numGroups);
 288                 for (int m = 0; m < simMatrix.size(); m++)      {
 289                         for (int j = 0; j < simMatrix.size(); j++)      {
 290                                 simMatrix[m].push_back(0.0);
 291                         }
 292                 }
 293
 294                 //go through sparse matrix and fill sims
 295                 //go through each cell in the sparsematrix
 296                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 297                         //similairity = -(distance-1)
 298                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 299                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 300                 }
 301
 302
 303         }
 304         catch(exception& e) {
 305                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 306                 exit(1);
 307         }
 308         catch(...) {
 309                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 310                 exit(1);
 311         }
 312 }
 313
 314 /***********************************************************/
 315 void TreeGroupCommand::makeSimsShared() {
 316         try {
 317                 int count = 1;
 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                 //create treemap class from groupmap for tree class to use
 326                 tmap = new TreeMap();
 327                 tmap->makeSim(globaldata->gGroupmap);
 328                 globaldata->gTreemap = tmap;
 329
 330                 set<string> processedLabels;
 331                 set<string> userLabels = globaldata->labels;
 332
 333                 //as long as you are not at the end of the file or done wih the lines you want
 334                 while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 335
 336                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 337                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 338                                 process(lookup);
 339
 340                                 processedLabels.insert(lookup[0]->getLabel());
 341                                 userLabels.erase(lookup[0]->getLabel());
 342                         }
 343
 344                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 345                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 346                                 process(lastLookup);
 347
 348                                 processedLabels.insert(lastLookup[0]->getLabel());
 349                                 userLabels.erase(lastLookup[0]->getLabel());
 350                         }
 351
 352                         //prevent memory leak
 353                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 354                         lastLookup = lookup;
 355
 356                         //get next line to process
 357                         lookup = input->getSharedRAbundVectors();
 358                         count++;
 359                 }
 360
 361                 //output error messages about any remaining user labels
 362                 set<string>::iterator it;
 363                 bool needToRun = false;
 364                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 365                         cout << "Your file does not include the label "<< *it;
 366                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 367                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 368                                 needToRun = true;
 369                         }else {
 370                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 371                         }
 372                 }
 373
 374                 //run last line if you need to
 375                 if (needToRun == true)  {
 376                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 377                         process(lastLookup);
 378                 }
 379
 380                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 381                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 382         }
 383         catch(exception& e) {
 384                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 385                 exit(1);
 386         }
 387         catch(...) {
 388                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 389                 exit(1);
 390         }
 391 }
 392
 393 /***********************************************************/
 394 void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 395         try{
 396                                 EstOutput data;
 397                                 vector<SharedRAbundVector*> subset;
 398                                 numGroups = globaldata->Groups.size();
 399
 400                                 //for each calculator
 401                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 402                                         //initialize simMatrix
 403                                         simMatrix.clear();
 404                                         simMatrix.resize(numGroups);
 405                                         for (int m = 0; m < simMatrix.size(); m++)      {
 406                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 407                                                         simMatrix[m].push_back(0.0);
 408                                                 }
 409                                         }
 410
 411                                         //initialize index
 412                                         index.clear();
 413                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 414
 415                                         //create a new filename
 416                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 417
 418                                         for (int k = 0; k < thisLookup.size(); k++) {
 419                                                 for (int l = k; l < thisLookup.size(); l++) {
 420                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 421                                                                 //get estimated similarity between 2 groups
 422
 423                                                                 subset.clear(); //clear out old pair of sharedrabunds
 424                                                                 //add new pair of sharedrabunds
 425                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 426
 427                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 428                                                                 //save values in similarity matrix
 429                                                                 simMatrix[k][l] = data[0];
 430                                                                 simMatrix[l][k] = data[0];
 431                                                         }
 432                                                 }
 433                                         }
 434
 435                                         //creates tree from similarity matrix and write out file
 436                                         createTree();
 437                                 }
 438
 439         }
 440         catch(exception& e) {
 441                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 442                 exit(1);
 443         }
 444         catch(...) {
 445                 cout << "An unknown error has occurred in the TreeGroupCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 446                 exit(1);
 447         }
 448 }
 449 /***********************************************************/
 450
 451
 452