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