5 * Created by Sarah Westcott on 1/22/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 /*****************************************************************/
17 globaldata = GlobalData::getInstance();
18 numLeaves = globaldata->gTreemap->getNumSeqs();
19 numNodes = 2*numLeaves - 1;
21 tree.resize(numNodes);
23 //initialize tree with correct number of nodes, name and group info.
24 for (int i = 0; i < numNodes; i++) {
25 //initialize leaf nodes
26 if (i <= (numLeaves-1)) {
27 tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
28 tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
29 //the node knows its index
31 //set pcount and pGroup for groupname to 1.
32 tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
33 tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
34 //Treemap knows name, group and index to speed up search
35 globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
37 //intialize non leaf nodes
38 }else if (i > (numLeaves-1)) {
41 //the node knows its index
47 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
51 cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
56 /*****************************************************************/
58 int Tree::getIndex(string searchName) {
60 //Treemap knows name, group and index to speed up search
61 // getIndex function will return the vector index or -1 if seq is not found.
62 int index = globaldata->gTreemap->getIndex(searchName);
67 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
71 cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
75 /*****************************************************************/
77 void Tree::setIndex(string searchName, int index) {
79 //set index in treemap
80 globaldata->gTreemap->setIndex(searchName, index);
83 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
87 cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
91 /*****************************************************************/
92 void Tree::assembleTree() {
94 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
95 for (int i = numLeaves; i < numNodes; i++) {
96 tree[i].pGroups = (mergeGroups(i));
97 tree[i].pcount = (mergeGcounts(i));
100 catch(exception& e) {
101 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
105 cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
109 /*****************************************************************/
110 void Tree::getCopy(Tree* copy) {
113 //for each node in the tree copy its info
114 for (int i = 0; i < numNodes; i++) {
116 tree[i].setName(copy->tree[i].getName());
119 tree[i].setGroup(copy->tree[i].getGroup());
122 tree[i].setBranchLength(copy->tree[i].getBranchLength());
125 tree[i].setParent(copy->tree[i].getParent());
128 tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
130 //copy index in node and tmap
131 tree[i].setIndex(copy->tree[i].getIndex());
132 setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
135 tree[i].pGroups = copy->tree[i].pGroups;
138 tree[i].pcount = copy->tree[i].pcount;
141 catch(exception& e) {
142 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
146 cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
150 /*****************************************************************/
151 //returns a map with a groupname and the number of times that group was seen in the children
152 //for instance if your children are white and black then it would return a map with 2 entries
153 // p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
154 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
156 map<string, int> Tree::mergeGroups(int i) {
158 int lc = tree[i].getLChild();
159 int rc = tree[i].getRChild();
161 //set parsimony groups to left child
162 map<string,int> parsimony = tree[lc].pGroups;
166 //look at right child groups and update maxPars if right child has something higher for that group.
167 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
168 it2 = parsimony.find(it->first);
169 if (it2 != parsimony.end()) {
170 parsimony[it->first]++;
172 parsimony[it->first] = 1;
175 if(parsimony[it->first] > maxPars){
176 maxPars = parsimony[it->first];
180 // this is true if right child had a greater parsimony for a certain group
182 //erase all the groups that are only 1 because you found something with 2.
183 for(it=parsimony.begin();it!=parsimony.end();it++){
185 parsimony.erase(it->first);
189 //set one remaining groups to 1
190 //so with our above example p[white] = 2 would be left and it would become p[white] = 1
191 for(it=parsimony.begin();it!=parsimony.end();it++){
192 parsimony[it->first] = 1;
199 catch(exception& e) {
200 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
204 cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
208 /*****************************************************************/
209 //returns a map with a groupname and the number of times that group was seen in the children
210 //for instance if your children are white and black then it would return a map with 2 entries
211 // p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
212 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
214 map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
217 int lc = tree[i].getLChild();
218 int rc = tree[i].getRChild();
220 //loop through nodes groups removing the ones the user doesn't want
221 for (it = tree[lc].pGroups.begin(); it != tree[lc].pGroups.end(); it++) {
222 if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); }
225 //loop through nodes groups removing the ones the user doesn't want
226 for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) {
227 if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
230 //set parsimony groups to left child
231 map<string,int> parsimony = tree[lc].pGroups;
235 //look at right child groups and update maxPars if right child has something higher for that group.
236 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
237 it2 = parsimony.find(it->first);
238 if (it2 != parsimony.end()) {
239 parsimony[it->first]++;
241 parsimony[it->first] = 1;
244 if(parsimony[it->first] > maxPars){
245 maxPars = parsimony[it->first];
249 // this is true if right child had a greater parsimony for a certain group
251 //erase all the groups that are only 1 because you found something with 2.
252 for(it=parsimony.begin();it!=parsimony.end();it++){
254 parsimony.erase(it->first);
258 //set one remaining groups to 1
259 //so with our above example p[white] = 2 would be left and it would become p[white] = 1
260 for(it=parsimony.begin();it!=parsimony.end();it++){
261 parsimony[it->first] = 1;
268 catch(exception& e) {
269 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
273 cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
279 /**************************************************************************************************/
281 map<string,int> Tree::mergeGcounts(int position) {
283 map<string,int>::iterator pos;
285 int lc = tree[position].getLChild();
286 int rc = tree[position].getRChild();
288 map<string,int> sum = tree[lc].pcount;
290 for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
291 sum[it->first] += it->second;
295 catch(exception& e) {
296 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
300 cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
304 /**************************************************************************************************/
306 void Tree::randomLabels(vector<string> g) {
309 for(int i = 0; i < numLeaves; i++){
311 //get random index to switch with
312 z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
314 //you only want to randomize the nodes that are from a group the user wants analyzed, so
315 //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.
318 treez = inUsersGroups(tree[z].getGroup(), g);
319 treei = inUsersGroups(tree[i].getGroup(), g);
321 if ((treez == true) && (treei == true)) {
322 //switches node i and node z's info.
323 map<string,int> lib_hold = tree[z].pGroups;
324 tree[z].pGroups = (tree[i].pGroups);
325 tree[i].pGroups = (lib_hold);
327 string zgroup = tree[z].getGroup();
328 tree[z].setGroup(tree[i].getGroup());
329 tree[i].setGroup(zgroup);
331 string zname = tree[z].getName();
332 tree[z].setName(tree[i].getName());
333 tree[i].setName(zname);
335 map<string,int> gcount_hold = tree[z].pcount;
336 tree[z].pcount = (tree[i].pcount);
337 tree[i].pcount = (gcount_hold);
341 catch(exception& e) {
342 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
346 cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
350 /**************************************************************************************************/
352 void Tree::randomLabels(string groupA, string groupB) {
354 int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
355 int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
357 vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
358 for(int i=numSeqsA;i<randomGroups.size();i++){
359 randomGroups[i] = groupB;
361 random_shuffle(randomGroups.begin(), randomGroups.end());
363 int randomCounter = 0;
364 for(int i=0;i<numLeaves;i++){
365 if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
366 tree[i].setGroup(randomGroups[randomCounter]);
367 tree[i].pcount.clear();
368 tree[i].pcount[randomGroups[randomCounter]] = 1;
369 tree[i].pGroups.clear();
370 tree[i].pGroups[randomGroups[randomCounter]] = 1;
375 catch(exception& e) {
376 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
380 cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
384 /**************************************************************************************************/
385 void Tree::randomBlengths() {
387 for(int i=numNodes-1;i>=0;i--){
388 int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
390 float bl_hold = tree[z].getBranchLength();
391 tree[z].setBranchLength(tree[i].getBranchLength());
392 tree[i].setBranchLength(bl_hold);
395 catch(exception& e) {
396 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
400 cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
404 /*************************************************************************************************/
405 void Tree::assembleRandomUnifracTree(vector<string> g) {
409 /*************************************************************************************************/
410 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
411 randomLabels(groupA, groupB);
415 /*************************************************************************************************/
416 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
417 void Tree::assembleRandomTree() {
421 /**************************************************************************************************/
423 void Tree::randomTopology() {
425 for(int i=0;i<numNodes;i++){
426 tree[i].setParent(-1);
428 for(int i=numLeaves;i<numNodes;i++){
429 tree[i].setChildren(-1, -1);
432 for(int i=numLeaves;i<numNodes;i++){
434 int rnd_index1, rnd_index2;
436 rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
437 if(tree[rnd_index1].getParent() == -1){escape = 1;}
442 rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
443 if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
448 tree[i].setChildren(rnd_index1,rnd_index2);
449 tree[i].setParent(-1);
450 tree[rnd_index1].setParent(i);
451 tree[rnd_index2].setParent(i);
454 catch(exception& e) {
455 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
459 cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
464 /*****************************************************************/
465 // This prints out the tree in Newick form.
466 void Tree::createNewickFile(string f) {
468 int root = findRoot();
469 //filename = getRootName(globaldata->getTreeFile()) + "newick";
471 openOutputFile(filename, out);
475 // you are at the end of the tree
479 catch(exception& e) {
480 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
484 cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
489 /*****************************************************************/
490 //This function finds the index of the root node.
492 int Tree::findRoot() {
494 for (int i = 0; i < numNodes; i++) {
496 if (tree[i].getParent() == -1) { return i; }
500 catch(exception& e) {
501 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
505 cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
510 /*****************************************************************/
511 void Tree::printBranch(int node) {
514 // you are not a leaf
515 if (tree[node].getLChild() != -1) {
517 printBranch(tree[node].getLChild());
519 printBranch(tree[node].getRChild());
521 }else { //you are a leaf
522 out << tree[node].getGroup() << ":" << tree[node].getBranchLength();
526 catch(exception& e) {
527 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
531 cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
536 /*****************************************************************/
538 void Tree::printTree() {
540 for(int i=0;i<numNodes;i++){
547 /*****************************************************************/