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 Tree::Tree(int num, TreeMap* t) : tmap(t) {
  14         try {
  15                 m = MothurOut::getInstance();
  16
  17                 numLeaves = num;
  18                 numNodes = 2*numLeaves - 1;
  19
  20                 tree.resize(numNodes);
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "Tree", "Tree - numNodes");
  24                 exit(1);
  25         }
  26 }
  27 /*****************************************************************/
  28 Tree::Tree(string g) { //do not use tree generated by this its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
  29         try {
  30                 m = MothurOut::getInstance();
  31                 parseTreeFile();  m->runParse = false;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "Tree", "Tree - just parse");
  35                 exit(1);
  36         }
  37 }
  38 /*****************************************************************/
  39 Tree::Tree(TreeMap* t) : tmap(t) {
  40         try {
  41                 m = MothurOut::getInstance();
  42
  43                 if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }
  44 //for(int i = 0; i <    globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }
  45                 numLeaves = m->Treenames.size();
  46                 numNodes = 2*numLeaves - 1;
  47
  48                 tree.resize(numNodes);
  49
  50                 //initialize groupNodeInfo
  51                 for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
  52                         groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
  53                 }
  54
  55                 //initialize tree with correct number of nodes, name and group info.
  56                 for (int i = 0; i < numNodes; i++) {
  57                         //initialize leaf nodes
  58                         if (i <= (numLeaves-1)) {
  59                                 tree[i].setName(m->Treenames[i]);
  60
  61                                 //save group info
  62                                 string group = tmap->getGroup(m->Treenames[i]);
  63
  64                                 vector<string> tempGroups; tempGroups.push_back(group);
  65                                 tree[i].setGroup(tempGroups);
  66                                 groupNodeInfo[group].push_back(i);
  67
  68                                 //set pcount and pGroup for groupname to 1.
  69                                 tree[i].pcount[group] = 1;
  70                                 tree[i].pGroups[group] = 1;
  71
  72                                 //Treemap knows name, group and index to speed up search
  73                                 tmap->setIndex(m->Treenames[i], i);
  74
  75                         //intialize non leaf nodes
  76                         }else if (i > (numLeaves-1)) {
  77                                 tree[i].setName("");
  78                                 vector<string> tempGroups;
  79                                 tree[i].setGroup(tempGroups);
  80                         }
  81                 }
  82
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "Tree", "Tree");
  86                 exit(1);
  87         }
  88 }
  89 /*****************************************************************/
  90 Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
  91         try {
  92                 m = MothurOut::getInstance();
  93
  94                 if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }
  95                 numLeaves = m->Treenames.size();
  96                 numNodes = 2*numLeaves - 1;
  97
  98                 tree.resize(numNodes);
  99
 100                 //initialize groupNodeInfo
 101                 for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
 102                         groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
 103                 }
 104
 105                 //initialize tree with correct number of nodes, name and group info.
 106                 for (int i = 0; i < numNodes; i++) {
 107                         //initialize leaf nodes
 108                         if (i <= (numLeaves-1)) {
 109                                 tree[i].setName(m->Treenames[i]);
 110
 111                                 //save group info
 112                                 string group = tmap->getGroup(m->Treenames[i]);
 113
 114                                 vector<string> tempGroups; tempGroups.push_back(group);
 115                                 tree[i].setGroup(tempGroups);
 116                                 groupNodeInfo[group].push_back(i);
 117
 118                                 //set pcount and pGroup for groupname to 1.
 119                                 tree[i].pcount[group] = 1;
 120                                 tree[i].pGroups[group] = 1;
 121
 122                                 //Treemap knows name, group and index to speed up search
 123                                 tmap->setIndex(m->Treenames[i], i);
 124
 125                 //intialize non leaf nodes
 126                         }else if (i > (numLeaves-1)) {
 127                                 tree[i].setName("");
 128                                 vector<string> tempGroups;
 129                                 tree[i].setGroup(tempGroups);
 130                         }
 131                 }
 132
 133         //build tree from matrix
 134         //initialize indexes
 135         map<int, int> indexes;  //maps row in simMatrix to vector index in the tree
 136         for (int g = 0; g < numLeaves; g++) {   indexes[g] = g; }
 137
 138                 //do merges and create tree structure by setting parents and children
 139                 //there are numGroups - 1 merges to do
 140                 for (int i = 0; i < (numLeaves - 1); i++) {
 141                         float largest = -1000.0;
 142
 143                         if (m->control_pressed) { break; }
 144
 145                         int row, column;
 146                         //find largest value in sims matrix by searching lower triangle
 147                         for (int j = 1; j < sims.size(); j++) {
 148                                 for (int k = 0; k < j; k++) {
 149                                         if (sims[j][k] > largest) {  largest = sims[j][k]; row = j; column = k;  }
 150                                 }
 151                         }
 152
 153                         //set non-leaf node info and update leaves to know their parents
 154                         //non-leaf
 155                         tree[numLeaves + i].setChildren(indexes[row], indexes[column]);
 156
 157                         //parents
 158                         tree[indexes[row]].setParent(numLeaves + i);
 159                         tree[indexes[column]].setParent(numLeaves + i);
 160
 161                         //blength = distance / 2;
 162                         float blength = ((1.0 - largest) / 2);
 163
 164                         //branchlengths
 165                         tree[indexes[row]].setBranchLength(blength - tree[indexes[row]].getLengthToLeaves());
 166                         tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves());
 167
 168                         //set your length to leaves to your childs length plus branchlength
 169                         tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
 170
 171
 172                         //update index
 173                         indexes[row] = numLeaves+i;
 174                         indexes[column] = numLeaves+i;
 175
 176                         //remove highest value that caused the merge.
 177                         sims[row][column] = -1000.0;
 178                         sims[column][row] = -1000.0;
 179
 180                         //merge values in simsMatrix
 181                         for (int n = 0; n < sims.size(); n++)   {
 182                                 //row becomes merge of 2 groups
 183                                 sims[row][n] = (sims[row][n] + sims[column][n]) / 2;
 184                                 sims[n][row] = sims[row][n];
 185                                 //delete column
 186                                 sims[column][n] = -1000.0;
 187                                 sims[n][column] = -1000.0;
 188                         }
 189                 }
 190
 191                 //adjust tree to make sure root to tip length is .5
 192                 int root = findRoot();
 193                 tree[root].setBranchLength((0.5 - tree[root].getLengthToLeaves()));
 194
 195     }
 196         catch(exception& e) {
 197                 m->errorOut(e, "Tree", "Tree");
 198                 exit(1);
 199         }
 200 }
 201 /*****************************************************************/
 202 Tree::~Tree() {}
 203 /*****************************************************************/
 204 void Tree::addNamesToCounts(map<string, string> nameMap) {
 205         try {
 206                 //ex. seq1      seq2,seq3,se4
 207                 //              seq1 = pasture
 208                 //              seq2 = forest
 209                 //              seq4 = pasture
 210                 //              seq3 = ocean
 211
 212                 //before this function seq1.pcount = pasture -> 1
 213                 //after                            seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
 214
 215                 //before this function seq1.pgroups = pasture -> 1
 216                 //after                            seq1.pgroups = pasture -> 1 since that is the dominant group
 217
 218
 219                 //go through each leaf and update its pcounts and pgroups
 220
 221                 //float A = clock();
 222
 223                 for (int i = 0; i < numLeaves; i++) {
 224
 225                         string name = tree[i].getName();
 226
 227                         map<string, string>::iterator itNames = nameMap.find(name);
 228
 229                         if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
 230                         else {
 231                                 vector<string> dupNames;
 232                                 m->splitAtComma(nameMap[name], dupNames);
 233
 234                                 map<string, int>::iterator itCounts;
 235                                 int maxPars = 1;
 236                                 set<string> groupsAddedForThisNode;
 237                                 for (int j = 0; j < dupNames.size(); j++) {
 238
 239                                         string group = tmap->getGroup(dupNames[j]);
 240
 241                                         if (dupNames[j] != name) {//you already added yourself in the constructor
 242
 243                                                 if (groupsAddedForThisNode.count(group) == 0)  {  groupNodeInfo[group].push_back(i);  groupsAddedForThisNode.insert(group);  } //if you have not already added this node for this group, then add it
 244
 245                                                 //update pcounts
 246                                                 itCounts = tree[i].pcount.find(group);
 247                                                 if (itCounts == tree[i].pcount.end()) { //new group, add it
 248                                                         tree[i].pcount[group] = 1;
 249                                                 }else {
 250                                                         tree[i].pcount[group]++;
 251                                                 }
 252
 253                                                 //update pgroups
 254                                                 itCounts = tree[i].pGroups.find(group);
 255                                                 if (itCounts == tree[i].pGroups.end()) { //new group, add it
 256                                                         tree[i].pGroups[group] = 1;
 257                                                 }else{
 258                                                         tree[i].pGroups[group]++;
 259                                                 }
 260
 261                                                 //keep highest group
 262                                                 if(tree[i].pGroups[group] > maxPars){
 263                                                         maxPars = tree[i].pGroups[group];
 264                                                 }
 265                                         }else {  groupsAddedForThisNode.insert(group);  } //add it so you don't add it to groupNodeInfo again
 266                                 }//end for
 267
 268                                 if (maxPars > 1) { //then we have some more dominant groups
 269                                         //erase all the groups that are less than maxPars because you found a more dominant group.
 270                                         for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
 271                                                 if(it->second < maxPars){
 272                                                         tree[i].pGroups.erase(it++);
 273                                                 }else { it++; }
 274                                         }
 275                                         //set one remaining groups to 1
 276                                         for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
 277                                                 tree[i].pGroups[it->first] = 1;
 278                                         }
 279                                 }//end if
 280
 281                                 //update groups to reflect all the groups this node represents
 282                                 vector<string> nodeGroups;
 283                                 map<string, int>::iterator itGroups;
 284                                 for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
 285                                         nodeGroups.push_back(itGroups->first);
 286                                 }
 287                                 tree[i].setGroup(nodeGroups);
 288
 289                         }//end else
 290                 }//end for
 291
 292                 //float B = clock();
 293                 //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
 294
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "Tree", "addNamesToCounts");
 298                 exit(1);
 299         }
 300 }
 301 /*****************************************************************/
 302 int Tree::getIndex(string searchName) {
 303         try {
 304                 //Treemap knows name, group and index to speed up search
 305                 // getIndex function will return the vector index or -1 if seq is not found.
 306                 int index = tmap->getIndex(searchName);
 307                 return index;
 308
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "Tree", "getIndex");
 312                 exit(1);
 313         }
 314 }
 315 /*****************************************************************/
 316
 317 void Tree::setIndex(string searchName, int index) {
 318         try {
 319                 //set index in treemap
 320                 tmap->setIndex(searchName, index);
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "Tree", "setIndex");
 324                 exit(1);
 325         }
 326 }
 327 /*****************************************************************/
 328 int Tree::assembleTree(map<string, string> nameMap) {
 329         try {
 330                 //save for later
 331         names = nameMap;
 332
 333                 //if user has given a names file we want to include that info in the pgroups and pcount info.
 334                 if(nameMap.size() != 0) {  addNamesToCounts(nameMap);  }
 335
 336                 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 337                 for (int i = numLeaves; i < numNodes; i++) {
 338                         if (m->control_pressed) { return 1; }
 339
 340                         tree[i].pGroups = (mergeGroups(i));
 341                         tree[i].pcount = (mergeGcounts(i));
 342                 }
 343
 344                 return 0;
 345         }
 346         catch(exception& e) {
 347                 m->errorOut(e, "Tree", "assembleTree");
 348                 exit(1);
 349         }
 350 }
 351 /*****************************************************************
 352 int Tree::assembleTree(string n) {
 353         try {
 354
 355                 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 356                 for (int i = numLeaves; i < numNodes; i++) {
 357                         if (m->control_pressed) { return 1; }
 358
 359                         tree[i].pGroups = (mergeGroups(i));
 360                         tree[i].pcount = (mergeGcounts(i));
 361                 }
 362                 //float B = clock();
 363                 //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
 364                 return 0;
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "Tree", "assembleTree");
 368                 exit(1);
 369         }
 370 }
 371 /*****************************************************************/
 372 //assumes leaf node names are in groups and no names file - used by indicator command
 373 void Tree::getSubTree(Tree* Ctree, vector<string> Groups) {
 374         try {
 375
 376         //copy Tree since we are going to destroy it
 377         Tree* copy = new Tree(tmap);
 378         copy->getCopy(Ctree);
 379         map<string, string> empty;
 380         copy->assembleTree(empty);
 381
 382                 //we want to select some of the leaf nodes to create the output tree
 383                 //go through the input Tree starting at parents of leaves
 384                 for (int i = 0; i < numNodes; i++) {
 385
 386                         //initialize leaf nodes
 387                         if (i <= (numLeaves-1)) {
 388                                 tree[i].setName(Groups[i]);
 389
 390                                 //save group info
 391                                 string group = tmap->getGroup(Groups[i]);
 392                                 vector<string> tempGroups; tempGroups.push_back(group);
 393                                 tree[i].setGroup(tempGroups);
 394                                 groupNodeInfo[group].push_back(i);
 395
 396                                 //set pcount and pGroup for groupname to 1.
 397                                 tree[i].pcount[group] = 1;
 398                                 tree[i].pGroups[group] = 1;
 399
 400                                 //Treemap knows name, group and index to speed up search
 401                                 tmap->setIndex(Groups[i], i);
 402
 403                                 //intialize non leaf nodes
 404                         }else if (i > (numLeaves-1)) {
 405                                 tree[i].setName("");
 406                                 vector<string> tempGroups;
 407                                 tree[i].setGroup(tempGroups);
 408                         }
 409                 }
 410
 411                 set<int> removedLeaves;
 412                 for (int i = 0; i < copy->getNumLeaves(); i++) {
 413
 414                         if (removedLeaves.count(i) == 0) {
 415
 416                         //am I in the group
 417                         int parent = copy->tree[i].getParent();
 418
 419                         if (parent != -1) {
 420
 421                                 if (m->inUsersGroups(copy->tree[i].getName(), Groups)) {
 422                                         //find my siblings name
 423                                         int parentRC = copy->tree[parent].getRChild();
 424                                         int parentLC = copy->tree[parent].getLChild();
 425
 426                                         //if I am the right child, then my sib is the left child
 427                                         int sibIndex = parentRC;
 428                                         if (parentRC == i) { sibIndex = parentLC; }
 429
 430                                         string sibsName = copy->tree[sibIndex].getName();
 431
 432                                         //if yes, is my sibling
 433                                         if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
 434                                                 //we both are okay no trimming required
 435                                         }else{
 436                                                 //i am, my sib is not, so remove sib by setting my parent to my grandparent
 437                                                 int grandparent = copy->tree[parent].getParent();
 438                                                 int grandparentLC = copy->tree[grandparent].getLChild();
 439                                                 int grandparentRC = copy->tree[grandparent].getRChild();
 440
 441                                                 //whichever of my granparents children was my parent now equals me
 442                                                 if (grandparentLC == parent) { grandparentLC = i; }
 443                                                 else { grandparentRC = i; }
 444
 445                                                 copy->tree[i].setParent(grandparent);
 446                                                 copy->tree[i].setBranchLength((copy->tree[i].getBranchLength()+copy->tree[parent].getBranchLength()));
 447                                                 if (grandparent != -1) {
 448                                                         copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
 449                                                 }
 450                                                 removedLeaves.insert(sibIndex);
 451                                         }
 452                                 }else{
 453                                         //find my siblings name
 454                                         int parentRC = copy->tree[parent].getRChild();
 455                                         int parentLC = copy->tree[parent].getLChild();
 456
 457                                         //if I am the right child, then my sib is the left child
 458                                         int sibIndex = parentRC;
 459                                         if (parentRC == i) { sibIndex = parentLC; }
 460
 461                                         string sibsName = copy->tree[sibIndex].getName();
 462
 463                                         //if no is my sibling
 464                                         if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
 465                                                 //i am not, but my sib is
 466                                                 int grandparent = copy->tree[parent].getParent();
 467                                                 int grandparentLC = copy->tree[grandparent].getLChild();
 468                                                 int grandparentRC = copy->tree[grandparent].getRChild();
 469
 470                                                 //whichever of my granparents children was my parent now equals my sib
 471                                                 if (grandparentLC == parent) { grandparentLC = sibIndex; }
 472                                                 else { grandparentRC = sibIndex; }
 473
 474                                                 copy->tree[sibIndex].setParent(grandparent);
 475                                                 copy->tree[sibIndex].setBranchLength((copy->tree[sibIndex].getBranchLength()+copy->tree[parent].getBranchLength()));
 476                                                 if (grandparent != -1) {
 477                                                         copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
 478                                                 }
 479                                                 removedLeaves.insert(i);
 480                                         }else{
 481                                                 //neither of us are, so we want to eliminate ourselves and our parent
 482                                                 //so set our parents sib to our great-grandparent
 483                                                 int parent = copy->tree[i].getParent();
 484                                                 int grandparent = copy->tree[parent].getParent();
 485                                                 int parentsSibIndex;
 486                                                 if (grandparent != -1) {
 487                                                         int greatgrandparent = copy->tree[grandparent].getParent();
 488                                                         int greatgrandparentLC, greatgrandparentRC;
 489                                                         if (greatgrandparent != -1) {
 490                                                                 greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
 491                                                                 greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
 492                                                         }
 493
 494                                                         int grandparentLC = copy->tree[grandparent].getLChild();
 495                                                         int grandparentRC = copy->tree[grandparent].getRChild();
 496
 497                                                         parentsSibIndex = grandparentLC;
 498                                                         if (grandparentLC == parent) { parentsSibIndex = grandparentRC; }
 499
 500                                                         //whichever of my greatgrandparents children was my grandparent
 501                                                         if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
 502                                                         else { greatgrandparentRC = parentsSibIndex; }
 503
 504                                                         copy->tree[parentsSibIndex].setParent(greatgrandparent);
 505                                                         copy->tree[parentsSibIndex].setBranchLength((copy->tree[parentsSibIndex].getBranchLength()+copy->tree[grandparent].getBranchLength()));
 506                                                         if (greatgrandparent != -1) {
 507                                                                 copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
 508                                                         }
 509                                                 }else{
 510                                                         copy->tree[parent].setParent(-1);
 511                                                         //cout << "issues with making subtree" << endl;
 512                                                 }
 513                                                 removedLeaves.insert(sibIndex);
 514                                                 removedLeaves.insert(i);
 515                                         }
 516                                 }
 517                         }
 518                         }
 519                 }
 520
 521                 int root = 0;
 522                 for (int i = 0; i < copy->getNumNodes(); i++) {
 523                         //you found the root
 524                         if (copy->tree[i].getParent() == -1) { root = i; break; }
 525                 }
 526
 527                 int nextSpot = numLeaves;
 528                 populateNewTree(copy->tree, root, nextSpot);
 529
 530         delete copy;
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "Tree", "getSubTree");
 534                 exit(1);
 535         }
 536 }
 537 /*****************************************************************/
 538 //assumes nameMap contains unique names as key or is empty.
 539 //assumes numLeaves defined in tree constructor equals size of seqsToInclude and seqsToInclude only contains unique seqs.
 540 int Tree::getSubTree(Tree* copy, vector<string> seqsToInclude, map<string, string> nameMap) {
 541         try {
 542
 543         if (numLeaves != seqsToInclude.size()) { m->mothurOut("[ERROR]: numLeaves does not equal numUniques, cannot create subtree.\n"); m->control_pressed = true; return 0; }
 544
 545         getSubTree(copy, seqsToInclude);
 546         if (nameMap.size() != 0) {  addNamesToCounts(nameMap);  }
 547
 548         //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 549                 for (int i = numLeaves; i < numNodes; i++) {
 550                         if (m->control_pressed) { return 1; }
 551
 552                         tree[i].pGroups = (mergeGroups(i));
 553                         tree[i].pcount = (mergeGcounts(i));
 554                 }
 555
 556         return 0;
 557     }
 558         catch(exception& e) {
 559                 m->errorOut(e, "Tree", "getSubTree");
 560                 exit(1);
 561         }
 562 }
 563 /*****************************************************************/
 564 int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
 565         try {
 566
 567                 if (oldtree[node].getLChild() != -1) {
 568                         int rc = populateNewTree(oldtree, oldtree[node].getLChild(), index);
 569                         int lc = populateNewTree(oldtree, oldtree[node].getRChild(), index);
 570
 571                         tree[index].setChildren(lc, rc);
 572                         tree[rc].setParent(index);
 573                         tree[lc].setParent(index);
 574
 575                         tree[index].setBranchLength(oldtree[node].getBranchLength());
 576                         tree[rc].setBranchLength(oldtree[oldtree[node].getLChild()].getBranchLength());
 577                         tree[lc].setBranchLength(oldtree[oldtree[node].getRChild()].getBranchLength());
 578
 579                         return (index++);
 580                 }else { //you are a leaf
 581                         int indexInNewTree = tmap->getIndex(oldtree[node].getName());
 582                         return indexInNewTree;
 583                 }
 584         }
 585         catch(exception& e) {
 586                 m->errorOut(e, "Tree", "populateNewTree");
 587                 exit(1);
 588         }
 589 }
 590 /*****************************************************************/
 591 void Tree::getCopy(Tree* copy, map<string, string> nameMap) {
 592         try {
 593
 594                 //for each node in the tree copy its info
 595                 for (int i = 0; i < numNodes; i++) {
 596                         //copy branch length
 597                         tree[i].setBranchLength(copy->tree[i].getBranchLength());
 598
 599                         //copy parent
 600                         tree[i].setParent(copy->tree[i].getParent());
 601
 602                         //copy children
 603                         tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
 604         }
 605
 606         if (nameMap.size() != 0) {  addNamesToCounts(nameMap);  }
 607
 608         //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 609                 for (int i = numLeaves; i < numNodes; i++) {
 610                         if (m->control_pressed) { break; }
 611
 612                         tree[i].pGroups = (mergeGroups(i));
 613                         tree[i].pcount = (mergeGcounts(i));
 614                 }
 615         }
 616         catch(exception& e) {
 617                 m->errorOut(e, "Tree", "getCopy");
 618                 exit(1);
 619         }
 620 }
 621 /*****************************************************************/
 622 void Tree::getCopy(Tree* copy) {
 623         try {
 624
 625                 //for each node in the tree copy its info
 626                 for (int i = 0; i < numNodes; i++) {
 627                         //copy name
 628                         tree[i].setName(copy->tree[i].getName());
 629
 630                         //copy group
 631                         tree[i].setGroup(copy->tree[i].getGroup());
 632
 633                         //copy branch length
 634                         tree[i].setBranchLength(copy->tree[i].getBranchLength());
 635
 636                         //copy parent
 637                         tree[i].setParent(copy->tree[i].getParent());
 638
 639                         //copy children
 640                         tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
 641
 642                         //copy index in node and tmap
 643                         tree[i].setIndex(copy->tree[i].getIndex());
 644                         setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
 645
 646                         //copy pGroups
 647                         tree[i].pGroups = copy->tree[i].pGroups;
 648
 649                         //copy pcount
 650                         tree[i].pcount = copy->tree[i].pcount;
 651                 }
 652
 653                 groupNodeInfo = copy->groupNodeInfo;
 654
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "Tree", "getCopy");
 658                 exit(1);
 659         }
 660 }
 661 /*****************************************************************/
 662 //returns a map with a groupname and the number of times that group was seen in the children
 663 //for instance if your children are white and black then it would return a map with 2 entries
 664 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 665 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 666
 667 map<string, int> Tree::mergeGroups(int i) {
 668         try {
 669                 int lc = tree[i].getLChild();
 670                 int rc = tree[i].getRChild();
 671
 672                 //set parsimony groups to left child
 673                 map<string,int> parsimony = tree[lc].pGroups;
 674
 675                 int maxPars = 1;
 676
 677                 //look at right child groups and update maxPars if right child has something higher for that group.
 678                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 679                         it2 = parsimony.find(it->first);
 680                         if (it2 != parsimony.end()) {
 681                                 parsimony[it->first]++;
 682                         }else {
 683                                 parsimony[it->first] = 1;
 684                         }
 685
 686                         if(parsimony[it->first] > maxPars){
 687                                 maxPars = parsimony[it->first];
 688                         }
 689                 }
 690
 691                 // this is true if right child had a greater parsimony for a certain group
 692                 if(maxPars > 1){
 693                         //erase all the groups that are only 1 because you found something with 2.
 694                         for(it=parsimony.begin();it!=parsimony.end();){
 695                                 if(it->second == 1){
 696                                         parsimony.erase(it++);
 697                                 }else { it++; }
 698                         }
 699                         //set one remaining groups to 1
 700                         //so with our above example p[white] = 2 would be left and it would become p[white] = 1
 701                         for(it=parsimony.begin();it!=parsimony.end();it++){
 702                                 parsimony[it->first] = 1;
 703                         }
 704
 705                 }
 706
 707                 return parsimony;
 708         }
 709         catch(exception& e) {
 710                 m->errorOut(e, "Tree", "mergeGroups");
 711                 exit(1);
 712         }
 713 }
 714 /*****************************************************************/
 715 //returns a map with a groupname and the number of times that group was seen in the children
 716 //for instance if your children are white and black then it would return a map with 2 entries
 717 // p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
 718 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
 719
 720 map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
 721         try {
 722
 723                 int lc = tree[i].getLChild();
 724                 int rc = tree[i].getRChild();
 725
 726                 //loop through nodes groups removing the ones the user doesn't want
 727                 for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
 728                                 if (m->inUsersGroups(it->first, g) != true) {
 729                                         tree[lc].pGroups.erase(it++);
 730                                 }else { it++; }
 731                 }
 732
 733                 //loop through nodes groups removing the ones the user doesn't want
 734                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
 735                                 if (m->inUsersGroups(it->first, g) != true) {
 736                                         tree[rc].pGroups.erase(it++);
 737                                 }else { it++; }
 738                 }
 739
 740                 //set parsimony groups to left child
 741                 map<string,int> parsimony = tree[lc].pGroups;
 742
 743                 int maxPars = 1;
 744
 745                 //look at right child groups and update maxPars if right child has something higher for that group.
 746                 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
 747                         it2 = parsimony.find(it->first);
 748                         if (it2 != parsimony.end()) {
 749                                 parsimony[it->first]++;
 750                         }else {
 751                                 parsimony[it->first] = 1;
 752                         }
 753
 754                         if(parsimony[it->first] > maxPars){
 755                                 maxPars = parsimony[it->first];
 756                         }
 757                 }
 758
 759                 // this is true if right child had a greater parsimony for a certain group
 760                 if(maxPars > 1){
 761                         //erase all the groups that are only 1 because you found something with 2.
 762                         for(it=parsimony.begin();it!=parsimony.end();){
 763                                 if(it->second == 1){
 764                                         parsimony.erase(it++);
 765                                 }else { it++; }
 766                         }
 767
 768                         for(it=parsimony.begin();it!=parsimony.end();it++){
 769                                 parsimony[it->first] = 1;
 770                         }
 771                 }
 772
 773                 return parsimony;
 774         }
 775         catch(exception& e) {
 776                 m->errorOut(e, "Tree", "mergeUserGroups");
 777                 exit(1);
 778         }
 779 }
 780
 781
 782 /**************************************************************************************************/
 783
 784 map<string,int> Tree::mergeGcounts(int position) {
 785         try{
 786                 map<string,int>::iterator pos;
 787
 788                 int lc = tree[position].getLChild();
 789                 int rc = tree[position].getRChild();
 790
 791                 map<string,int> sum = tree[lc].pcount;
 792
 793                 for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
 794                         sum[it->first] += it->second;
 795                 }
 796                 return sum;
 797         }
 798         catch(exception& e) {
 799                 m->errorOut(e, "Tree", "mergeGcounts");
 800                 exit(1);
 801         }
 802 }
 803 /**************************************************************************************************/
 804 void Tree::randomLabels(vector<string> g) {
 805         try {
 806
 807                 //initialize groupNodeInfo
 808                 for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
 809                         groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
 810                 }
 811
 812                 for(int i = 0; i < numLeaves; i++){
 813                         int z;
 814                         //get random index to switch with
 815                         z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 816
 817                         //you only want to randomize the nodes that are from a group the user wants analyzed, so
 818                         //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.
 819                         bool treez, treei;
 820
 821                         treez = m->inUsersGroups(tree[z].getGroup(), g);
 822                         treei = m->inUsersGroups(tree[i].getGroup(), g);
 823
 824                         if ((treez == true) && (treei == true)) {
 825                                 //switches node i and node z's info.
 826                                 map<string,int> lib_hold = tree[z].pGroups;
 827                                 tree[z].pGroups = (tree[i].pGroups);
 828                                 tree[i].pGroups = (lib_hold);
 829
 830                                 vector<string> zgroup = tree[z].getGroup();
 831                                 tree[z].setGroup(tree[i].getGroup());
 832                                 tree[i].setGroup(zgroup);
 833
 834                                 string zname = tree[z].getName();
 835                                 tree[z].setName(tree[i].getName());
 836                                 tree[i].setName(zname);
 837
 838                                 map<string,int> gcount_hold = tree[z].pcount;
 839                                 tree[z].pcount = (tree[i].pcount);
 840                                 tree[i].pcount = (gcount_hold);
 841                         }
 842
 843                         for (int k = 0; k < (tree[i].getGroup()).size(); k++) {  groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
 844                         for (int k = 0; k < (tree[z].getGroup()).size(); k++) {  groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
 845                 }
 846         }
 847         catch(exception& e) {
 848                 m->errorOut(e, "Tree", "randomLabels");
 849                 exit(1);
 850         }
 851 }
 852 /**************************************************************************************************/
 853 void Tree::randomBlengths()  {
 854         try {
 855                 for(int i=numNodes-1;i>=0;i--){
 856                         int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 857
 858                         float bl_hold = tree[z].getBranchLength();
 859                         tree[z].setBranchLength(tree[i].getBranchLength());
 860                         tree[i].setBranchLength(bl_hold);
 861                 }
 862         }
 863         catch(exception& e) {
 864                 m->errorOut(e, "Tree", "randomBlengths");
 865                 exit(1);
 866         }
 867 }
 868 /*************************************************************************************************/
 869 void Tree::assembleRandomUnifracTree(vector<string> g) {
 870         randomLabels(g);
 871     map<string, string> empty;
 872         assembleTree(empty);
 873 }
 874 /*************************************************************************************************/
 875 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
 876         vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
 877         randomLabels(temp);
 878     map<string, string> empty;
 879         assembleTree(empty);
 880 }
 881
 882 /*************************************************************************************************/
 883 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
 884 void Tree::assembleRandomTree() {
 885         randomTopology();
 886     map<string, string> empty;
 887         assembleTree(empty);
 888 }
 889 /**************************************************************************************************/
 890
 891 void Tree::randomTopology() {
 892         try {
 893                 for(int i=0;i<numNodes;i++){
 894                         tree[i].setParent(-1);
 895                 }
 896                 for(int i=numLeaves;i<numNodes;i++){
 897                         tree[i].setChildren(-1, -1);
 898                 }
 899
 900                 for(int i=numLeaves;i<numNodes;i++){
 901                         int escape =0;
 902                         int rnd_index1, rnd_index2;
 903                         while(escape == 0){
 904                                 rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
 905                                 if(tree[rnd_index1].getParent() == -1){escape = 1;}
 906                         }
 907
 908                         escape = 0;
 909                         while(escape == 0){
 910                                 rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
 911                                 if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
 912                                         escape = 1;
 913                                 }
 914                         }
 915
 916                         tree[i].setChildren(rnd_index1,rnd_index2);
 917                         tree[i].setParent(-1);
 918                         tree[rnd_index1].setParent(i);
 919                         tree[rnd_index2].setParent(i);
 920                 }
 921         }
 922         catch(exception& e) {
 923                 m->errorOut(e, "Tree", "randomTopology");
 924                 exit(1);
 925         }
 926 }
 927 /*****************************************************************/
 928 void Tree::print(ostream& out) {
 929         try {
 930                 int root = findRoot();
 931                 printBranch(root, out, "branch");
 932                 out << ";" << endl;
 933         }
 934         catch(exception& e) {
 935                 m->errorOut(e, "Tree", "print");
 936                 exit(1);
 937         }
 938 }
 939 /*****************************************************************/
 940 void Tree::print(ostream& out, map<string, string> nameMap) {
 941         try {
 942                 int root = findRoot();
 943                 printBranch(root, out, nameMap);
 944                 out << ";" << endl;
 945         }
 946         catch(exception& e) {
 947                 m->errorOut(e, "Tree", "print");
 948                 exit(1);
 949         }
 950 }
 951 /*****************************************************************/
 952 void Tree::print(ostream& out, string mode) {
 953         try {
 954                 int root = findRoot();
 955                 printBranch(root, out, mode);
 956                 out << ";" << endl;
 957         }
 958         catch(exception& e) {
 959                 m->errorOut(e, "Tree", "print");
 960                 exit(1);
 961         }
 962 }
 963 /*****************************************************************/
 964 // This prints out the tree in Newick form.
 965 void Tree::createNewickFile(string f) {
 966         try {
 967                 int root = findRoot();
 968
 969                 filename = f;
 970
 971                 m->openOutputFile(filename, out);
 972
 973                 printBranch(root, out, "branch");
 974
 975                 // you are at the end of the tree
 976                 out << ";" << endl;
 977                 out.close();
 978         }
 979         catch(exception& e) {
 980                 m->errorOut(e, "Tree", "createNewickFile");
 981                 exit(1);
 982         }
 983 }
 984
 985 /*****************************************************************/
 986 //This function finds the index of the root node.
 987
 988 int Tree::findRoot() {
 989         try {
 990                 for (int i = 0; i < numNodes; i++) {
 991                         //you found the root
 992                         if (tree[i].getParent() == -1) { return i; }
 993                         //cout << "i = " << i << endl;
 994                         //cout << "i's parent = " << tree[i].getParent() << endl;
 995                 }
 996                 return -1;
 997         }
 998         catch(exception& e) {
 999                 m->errorOut(e, "Tree", "findRoot");
1000                 exit(1);
1001         }
1002 }
1003 /*****************************************************************/
1004 void Tree::printBranch(int node, ostream& out, map<string, string> names) {
1005 try {
1006
1007 // you are not a leaf
1008                 if (tree[node].getLChild() != -1) {
1009                         out << "(";
1010                         printBranch(tree[node].getLChild(), out, names);
1011                         out << ",";
1012                         printBranch(tree[node].getRChild(), out, names);
1013                         out << ")";
1014
1015             //if there is a branch length then print it
1016             if (tree[node].getBranchLength() != -1) {
1017                 out << ":" << tree[node].getBranchLength();
1018             }
1019
1020                 }else { //you are a leaf
1021             map<string, string>::iterator itNames = names.find(tree[node].getName());
1022
1023             string outputString = "";
1024             if (itNames != names.end()) {
1025
1026                 vector<string> dupNames;
1027                 m->splitAtComma((itNames->second), dupNames);
1028
1029                 if (dupNames.size() == 1) {
1030                     outputString += tree[node].getName();
1031                     if (tree[node].getBranchLength() != -1) {
1032                         outputString += ":" + toString(tree[node].getBranchLength());
1033                     }
1034                 }else {
1035                     outputString += "(";
1036
1037                     for (int u = 0; u < dupNames.size()-1; u++) {
1038                         outputString += dupNames[u];
1039
1040                         if (tree[node].getBranchLength() != -1) {
1041                             outputString += ":" + toString(0.0);
1042                         }
1043                         outputString += ",";
1044                     }
1045
1046                     outputString += dupNames[dupNames.size()-1];
1047                     if (tree[node].getBranchLength() != -1) {
1048                         outputString += ":" + toString(0.0);
1049                     }
1050
1051                     outputString += ")";
1052                     if (tree[node].getBranchLength() != -1) {
1053                         outputString += ":" + toString(tree[node].getBranchLength());
1054                     }
1055                 }
1056             }else {
1057                 outputString = tree[node].getName();
1058                 //if there is a branch length then print it
1059                 if (tree[node].getBranchLength() != -1) {
1060                     outputString += ":" + toString(tree[node].getBranchLength());
1061                 }
1062
1063                 m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine();
1064             }
1065
1066             out << outputString;
1067                 }
1068
1069         }
1070         catch(exception& e) {
1071                 m->errorOut(e, "Tree", "printBranch");
1072                 exit(1);
1073         }
1074 }
1075 /*****************************************************************/
1076 void Tree::printBranch(int node, ostream& out, string mode) {
1077     try {
1078
1079         // you are not a leaf
1080                 if (tree[node].getLChild() != -1) {
1081                         out << "(";
1082                         printBranch(tree[node].getLChild(), out, mode);
1083                         out << ",";
1084                         printBranch(tree[node].getRChild(), out, mode);
1085                         out << ")";
1086                         if (mode == "branch") {
1087                                 //if there is a branch length then print it
1088                                 if (tree[node].getBranchLength() != -1) {
1089                                         out << ":" << tree[node].getBranchLength();
1090                                 }
1091                         }else if (mode == "boot") {
1092                                 //if there is a label then print it
1093                                 if (tree[node].getLabel() != -1) {
1094                                         out << tree[node].getLabel();
1095                                 }
1096                         }else if (mode == "both") {
1097                                 if (tree[node].getLabel() != -1) {
1098                                         out << tree[node].getLabel();
1099                                 }
1100                                 //if there is a branch length then print it
1101                                 if (tree[node].getBranchLength() != -1) {
1102                                         out << ":" << tree[node].getBranchLength();
1103                                 }
1104                         }
1105                 }else { //you are a leaf
1106                         string leafGroup = tmap->getGroup(tree[node].getName());
1107
1108                         if (mode == "branch") {
1109                                 out << leafGroup;
1110                                 //if there is a branch length then print it
1111                                 if (tree[node].getBranchLength() != -1) {
1112                                         out << ":" << tree[node].getBranchLength();
1113                                 }
1114                         }else if (mode == "boot") {
1115                                 out << leafGroup;
1116                                 //if there is a label then print it
1117                                 if (tree[node].getLabel() != -1) {
1118                                         out << tree[node].getLabel();
1119                                 }
1120                         }else if (mode == "both") {
1121                                 out << tree[node].getName();
1122                                 if (tree[node].getLabel() != -1) {
1123                                         out << tree[node].getLabel();
1124                                 }
1125                                 //if there is a branch length then print it
1126                                 if (tree[node].getBranchLength() != -1) {
1127                                         out << ":" << tree[node].getBranchLength();
1128                                 }
1129                         }
1130                 }
1131
1132         }
1133         catch(exception& e) {
1134                 m->errorOut(e, "Tree", "printBranch");
1135                 exit(1);
1136         }
1137 }
1138 /*****************************************************************/
1139 void Tree::printBranch(int node, ostream& out, string mode, vector<Node>& theseNodes) {
1140         try {
1141
1142                 // you are not a leaf
1143                 if (theseNodes[node].getLChild() != -1) {
1144                         out << "(";
1145                         printBranch(theseNodes[node].getLChild(), out, mode);
1146                         out << ",";
1147                         printBranch(theseNodes[node].getRChild(), out, mode);
1148                         out << ")";
1149                         if (mode == "branch") {
1150                                 //if there is a branch length then print it
1151                                 if (theseNodes[node].getBranchLength() != -1) {
1152                                         out << ":" << theseNodes[node].getBranchLength();
1153                                 }
1154                         }else if (mode == "boot") {
1155                                 //if there is a label then print it
1156                                 if (theseNodes[node].getLabel() != -1) {
1157                                         out << theseNodes[node].getLabel();
1158                                 }
1159                         }else if (mode == "both") {
1160                                 if (theseNodes[node].getLabel() != -1) {
1161                                         out << theseNodes[node].getLabel();
1162                                 }
1163                                 //if there is a branch length then print it
1164                                 if (theseNodes[node].getBranchLength() != -1) {
1165                                         out << ":" << theseNodes[node].getBranchLength();
1166                                 }
1167                         }
1168                 }else { //you are a leaf
1169                         string leafGroup = tmap->getGroup(theseNodes[node].getName());
1170
1171                         if (mode == "branch") {
1172                                 out << leafGroup;
1173                                 //if there is a branch length then print it
1174                                 if (theseNodes[node].getBranchLength() != -1) {
1175                                         out << ":" << theseNodes[node].getBranchLength();
1176                                 }
1177                         }else if (mode == "boot") {
1178                                 out << leafGroup;
1179                                 //if there is a label then print it
1180                                 if (theseNodes[node].getLabel() != -1) {
1181                                         out << theseNodes[node].getLabel();
1182                                 }
1183                         }else if (mode == "both") {
1184                                 out << theseNodes[node].getName();
1185                                 if (theseNodes[node].getLabel() != -1) {
1186                                         out << theseNodes[node].getLabel();
1187                                 }
1188                                 //if there is a branch length then print it
1189                                 if (theseNodes[node].getBranchLength() != -1) {
1190                                         out << ":" << theseNodes[node].getBranchLength();
1191                                 }
1192                         }
1193                 }
1194
1195         }
1196         catch(exception& e) {
1197                 m->errorOut(e, "Tree", "printBranch");
1198                 exit(1);
1199         }
1200 }
1201 /*****************************************************************/
1202
1203 void Tree::printTree() {
1204
1205         for(int i=0;i<numNodes;i++){
1206                 cout << i << '\t';
1207                 tree[i].printNode();
1208         }
1209
1210 }
1211
1212 /*****************************************************************/
1213 //this code is a mess and should be rethought...-slw
1214 void Tree::parseTreeFile() {
1215
1216         //only takes names from the first tree and assumes that all trees use the same names.
1217         try {
1218                 string filename = m->getTreeFile();
1219                 ifstream filehandle;
1220                 m->openInputFile(filename, filehandle);
1221                 int c, comment;
1222                 comment = 0;
1223                 int done = 1;
1224
1225                 //ifyou are not a nexus file
1226                 if((c = filehandle.peek()) != '#') {
1227                         while((c = filehandle.peek()) != ';') {
1228                                 while ((c = filehandle.peek()) != ';') {
1229                                         // get past comments
1230                                         if(c == '[') {
1231                                                 comment = 1;
1232                                         }
1233                                         if(c == ']'){
1234                                                 comment = 0;
1235                                         }
1236                                         if((c == '(') && (comment != 1)){ break; }
1237                                         filehandle.get();
1238                                 }
1239
1240                                 done = readTreeString(filehandle);
1241                                 if (done == 0) { break; }
1242                         }
1243                 //ifyou are a nexus file
1244                 }else if((c = filehandle.peek()) == '#') {
1245                         string holder = "";
1246
1247                         // get past comments
1248                         while(holder != "translate" && holder != "Translate"){
1249                                 if(holder == "[" || holder == "[!"){
1250                                         comment = 1;
1251                                 }
1252                                 if(holder == "]"){
1253                                         comment = 0;
1254                                 }
1255                                 filehandle >> holder;
1256
1257                                 //if there is no translate then you must read tree string otherwise use translate to get names
1258                                 if((holder == "tree") && (comment != 1)){
1259                                         //pass over the "tree rep.6878900 = "
1260                                         while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
1261
1262                                         if(c == EOF) { break; }
1263                                         filehandle.putback(c);  //put back first ( of tree.
1264                                         done = readTreeString(filehandle);
1265
1266                                         break;
1267                                 }
1268
1269                                 if (done == 0) { break;  }
1270                         }
1271
1272                         //use nexus translation rather than parsing tree to save time
1273                         if((holder == "translate") || (holder == "Translate")) {
1274
1275                                 string number, name, h;
1276                                 h = ""; // so it enters the loop the first time
1277                                 while((h != ";") && (number != ";")) {
1278                                         filehandle >> number;
1279                                         filehandle >> name;
1280
1281                                         //c = , until done with translation then c = ;
1282                                         h = name.substr(name.length()-1, name.length());
1283                                         name.erase(name.end()-1);  //erase the comma
1284                                         m->Treenames.push_back(number);
1285                                 }
1286                                 if(number == ";") { m->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
1287                         }
1288                 }
1289                 filehandle.close();
1290
1291                 //for (int i = 0; i < globaldata->Treenames.size(); i++) {
1292 //cout << globaldata->Treenames[i] << endl; }
1293 //cout << globaldata->Treenames.size() << endl;
1294         }
1295         catch(exception& e) {
1296                 m->errorOut(e, "Tree", "parseTreeFile");
1297                 exit(1);
1298         }
1299 }
1300 /*******************************************************/
1301
1302 /*******************************************************/
1303 int Tree::readTreeString(ifstream& filehandle)  {
1304         try {
1305                 int c;
1306                 string name;  //, k
1307
1308                 while((c = filehandle.peek()) != ';') {
1309 //k = c;
1310 //cout << " at beginning of while " <<  k << endl;
1311                         if(c == ')')  {
1312                                 //to pass over labels in trees
1313                                 c=filehandle.get();
1314                                 while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
1315                                 filehandle.putback(c);
1316                         }
1317                         if(c == ';') { return 0; }
1318                         if(c == -1) { return 0; }
1319                         //if you are a name
1320                         if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
1321                                 name = "";
1322                                 c = filehandle.get();
1323                         //k = c;
1324 //cout << k << endl;
1325                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
1326                                         name += c;
1327                                         c = filehandle.get();
1328                         //k = c;
1329 //cout << " in name while " << k << endl;
1330                                 }
1331
1332 //cout << "name = " << name << endl;
1333                                 m->Treenames.push_back(name);
1334                                 filehandle.putback(c);
1335 //k = c;
1336 //cout << " after putback" <<  k << endl;
1337                         }
1338
1339                         if(c  == ':') { //read until you reach the end of the branch length
1340                                 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
1341                                         c = filehandle.get();
1342         //k = c;
1343         //cout << " in branch while " << k << endl;
1344                                 }
1345                                 filehandle.putback(c);
1346                         }
1347
1348                         c = filehandle.get();
1349 //k = c;
1350         //cout << " here after get " << k << endl;
1351                         if(c == ';') { return 0; }
1352                         if(c == ')') { filehandle.putback(c); }
1353         //k = c;
1354 //cout << k << endl;
1355
1356                 }
1357                 return 0;
1358         }
1359         catch(exception& e) {
1360                 m->errorOut(e, "Tree", "readTreeString");
1361                 exit(1);
1362         }
1363 }
1364
1365 /*******************************************************/
1366
1367 /*******************************************************/
1368