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                 globaldata = GlobalData::getInstance();
  17                 m = MothurOut::getInstance();
  18
  19                 if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
  20 //for(int i = 0; i <    globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }
  21                 numLeaves = globaldata->Treenames.size();
  22                 numNodes = 2*numLeaves - 1;
  23
  24                 tree.resize(numNodes);
  25
  26                 //initialize tree with correct number of nodes, name and group info.
  27                 for (int i = 0; i < numNodes; i++) {
  28                         //initialize leaf nodes
  29                         if (i <= (numLeaves-1)) {
  30                                 tree[i].setName(globaldata->Treenames[i]);
  31                                 vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
  32                                 tree[i].setGroup(tempGroups);
  33                                 //set pcount and pGroup for groupname to 1.
  34                                 tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
  35                                 tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
  36                                 //Treemap knows name, group and index to speed up search
  37                                 globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
  38
  39                         //intialize non leaf nodes
  40                         }else if (i > (numLeaves-1)) {
  41                                 tree[i].setName("");
  42                                 vector<string> tempGroups;
  43                                 tree[i].setGroup(tempGroups);
  44                         }
  45                 }
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "Tree", "Tree");
  49                 exit(1);
  50         }
  51 }
  52
  53 /*****************************************************************/
  54 Tree::~Tree() {}
  55 /*****************************************************************/
  56 void Tree::addNamesToCounts() {
  57         try {
  58                 //ex. seq1      seq2,seq3,se4
  59                 //              seq1 = pasture
  60                 //              seq2 = forest
  61                 //              seq4 = pasture
  62                 //              seq3 = ocean
  63
  64                 //before this function seq1.pcount = pasture -> 1
  65                 //after                            seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
  66
  67                 //before this function seq1.pgroups = pasture -> 1
  68                 //after                            seq1.pgroups = pasture -> 1 since that is the dominant group
  69
  70
  71                 //go through each leaf and update its pcounts and pgroups
  72                 for (int i = 0; i < numLeaves; i++) {
  73                         string name = tree[i].getName();
  74
  75                         map<string, string>::iterator itNames = globaldata->names.find(name);
  76
  77                         if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
  78                         else {
  79                                 vector<string> dupNames;
  80                                 splitAtComma(globaldata->names[name], dupNames);
  81
  82                                 map<string, int>::iterator itCounts;
  83                                 int maxPars = 1;
  84                                 for (int j = 0; j < dupNames.size(); j++) {
  85
  86                                         if (dupNames[j] != name) {//you already added yourself in the constructor
  87                                                 string group = globaldata->gTreemap->getGroup(dupNames[j]);
  88
  89                                                 //update pcounts
  90                                                 itCounts = tree[i].pcount.find(group);
  91                                                 if (itCounts == tree[i].pcount.end()) { //new group, add it
  92                                                         tree[i].pcount[group] = 1;
  93                                                 }else {
  94                                                         tree[i].pcount[group]++;
  95                                                 }
  96
  97                                                 //update pgroups
  98                                                 itCounts = tree[i].pGroups.find(group);
  99                                                 if (itCounts == tree[i].pGroups.end()) { //new group, add it
 100                                                         tree[i].pGroups[group] = 1;
 101                                                 }else {
 102                                                         tree[i].pGroups[group]++;
 103                                                 }
 104
 105                                                 //keep highest group
 106                                                 if(tree[i].pGroups[group] > maxPars){
 107                                                         maxPars = tree[i].pGroups[group];
 108                                                 }
 109                                         }//end if
 110                                 }//end for
 111
 112                                 if (maxPars > 1) { //then we have some more dominant groups
 113                                         //erase all the groups that are less than maxPars because you found a more dominant group.
 114                                         for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
 115                                                 if(it->second < maxPars){
 116                                                         tree[i].pGroups.erase(it++);
 117                                                 }else { it++; }
 118                                         }
 119                                         //set one remaining groups to 1
 120                                         for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
 121                                                 tree[i].pGroups[it->first] = 1;
 122                                         }
 123                                 }//end if
 124
 125                                 //update groups to reflect all the groups this node represents
 126                                 vector<string> nodeGroups;
 127                                 map<string, int>::iterator itGroups;
 128                                 for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
 129                                         nodeGroups.push_back(itGroups->first);
 130                                 }
 131                                 tree[i].setGroup(nodeGroups);
 132
 133                         }//end else
 134                 }//end for
 135
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "Tree", "addNamesToCounts");
 139                 exit(1);
 140         }
 141 }
 142 /*****************************************************************/
 143 int Tree::getIndex(string searchName) {
 144         try {
 145                 //Treemap knows name, group and index to speed up search
 146                 // getIndex function will return the vector index or -1 if seq is not found.
 147                 int index = globaldata->gTreemap->getIndex(searchName);
 148                 return index;
 149
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "Tree", "getIndex");
 153                 exit(1);
 154         }
 155 }
 156 /*****************************************************************/
 157
 158 void Tree::setIndex(string searchName, int index) {
 159         try {
 160                 //set index in treemap
 161                 globaldata->gTreemap->setIndex(searchName, index);
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "Tree", "setIndex");
 165                 exit(1);
 166         }
 167 }
 168 /*****************************************************************/
 169 void Tree::assembleTree() {
 170         try {
 171
 172                 //if user has given a names file we want to include that info in the pgroups and pcount info.
 173                 if(globaldata->names.size() != 0) {  addNamesToCounts();  }
 174
 175                 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 176                 for (int i = numLeaves; i < numNodes; i++) {
 177                         tree[i].pGroups = (mergeGroups(i));
 178                         tree[i].pcount = (mergeGcounts(i));
 179                 }
 180         }
 181         catch(exception& e) {
 182                 m->errorOut(e, "Tree", "assembleTree");
 183                 exit(1);
 184         }
 185 }
 186 /*****************************************************************/
 187 void Tree::getCopy(Tree* copy) {
 188         try {
 189
 190                 //for each node in the tree copy its info
 191                 for (int i = 0; i < numNodes; i++) {
 192                         //copy name
 193                         tree[i].setName(copy->tree[i].getName());
 194
 195                         //copy group
 196                         tree[i].setGroup(copy->tree[i].getGroup());
 197
 198                         //copy branch length
 199                         tree[i].setBranchLength(copy->tree[i].getBranchLength());
 200
 201                         //copy parent
 202                         tree[i].setParent(copy->tree[i].getParent());
 203
 204                         //copy children
 205                         tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
 206
 207                         //copy index in node and tmap
 208                         tree[i].setIndex(copy->tree[i].getIndex());
 209                         setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
 210
 211                         //copy pGroups
 212                         tree[i].pGroups = copy->tree[i].pGroups;
 213
 214                         //copy pcount
 215                         tree[i].pcount = copy->tree[i].pcount;
 216                 }
 217
 218         }
 219         catch(exception& e) {
 220                 m->errorOut(e, "Tree", "getCopy");
 221                 exit(1);
 222         }
 223 }
 224 /*****************************************************************/
 225 //returns a map with a groupname and the number of times that group was seen in the children
 226 //for instance if your children are white and black then it would return a map with 2 entries
 227 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 228 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 229
 230 map<string, int> Tree::mergeGroups(int i) {
 231         try {
 232                 int lc = tree[i].getLChild();
 233                 int rc = tree[i].getRChild();
 234
 235                 //set parsimony groups to left child
 236                 map<string,int> parsimony = tree[lc].pGroups;
 237
 238                 int maxPars = 1;
 239
 240                 //look at right child groups and update maxPars if right child has something higher for that group.
 241                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 242                         it2 = parsimony.find(it->first);
 243                         if (it2 != parsimony.end()) {
 244                                 parsimony[it->first]++;
 245                         }else {
 246                                 parsimony[it->first] = 1;
 247                         }
 248
 249                         if(parsimony[it->first] > maxPars){
 250                                 maxPars = parsimony[it->first];
 251                         }
 252                 }
 253
 254                 // this is true if right child had a greater parsimony for a certain group
 255                 if(maxPars > 1){
 256                         //erase all the groups that are only 1 because you found something with 2.
 257                         for(it=parsimony.begin();it!=parsimony.end();){
 258                                 if(it->second == 1){
 259                                         parsimony.erase(it++);
 260                                 }else { it++; }
 261                         }
 262                         //set one remaining groups to 1
 263                         //so with our above example p[white] = 2 would be left and it would become p[white] = 1
 264                         for(it=parsimony.begin();it!=parsimony.end();it++){
 265                                 parsimony[it->first] = 1;
 266                         }
 267
 268                 }
 269
 270                 return parsimony;
 271         }
 272         catch(exception& e) {
 273                 m->errorOut(e, "Tree", "mergeGroups");
 274                 exit(1);
 275         }
 276 }
 277 /*****************************************************************/
 278 //returns a map with a groupname and the number of times that group was seen in the children
 279 //for instance if your children are white and black then it would return a map with 2 entries
 280 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 281 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 282
 283 map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
 284         try {
 285
 286                 int lc = tree[i].getLChild();
 287                 int rc = tree[i].getRChild();
 288
 289                 //loop through nodes groups removing the ones the user doesn't want
 290                 for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
 291                                 if (inUsersGroups(it->first, g) != true) {
 292                                         tree[lc].pGroups.erase(it++);
 293                                 }else { it++; }
 294                 }
 295
 296                 //loop through nodes groups removing the ones the user doesn't want
 297                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
 298                                 if (inUsersGroups(it->first, g) != true) {
 299                                         tree[rc].pGroups.erase(it++);
 300                                 }else { it++; }
 301                 }
 302
 303                 //set parsimony groups to left child
 304                 map<string,int> parsimony = tree[lc].pGroups;
 305
 306                 int maxPars = 1;
 307
 308                 //look at right child groups and update maxPars if right child has something higher for that group.
 309                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 310                         it2 = parsimony.find(it->first);
 311                         if (it2 != parsimony.end()) {
 312                                 parsimony[it->first]++;
 313                         }else {
 314                                 parsimony[it->first] = 1;
 315                         }
 316
 317                         if(parsimony[it->first] > maxPars){
 318                                 maxPars = parsimony[it->first];
 319                         }
 320                 }
 321
 322                 // this is true if right child had a greater parsimony for a certain group
 323                 if(maxPars > 1){
 324                         //erase all the groups that are only 1 because you found something with 2.
 325                         for(it=parsimony.begin();it!=parsimony.end();){
 326                                 if(it->second == 1){
 327                                         parsimony.erase(it++);
 328                                 }else { it++; }
 329                         }
 330
 331                         for(it=parsimony.begin();it!=parsimony.end();it++){
 332                                 parsimony[it->first] = 1;
 333                         }
 334                 }
 335
 336                 return parsimony;
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "Tree", "mergeUserGroups");
 340                 exit(1);
 341         }
 342 }
 343
 344
 345 /**************************************************************************************************/
 346
 347 map<string,int> Tree::mergeGcounts(int position) {
 348         try{
 349                 map<string,int>::iterator pos;
 350
 351                 int lc = tree[position].getLChild();
 352                 int rc = tree[position].getRChild();
 353
 354                 map<string,int> sum = tree[lc].pcount;
 355
 356                 for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
 357                         sum[it->first] += it->second;
 358                 }
 359                 return sum;
 360         }
 361         catch(exception& e) {
 362                 m->errorOut(e, "Tree", "mergeGcounts");
 363                 exit(1);
 364         }
 365 }
 366 /**************************************************************************************************/
 367
 368 void Tree::randomLabels(vector<string> g) {
 369         try {
 370
 371                 for(int i = 0; i < numLeaves; i++){
 372                         int z;
 373                         //get random index to switch with
 374                         z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 375
 376                         //you only want to randomize the nodes that are from a group the user wants analyzed, so
 377                         //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.
 378                         bool treez, treei;
 379
 380                         treez = inUsersGroups(tree[z].getGroup(), g);
 381                         treei = inUsersGroups(tree[i].getGroup(), g);
 382
 383                         if ((treez == true) && (treei == true)) {
 384                                 //switches node i and node z's info.
 385                                 map<string,int> lib_hold = tree[z].pGroups;
 386                                 tree[z].pGroups = (tree[i].pGroups);
 387                                 tree[i].pGroups = (lib_hold);
 388
 389                                 vector<string> zgroup = tree[z].getGroup();
 390                                 tree[z].setGroup(tree[i].getGroup());
 391                                 tree[i].setGroup(zgroup);
 392
 393                                 string zname = tree[z].getName();
 394                                 tree[z].setName(tree[i].getName());
 395                                 tree[i].setName(zname);
 396
 397                                 map<string,int> gcount_hold = tree[z].pcount;
 398                                 tree[z].pcount = (tree[i].pcount);
 399                                 tree[i].pcount = (gcount_hold);
 400                         }
 401                 }
 402         }
 403         catch(exception& e) {
 404                 m->errorOut(e, "Tree", "randomLabels");
 405                 exit(1);
 406         }
 407 }
 408 /**************************************************************************************************
 409
 410 void Tree::randomLabels(string groupA, string groupB) {
 411         try {
 412                 int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
 413                 int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
 414
 415                 vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
 416                 for(int i=numSeqsA;i<randomGroups.size();i++){
 417                         randomGroups[i] = groupB;
 418                 }
 419                 random_shuffle(randomGroups.begin(), randomGroups.end());
 420
 421                 int randomCounter = 0;
 422                 for(int i=0;i<numLeaves;i++){
 423                         if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
 424                                 tree[i].setGroup(randomGroups[randomCounter]);
 425                                 tree[i].pcount.clear();
 426                                 tree[i].pcount[randomGroups[randomCounter]] = 1;
 427                                 tree[i].pGroups.clear();
 428                                 tree[i].pGroups[randomGroups[randomCounter]] = 1;
 429                                 randomCounter++;
 430                         }
 431                 }
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "Tree", "randomLabels");
 435                 exit(1);
 436         }
 437 }
 438 /**************************************************************************************************/
 439 void Tree::randomBlengths()  {
 440         try {
 441                 for(int i=numNodes-1;i>=0;i--){
 442                         int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 443
 444                         float bl_hold = tree[z].getBranchLength();
 445                         tree[z].setBranchLength(tree[i].getBranchLength());
 446                         tree[i].setBranchLength(bl_hold);
 447                 }
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "Tree", "randomBlengths");
 451                 exit(1);
 452         }
 453 }
 454 /*************************************************************************************************/
 455 void Tree::assembleRandomUnifracTree(vector<string> g) {
 456         randomLabels(g);
 457         assembleTree();
 458 }
 459 /*************************************************************************************************/
 460 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
 461
 462         vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
 463         randomLabels(temp);
 464         assembleTree();
 465 }
 466
 467 /*************************************************************************************************/
 468 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
 469 void Tree::assembleRandomTree() {
 470         randomTopology();
 471         assembleTree();
 472 }
 473 /**************************************************************************************************/
 474
 475 void Tree::randomTopology() {
 476         try {
 477                 for(int i=0;i<numNodes;i++){
 478                         tree[i].setParent(-1);
 479                 }
 480                 for(int i=numLeaves;i<numNodes;i++){
 481                         tree[i].setChildren(-1, -1);
 482                 }
 483
 484                 for(int i=numLeaves;i<numNodes;i++){
 485                         int escape =0;
 486                         int rnd_index1, rnd_index2;
 487                         while(escape == 0){
 488                                 rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
 489                                 if(tree[rnd_index1].getParent() == -1){escape = 1;}
 490                         }
 491
 492                         escape = 0;
 493                         while(escape == 0){
 494                                 rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
 495                                 if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
 496                                         escape = 1;
 497                                 }
 498                         }
 499
 500                         tree[i].setChildren(rnd_index1,rnd_index2);
 501                         tree[i].setParent(-1);
 502                         tree[rnd_index1].setParent(i);
 503                         tree[rnd_index2].setParent(i);
 504                 }
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "Tree", "randomTopology");
 508                 exit(1);
 509         }
 510 }
 511 /*****************************************************************/
 512 void Tree::print(ostream& out) {
 513         try {
 514                 int root = findRoot();
 515                 printBranch(root, out, "branch");
 516                 out << ";" << endl;
 517         }
 518         catch(exception& e) {
 519                 m->errorOut(e, "Tree", "print");
 520                 exit(1);
 521         }
 522 }
 523 /*****************************************************************/
 524 void Tree::printForBoot(ostream& out) {
 525         try {
 526                 int root = findRoot();
 527                 printBranch(root, out, "boot");
 528                 out << ";" << endl;
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "Tree", "printForBoot");
 532                 exit(1);
 533         }
 534 }
 535
 536 /*****************************************************************/
 537 // This prints out the tree in Newick form.
 538 void Tree::createNewickFile(string f) {
 539         try {
 540                 int root = findRoot();
 541                 //filename = getRootName(globaldata->getTreeFile()) + "newick";
 542                 filename = f;
 543
 544                 openOutputFile(filename, out);
 545
 546                 printBranch(root, out, "branch");
 547
 548                 // you are at the end of the tree
 549                 out << ";" << endl;
 550                 out.close();
 551         }
 552         catch(exception& e) {
 553                 m->errorOut(e, "Tree", "createNewickFile");
 554                 exit(1);
 555         }
 556 }
 557
 558 /*****************************************************************/
 559 //This function finds the index of the root node.
 560
 561 int Tree::findRoot() {
 562         try {
 563                 for (int i = 0; i < numNodes; i++) {
 564                         //you found the root
 565                         if (tree[i].getParent() == -1) { return i; }
 566                         //cout << "i = " << i << endl;
 567                         //cout << "i's parent = " << tree[i].getParent() << endl;
 568                 }
 569                 return -1;
 570         }
 571         catch(exception& e) {
 572                 m->errorOut(e, "Tree", "findRoot");
 573                 exit(1);
 574         }
 575 }
 576
 577 /*****************************************************************/
 578 void Tree::printBranch(int node, ostream& out, string mode) {
 579         try {
 580
 581                 // you are not a leaf
 582                 if (tree[node].getLChild() != -1) {
 583                         out << "(";
 584                         printBranch(tree[node].getLChild(), out, mode);
 585                         out << ",";
 586                         printBranch(tree[node].getRChild(), out, mode);
 587                         out << ")";
 588                         if (mode == "branch") {
 589                                 //if there is a branch length then print it
 590                                 if (tree[node].getBranchLength() != -1) {
 591                                         out << ":" << tree[node].getBranchLength();
 592                                 }
 593                         }else if (mode == "boot") {
 594                                 //if there is a label then print it
 595                                 if (tree[node].getLabel() != -1) {
 596                                         out << tree[node].getLabel();
 597                                 }
 598                         }
 599                 }else { //you are a leaf
 600                         string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
 601
 602                         out << leafGroup;
 603                         if (mode == "branch") {
 604                                 //if there is a branch length then print it
 605                                 if (tree[node].getBranchLength() != -1) {
 606                                         out << ":" << tree[node].getBranchLength();
 607                                 }
 608                         }else if (mode == "boot") {
 609                                 //if there is a label then print it
 610                                 if (tree[node].getLabel() != -1) {
 611                                         out << tree[node].getLabel();
 612                                 }
 613                         }
 614                 }
 615
 616         }
 617         catch(exception& e) {
 618                 m->errorOut(e, "Tree", "printBranch");
 619                 exit(1);
 620         }
 621 }
 622
 623 /*****************************************************************/
 624
 625 void Tree::printTree() {
 626
 627         for(int i=0;i<numNodes;i++){
 628                 cout << i << '\t';
 629                 tree[i].printNode();
 630         }
 631
 632 }
 633
 634 /*****************************************************************/
 635 //this code is a mess and should be rethought...-slw
 636 void Tree::parseTreeFile() {
 637
 638         //only takes names from the first tree and assumes that all trees use the same names.
 639         try {
 640                 string filename = globaldata->getTreeFile();
 641                 ifstream filehandle;
 642                 openInputFile(filename, filehandle);
 643                 int c, comment;
 644                 comment = 0;
 645                 int done = 1;
 646
 647                 //ifyou are not a nexus file
 648                 if((c = filehandle.peek()) != '#') {
 649                         while((c = filehandle.peek()) != ';') {
 650                                 while ((c = filehandle.peek()) != ';') {
 651                                         // get past comments
 652                                         if(c == '[') {
 653                                                 comment = 1;
 654                                         }
 655                                         if(c == ']'){
 656                                                 comment = 0;
 657                                         }
 658                                         if((c == '(') && (comment != 1)){ break; }
 659                                         filehandle.get();
 660                                 }
 661
 662                                 done = readTreeString(filehandle);
 663                                 if (done == 0) { break; }
 664                         }
 665                 //ifyou are a nexus file
 666                 }else if((c = filehandle.peek()) == '#') {
 667                         string holder = "";
 668
 669                         // get past comments
 670                         while(holder != "translate" && holder != "Translate"){
 671                                 if(holder == "[" || holder == "[!"){
 672                                         comment = 1;
 673                                 }
 674                                 if(holder == "]"){
 675                                         comment = 0;
 676                                 }
 677                                 filehandle >> holder;
 678
 679                                 //if there is no translate then you must read tree string otherwise use translate to get names
 680                                 if((holder == "tree") && (comment != 1)){
 681                                         //pass over the "tree rep.6878900 = "
 682                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
 683
 684                                         if(c == EOF) { break; }
 685                                         filehandle.putback(c);  //put back first ( of tree.
 686                                         done = readTreeString(filehandle);
 687
 688                                         break;
 689                                 }
 690
 691                                 if (done == 0) { break;  }
 692                         }
 693
 694                         //use nexus translation rather than parsing tree to save time
 695                         if((holder == "translate") || (holder == "Translate")) {
 696
 697                                 string number, name, h;
 698                                 h = ""; // so it enters the loop the first time
 699                                 while((h != ";") && (number != ";")) {
 700                                         filehandle >> number;
 701                                         filehandle >> name;
 702
 703                                         //c = , until done with translation then c = ;
 704                                         h = name.substr(name.length()-1, name.length());
 705                                         name.erase(name.end()-1);  //erase the comma
 706                                         globaldata->Treenames.push_back(number);
 707                                 }
 708                                 if(number == ";") { globaldata->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
 709                         }
 710                 }
 711                 filehandle.close();
 712         }
 713         catch(exception& e) {
 714                 m->errorOut(e, "Tree", "parseTreeFile");
 715                 exit(1);
 716         }
 717 }
 718 /*******************************************************/
 719
 720 /*******************************************************/
 721 int Tree::readTreeString(ifstream& filehandle)  {
 722         try {
 723                 int c;
 724                 string name;  //, k
 725
 726                 while((c = filehandle.peek()) != ';') {
 727 //k = c;
 728 //cout << " at beginning of while " <<  k << endl;
 729                         if(c == ')')  {
 730                                 //to pass over labels in trees
 731                                 c=filehandle.get();
 732                                 while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
 733                                 filehandle.putback(c);
 734                         }
 735                         if(c == ';') { return 0; }
 736                         if(c == -1) { return 0; }
 737                         //if you are a name
 738                         if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
 739                                 name = "";
 740                                 c = filehandle.get();
 741                         //k = c;
 742 //cout << k << endl;
 743                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
 744                                         name += c;
 745                                         c = filehandle.get();
 746                         //k = c;
 747 //cout << " in name while " << k << endl;
 748                                 }
 749
 750 //cout << "name = " << name << endl;
 751                                 globaldata->Treenames.push_back(name);
 752                                 filehandle.putback(c);
 753 //k = c;
 754 //cout << " after putback" <<  k << endl;
 755                         }
 756
 757                         if(c  == ':') { //read until you reach the end of the branch length
 758                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
 759                                         c = filehandle.get();
 760         //k = c;
 761         //cout << " in branch while " << k << endl;
 762                                 }
 763                                 filehandle.putback(c);
 764                         }
 765
 766                         c = filehandle.get();
 767 //k = c;
 768         //cout << " here after get " << k << endl;
 769                         if(c == ';') { return 0; }
 770                         if(c == ')') { filehandle.putback(c); }
 771         //k = c;
 772 //cout << k << endl;
 773
 774                 }
 775                 return 0;
 776         }
 777         catch(exception& e) {
 778                 m->errorOut(e, "Tree", "readTreeString");
 779                 exit(1);
 780         }
 781 }
 782
 783 /*******************************************************/
 784
 785 /*******************************************************/
 786