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
  98                         if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
  99
 100                         //create tree file
 101                         makeSimsShared();
 102                 }else{
 103                         //read in dist file
 104                         filename = globaldata->inputFileName;
 105
 106                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 107                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 108
 109                         if(globaldata->getPrecision() != ""){
 110                                 convert(globaldata->getPrecision(), precision);
 111                         }
 112
 113                         if(globaldata->getCutOff() != ""){
 114                                 convert(globaldata->getCutOff(), cutoff);
 115                                 cutoff += (5 / (precision * 10.0));
 116                         }
 117                         readMatrix->setCutoff(cutoff);
 118
 119                         if(globaldata->getNameFile() != ""){
 120                                 nameMap = new NameAssignment(globaldata->getNameFile());
 121                                 nameMap->readMap(1,2);
 122                         }
 123                         else{
 124                                 nameMap = NULL;
 125                         }
 126
 127                         readMatrix->read(nameMap);
 128                         list = readMatrix->getListVector();
 129                         matrix = readMatrix->getMatrix();
 130
 131                         //make treemap
 132                         tmap = new TreeMap();
 133                         tmap->makeSim(list);
 134                         globaldata->gTreemap = tmap;
 135
 136                         globaldata->Groups = tmap->namesOfGroups;
 137
 138                         //clear globaldatas old tree names if any
 139                         globaldata->Treenames.clear();
 140
 141                         //fills globaldatas tree names
 142                         globaldata->Treenames = globaldata->Groups;
 143
 144                         makeSimsDist();
 145
 146                         //create a new filename
 147                         outputFile = getRootName(globaldata->inputFileName) + "tre";
 148
 149                         createTree();
 150                 }
 151
 152                 //reset groups parameter
 153                 globaldata->Groups.clear();  globaldata->setGroups("");
 154
 155                 return 0;
 156         }
 157         catch(exception& e) {
 158                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 159                 exit(1);
 160         }
 161         catch(...) {
 162                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 163                 exit(1);
 164         }
 165 }
 166 //**********************************************************************************************************************
 167
 168 void TreeGroupCommand::createTree(){
 169         try {
 170                 //create tree
 171                 t = new Tree();
 172
 173                 //do merges and create tree structure by setting parents and children
 174                 //there are numGroups - 1 merges to do
 175                 for (int i = 0; i < (numGroups - 1); i++) {
 176                         float largest = -1000.0;
 177
 178                         int row, column;
 179                         //find largest value in sims matrix by searching lower triangle
 180                         for (int j = 1; j < simMatrix.size(); j++) {
 181                                 for (int k = 0; k < j; k++) {
 182                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 183                                 }
 184                         }
 185
 186                         //set non-leaf node info and update leaves to know their parents
 187                         //non-leaf
 188                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 189
 190                         //parents
 191                         t->tree[index[row]].setParent(numGroups + i);
 192                         t->tree[index[column]].setParent(numGroups + i);
 193
 194                         //blength = distance / 2;
 195                         float blength = ((1.0 - largest) / 2);
 196
 197                         //branchlengths
 198                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 199                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 200
 201                         //set your length to leaves to your childs length plus branchlength
 202                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 203
 204
 205                         //update index
 206                         index[row] = numGroups+i;
 207                         index[column] = numGroups+i;
 208
 209                         //remove highest value that caused the merge.
 210                         simMatrix[row][column] = -1000.0;
 211                         simMatrix[column][row] = -1000.0;
 212
 213                         //merge values in simsMatrix
 214                         for (int n = 0; n < simMatrix.size(); n++)      {
 215                                 //row becomes merge of 2 groups
 216                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 217                                 simMatrix[n][row] = simMatrix[row][n];
 218                                 //delete column
 219                                 simMatrix[column][n] = -1000.0;
 220                                 simMatrix[n][column] = -1000.0;
 221                         }
 222                 }
 223
 224                 //adjust tree to make sure root to tip length is .5
 225                 int root = t->findRoot();
 226                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 227
 228                 //assemble tree
 229                 t->assembleTree();
 230
 231                 //print newick file
 232                 t->createNewickFile(outputFile);
 233
 234                 //delete tree
 235                 delete t;
 236
 237         }
 238         catch(exception& e) {
 239                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 240                 exit(1);
 241         }
 242         catch(...) {
 243                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 244                 exit(1);
 245         }
 246 }
 247 /***********************************************************/
 248 void TreeGroupCommand::printSims(ostream& out) {
 249         try {
 250
 251                 //output column headers
 252                 //out << '\t';
 253                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 254                 //out << endl;
 255
 256
 257                 for (int m = 0; m < simMatrix.size(); m++)      {
 258                         //out << lookup[m]->getGroup() << '\t';
 259                         for (int n = 0; n < simMatrix.size(); n++)      {
 260                                 out << simMatrix[m][n] << '\t';
 261                         }
 262                         out << endl;
 263                 }
 264
 265         }
 266         catch(exception& e) {
 267                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 268                 exit(1);
 269         }
 270         catch(...) {
 271                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 272                 exit(1);
 273         }
 274 }
 275 /***********************************************************/
 276 void TreeGroupCommand::makeSimsDist() {
 277         try {
 278                 numGroups = list->size();
 279
 280                 //initialize index
 281                 index.clear();
 282                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 283
 284                 //initialize simMatrix
 285                 simMatrix.clear();
 286                 simMatrix.resize(numGroups);
 287                 for (int m = 0; m < simMatrix.size(); m++)      {
 288                         for (int j = 0; j < simMatrix.size(); j++)      {
 289                                 simMatrix[m].push_back(0.0);
 290                         }
 291                 }
 292
 293                 //go through sparse matrix and fill sims
 294                 //go through each cell in the sparsematrix
 295                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 296                         //similairity = -(distance-1)
 297                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 298                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 299                 }
 300
 301
 302         }
 303         catch(exception& e) {
 304                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 305                 exit(1);
 306         }
 307         catch(...) {
 308                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 309                 exit(1);
 310         }
 311 }
 312
 313 /***********************************************************/
 314 void TreeGroupCommand::makeSimsShared() {
 315         try {
 316                 int count = 1;
 317                 EstOutput data;
 318                 vector<SharedRAbundVector*> subset;
 319
 320                 numGroups = globaldata->Groups.size();
 321
 322                 //clear globaldatas old tree names if any
 323                 globaldata->Treenames.clear();
 324
 325                 //fills globaldatas tree names
 326                 globaldata->Treenames = globaldata->Groups;
 327
 328                 //create treemap class from groupmap for tree class to use
 329                 tmap = new TreeMap();
 330                 tmap->makeSim(globaldata->gGroupmap);
 331                 globaldata->gTreemap = tmap;
 332
 333                 while(lookup[0] != NULL){
 334
 335                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 336
 337                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 338
 339                                 //for each calculator
 340                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 341                                         //initialize simMatrix
 342                                         simMatrix.clear();
 343                                         simMatrix.resize(numGroups);
 344                                         for (int m = 0; m < simMatrix.size(); m++)      {
 345                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 346                                                         simMatrix[m].push_back(0.0);
 347                                                 }
 348                                         }
 349
 350                                         //initialize index
 351                                         index.clear();
 352                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 353
 354                                         //create a new filename
 355                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
 356
 357                                         for (int k = 0; k < lookup.size(); k++) {
 358                                                 for (int l = k; l < lookup.size(); l++) {
 359                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 360                                                                 //get estimated similarity between 2 groups
 361
 362                                                                 subset.clear(); //clear out old pair of sharedrabunds
 363                                                                 //add new pair of sharedrabunds
 364                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 365
 366                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 367                                                                 //save values in similarity matrix
 368                                                                 simMatrix[k][l] = data[0];
 369                                                                 simMatrix[l][k] = data[0];
 370                                                         }
 371                                                 }
 372                                         }
 373
 374                                         //creates tree from similarity matrix and write out file
 375                                         createTree();
 376                                 }
 377                         }
 378
 379                         //prevent memory leak
 380                         for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
 381
 382                         //get next line to process
 383                         lookup = input->getSharedRAbundVectors();
 384                         count++;
 385                 }
 386
 387                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 388         }
 389         catch(exception& e) {
 390                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 391                 exit(1);
 392         }
 393         catch(...) {
 394                 cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 395                 exit(1);
 396         }
 397 }
 398
 399 /***********************************************************/
 400
 401