tree.cpp

   1 /*
   2  *  tree.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/22/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "tree.h"
  11
  12
  13 /*****************************************************************/
  14 Tree::Tree() {
  15         try {
  16
  17                 globaldata = GlobalData::getInstance();
  18                 numLeaves = globaldata->gTreemap->getNumSeqs();
  19                 numNodes = 2*numLeaves - 1;
  20
  21                 tree.resize(numNodes);
  22
  23                 //initialize tree with correct number of nodes, name and group info.
  24                 for (int i = 0; i < numNodes; i++) {
  25                         //initialize leaf nodes
  26                         if (i <= (numLeaves-1)) {
  27                                 tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
  28                                 tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
  29                                 //set pcount and pGroup for groupname to 1.
  30                                 tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
  31                                 tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
  32                                 //Treemap knows name, group and index to speed up search
  33                                 globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
  34
  35                         //intialize non leaf nodes
  36                         }else if (i > (numLeaves-1)) {
  37                                 tree[i].setName("");
  38                                 tree[i].setGroup("");
  39                         }
  40                 }
  41         }
  42         catch(exception& e) {
  43                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46         catch(...) {
  47                 cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  48                 exit(1);
  49         }
  50 }
  51
  52 /*****************************************************************/
  53 int Tree::getIndex(string searchName) {
  54         try {
  55                 //Treemap knows name, group and index to speed up search
  56                 // getIndex function will return the vector index or -1 if seq is not found.
  57                 int index = globaldata->gTreemap->getIndex(searchName);
  58                 return index;
  59
  60         }
  61         catch(exception& e) {
  62                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65         catch(...) {
  66                 cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  67                 exit(1);
  68         }
  69 }
  70 /*****************************************************************/
  71
  72 void Tree::setIndex(string searchName, int index) {
  73         try {
  74                 //set index in treemap
  75                 globaldata->gTreemap->setIndex(searchName, index);
  76         }
  77         catch(exception& e) {
  78                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81         catch(...) {
  82                 cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85 }
  86 /*****************************************************************/
  87 void Tree::assembleTree() {
  88         try {
  89                 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
  90                 for (int i = numLeaves; i < numNodes; i++) {
  91                         tree[i].pGroups = (mergeGroups(i));
  92                         tree[i].pcount = (mergeGcounts(i));
  93                 }
  94         }
  95         catch(exception& e) {
  96                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99         catch(...) {
 100                 cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 101                 exit(1);
 102         }
 103 }
 104 /*****************************************************************/
 105 void Tree::getCopy(Tree* copy) {
 106         try {
 107
 108                 //for each node in the tree copy its info
 109                 for (int i = 0; i < numNodes; i++) {
 110                         //copy name
 111                         tree[i].setName(copy->tree[i].getName());
 112
 113                         //copy group
 114                         tree[i].setGroup(copy->tree[i].getGroup());
 115
 116                         //copy branch length
 117                         tree[i].setBranchLength(copy->tree[i].getBranchLength());
 118
 119                         //copy parent
 120                         tree[i].setParent(copy->tree[i].getParent());
 121
 122                         //copy children
 123                         tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
 124
 125                         //copy index in node and tmap
 126                         tree[i].setIndex(copy->tree[i].getIndex());
 127                         setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
 128
 129                         //copy pGroups
 130                         tree[i].pGroups = copy->tree[i].pGroups;
 131
 132                         //copy pcount
 133                         tree[i].pcount = copy->tree[i].pcount;
 134                 }
 135         }
 136         catch(exception& e) {
 137                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 138                 exit(1);
 139         }
 140         catch(...) {
 141                 cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144 }
 145 /*****************************************************************/
 146 //returns a map with a groupname and the number of times that group was seen in the children
 147 //for instance if your children are white and black then it would return a map with 2 entries
 148 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 149 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 150
 151 map<string, int> Tree::mergeGroups(int i) {
 152         try {
 153                 int lc = tree[i].getLChild();
 154                 int rc = tree[i].getRChild();
 155
 156                 //set parsimony groups to left child
 157                 map<string,int> parsimony = tree[lc].pGroups;
 158
 159                 int maxPars = 1;
 160
 161                 //look at right child groups and update maxPars if right child has something higher for that group.
 162                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 163                         it2 = parsimony.find(it->first);
 164                         if (it2 != parsimony.end()) {
 165                                 parsimony[it->first]++;
 166                         }else {
 167                                 parsimony[it->first] = 1;
 168                         }
 169
 170                         if(parsimony[it->first] > maxPars){
 171                                 maxPars = parsimony[it->first];
 172                         }
 173                 }
 174
 175                 // this is true if right child had a greater parsimony for a certain group
 176                 if(maxPars > 1){
 177                         //erase all the groups that are only 1 because you found something with 2.
 178                         for(it=parsimony.begin();it!=parsimony.end();it++){
 179                                 if(it->second == 1){
 180                                         parsimony.erase(it->first);
 181 //                                      it--;
 182                                 }
 183                         }
 184                         //set one remaining groups to 1
 185                         //so with our above example p[white] = 2 would be left and it would become p[white] = 1
 186                         for(it=parsimony.begin();it!=parsimony.end();it++){
 187                                 parsimony[it->first] = 1;
 188                         }
 189
 190                 }
 191
 192                 return parsimony;
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203 /*****************************************************************/
 204 //returns a map with a groupname and the number of times that group was seen in the children
 205 //for instance if your children are white and black then it would return a map with 2 entries
 206 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 207 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 208
 209 map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
 210         try {
 211
 212                 int lc = tree[i].getLChild();
 213                 int rc = tree[i].getRChild();
 214
 215                 //loop through nodes groups removing the ones the user doesn't want
 216                 for (it = tree[lc].pGroups.begin(); it != tree[lc].pGroups.end(); it++) {
 217                         if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); }
 218                 }
 219
 220                 //loop through nodes groups removing the ones the user doesn't want
 221                 for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) {
 222                         if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
 223                 }
 224
 225                 //set parsimony groups to left child
 226                 map<string,int> parsimony = tree[lc].pGroups;
 227
 228                 int maxPars = 1;
 229
 230                 //look at right child groups and update maxPars if right child has something higher for that group.
 231                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 232                         it2 = parsimony.find(it->first);
 233                         if (it2 != parsimony.end()) {
 234                                 parsimony[it->first]++;
 235                         }else {
 236                                 parsimony[it->first] = 1;
 237                         }
 238
 239                         if(parsimony[it->first] > maxPars){
 240                                 maxPars = parsimony[it->first];
 241                         }
 242                 }
 243
 244                 // this is true if right child had a greater parsimony for a certain group
 245                 if(maxPars > 1){
 246                         //erase all the groups that are only 1 because you found something with 2.
 247                         for(it=parsimony.begin();it!=parsimony.end();it++){
 248                                 if(it->second == 1){
 249                                         parsimony.erase(it->first);
 250                                 }
 251                         }
 252                         for(it=parsimony.begin();it!=parsimony.end();it++){
 253                                 parsimony[it->first] = 1;
 254                         }
 255                 }
 256
 257                 return parsimony;
 258         }
 259         catch(exception& e) {
 260                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 261                 exit(1);
 262         }
 263         catch(...) {
 264                 cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 265                 exit(1);
 266         }
 267 }
 268
 269
 270 /**************************************************************************************************/
 271
 272 map<string,int> Tree::mergeGcounts(int position) {
 273         try{
 274                 map<string,int>::iterator pos;
 275
 276                 int lc = tree[position].getLChild();
 277                 int rc = tree[position].getRChild();
 278
 279                 map<string,int> sum = tree[lc].pcount;
 280
 281                 for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
 282                         sum[it->first] += it->second;
 283                 }
 284                 return sum;
 285         }
 286         catch(exception& e) {
 287                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 288                 exit(1);
 289         }
 290         catch(...) {
 291                 cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 292                 exit(1);
 293         }
 294 }
 295 /**************************************************************************************************/
 296
 297 void Tree::randomLabels(vector<string> g) {
 298         try {
 299
 300                 for(int i = 0; i < numLeaves; i++){
 301                         int z;
 302                         //get random index to switch with
 303                         z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 304
 305                         //you only want to randomize the nodes that are from a group the user wants analyzed, so
 306                         //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
 307                         bool treez, treei;
 308
 309                         treez = inUsersGroups(tree[z].getGroup(), g);
 310                         treei = inUsersGroups(tree[i].getGroup(), g);
 311
 312                         if ((treez == true) && (treei == true)) {
 313                                 //switches node i and node z's info.
 314                                 map<string,int> lib_hold = tree[z].pGroups;
 315                                 tree[z].pGroups = (tree[i].pGroups);
 316                                 tree[i].pGroups = (lib_hold);
 317
 318                                 string zgroup = tree[z].getGroup();
 319                                 tree[z].setGroup(tree[i].getGroup());
 320                                 tree[i].setGroup(zgroup);
 321
 322                                 string zname = tree[z].getName();
 323                                 tree[z].setName(tree[i].getName());
 324                                 tree[i].setName(zname);
 325
 326                                 map<string,int> gcount_hold = tree[z].pcount;
 327                                 tree[z].pcount = (tree[i].pcount);
 328                                 tree[i].pcount = (gcount_hold);
 329                         }
 330                 }
 331         }
 332         catch(exception& e) {
 333                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 334                 exit(1);
 335         }
 336         catch(...) {
 337                 cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 338                 exit(1);
 339         }
 340 }
 341 /**************************************************************************************************/
 342
 343 void Tree::randomLabels(string groupA, string groupB) {
 344         try {
 345                 int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
 346                 int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
 347
 348                 vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
 349                 for(int i=numSeqsA;i<randomGroups.size();i++){
 350                         randomGroups[i] = groupB;
 351                 }
 352                 random_shuffle(randomGroups.begin(), randomGroups.end());
 353
 354                 int randomCounter = 0;
 355                 for(int i=0;i<numLeaves;i++){
 356                         if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
 357                                 tree[i].setGroup(randomGroups[randomCounter]);
 358                                 tree[i].pcount.clear();
 359                                 tree[i].pcount[randomGroups[randomCounter]] = 1;
 360                                 tree[i].pGroups.clear();
 361                                 tree[i].pGroups[randomGroups[randomCounter]] = 1;
 362                                 randomCounter++;
 363                         }
 364                 }
 365         }
 366         catch(exception& e) {
 367                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 368                 exit(1);
 369         }
 370         catch(...) {
 371                 cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 372                 exit(1);
 373         }
 374 }
 375 /**************************************************************************************************/
 376 void Tree::randomBlengths()  {
 377         try {
 378                 for(int i=numNodes-1;i>=0;i--){
 379                         int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 380
 381                         float bl_hold = tree[z].getBranchLength();
 382                         tree[z].setBranchLength(tree[i].getBranchLength());
 383                         tree[i].setBranchLength(bl_hold);
 384                 }
 385         }
 386         catch(exception& e) {
 387                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 388                 exit(1);
 389         }
 390         catch(...) {
 391                 cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 392                 exit(1);
 393         }
 394 }
 395 /*************************************************************************************************/
 396 void Tree::assembleRandomUnifracTree(vector<string> g) {
 397         randomLabels(g);
 398         assembleTree();
 399 }
 400 /*************************************************************************************************/
 401 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
 402         randomLabels(groupA, groupB);
 403         assembleTree();
 404 }
 405
 406 /*************************************************************************************************/
 407 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
 408 void Tree::assembleRandomTree() {
 409         randomTopology();
 410         assembleTree();
 411 }
 412 /**************************************************************************************************/
 413
 414 void Tree::randomTopology() {
 415         try {
 416                 for(int i=0;i<numNodes;i++){
 417                         tree[i].setParent(-1);
 418                 }
 419                 for(int i=numLeaves;i<numNodes;i++){
 420                         tree[i].setChildren(-1, -1);
 421                 }
 422
 423                 for(int i=numLeaves;i<numNodes;i++){
 424                         int escape =0;
 425                         int rnd_index1, rnd_index2;
 426                         while(escape == 0){
 427                                 rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
 428                                 if(tree[rnd_index1].getParent() == -1){escape = 1;}
 429                         }
 430
 431                         escape = 0;
 432                         while(escape == 0){
 433                                 rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
 434                                 if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
 435                                         escape = 1;
 436                                 }
 437                         }
 438
 439                         tree[i].setChildren(rnd_index1,rnd_index2);
 440                         tree[i].setParent(-1);
 441                         tree[rnd_index1].setParent(i);
 442                         tree[rnd_index2].setParent(i);
 443                 }
 444         }
 445         catch(exception& e) {
 446                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 447                 exit(1);
 448         }
 449         catch(...) {
 450                 cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 451                 exit(1);
 452         }
 453 }
 454
 455 /*****************************************************************/
 456 // This prints out the tree in Newick form.
 457 void Tree::createNewickFile(string f) {
 458         try {
 459                 int root = findRoot();
 460                 //filename = getRootName(globaldata->getTreeFile()) + "newick";
 461                 filename = f;
 462                 openOutputFile(filename, out);
 463
 464                 printBranch(root);
 465
 466                 // you are at the end of the tree
 467                 out << ";" << endl;
 468                 out.close();
 469         }
 470         catch(exception& e) {
 471                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 472                 exit(1);
 473         }
 474         catch(...) {
 475                 cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 476                 exit(1);
 477         }
 478 }
 479
 480 /*****************************************************************/
 481 //This function finds the index of the root node.
 482
 483 int Tree::findRoot() {
 484         try {
 485                 for (int i = 0; i < numNodes; i++) {
 486                         //you found the root
 487                         if (tree[i].getParent() == -1) { return i; }
 488                 }
 489                 return -1;
 490         }
 491         catch(exception& e) {
 492                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 493                 exit(1);
 494         }
 495         catch(...) {
 496                 cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 497                 exit(1);
 498         }
 499 }
 500
 501 /*****************************************************************/
 502 void Tree::printBranch(int node) {
 503         try {
 504
 505                 // you are not a leaf
 506                 if (tree[node].getLChild() != -1) {
 507                         out << "(";
 508                         printBranch(tree[node].getLChild());
 509                         out << ",";
 510                         printBranch(tree[node].getRChild());
 511                         out << ")";
 512                 }else { //you are a leaf
 513                         out << tree[node].getGroup() << ":" << tree[node].getBranchLength();
 514                 }
 515
 516         }
 517         catch(exception& e) {
 518                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 519                 exit(1);
 520         }
 521         catch(...) {
 522                 cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 523                 exit(1);
 524         }
 525 }
 526
 527 /*****************************************************************/
 528
 529 void Tree::printTree() {
 530
 531         for(int i=0;i<numNodes;i++){
 532                 cout << i << '\t';
 533                 tree[i].printNode();
 534         }
 535
 536 }
 537
 538 /*****************************************************************/
 539
 540