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