/*****************************************************************/
Tree::Tree() {
try {
+
globaldata = GlobalData::getInstance();
-
numLeaves = globaldata->gTreemap->getNumSeqs();
numNodes = 2*numLeaves - 1;
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
-
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
//the node knows its index
tree[i].setIndex(i);
+ //set pcount and pGroup for groupname to 1.
+ tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+ tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
//Treemap knows name, group and index to speed up search
globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
exit(1);
}
}
+/*****************************************************************/
+void Tree::assembleTree() {
+ try {
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::getCopy(Tree* copy) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //copy name
+ tree[i].setName(copy->tree[i].getName());
+
+ //copy group
+ tree[i].setGroup(copy->tree[i].getGroup());
+
+ //copy branch length
+ tree[i].setBranchLength(copy->tree[i].getBranchLength());
+
+ //copy parent
+ tree[i].setParent(copy->tree[i].getParent());
+
+ //copy children
+ tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+
+ //copy index in node and tmap
+ tree[i].setIndex(copy->tree[i].getIndex());
+ setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
+
+ //copy pGroups
+ tree[i].pGroups = copy->tree[i].pGroups;
+
+ //copy pcount
+ tree[i].pcount = copy->tree[i].pcount;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeGroups(int i) {
+ try {
+
+ int lc = tree[i].getLChild();
+ int rc = tree[i].getRChild();
+
+ //set parsimony groups to left child
+ map<string,int> parsimony = tree[lc].pGroups;
+
+ int maxPars = 1;
+
+ //look at right child groups and update maxPars if right child has something higher for that group.
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+ parsimony[it->first]++;
+
+ if(parsimony[it->first] > maxPars){
+ maxPars = parsimony[it->first];
+ }
+ }
+
+ // this is true if right child had a greater parsimony for a certain group
+ if(maxPars > 1){
+ //erase all the groups that are only 1 because you found something with 2.
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ if(it->second == 1){
+ parsimony.erase(it->first);
+ it--;
+ }
+ }
+ //set one remaining groups to 1
+ //so with our above example p[white] = 2 would be left and it would become p[white] = 1
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ parsimony[it->first] = 1;
+ }
+
+ }
+
+ return parsimony;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+map<string,int> Tree::mergeGcounts(int position) {
+ try{
+ map<string,int>::iterator pos;
+
+ int lc = tree[position].getLChild();
+ int rc = tree[position].getRChild();
+
+ map<string,int> sum = tree[lc].pcount;
+
+ for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
+ sum[it->first] += it->second;
+ }
+ return sum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void Tree::randomLabels() {
+ try {
+ for(int i=numLeaves-1;i>=0;i--){
+ if(tree[i].pGroups.size() == 0){
+ continue;
+ }
+
+ int escape = 1;
+ int z;
+
+ while(escape == 1){
+ z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ if(tree[z].pGroups.size() != 0){
+ escape = 0;
+ }
+ }
+
+
+ map<string,int> lib_hold = tree[z].pGroups;
+ tree[z].pGroups = (tree[i].pGroups);
+ tree[i].pGroups = (lib_hold);
+
+ tree[z].setGroup(tree[z].pGroups.begin()->first);
+ tree[i].setGroup(tree[i].pGroups.begin()->first);
+
+ map<string,int> gcount_hold = tree[z].pcount;
+ tree[z].pcount = (tree[i].pcount);
+ tree[i].pcount = (gcount_hold);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void Tree::randomBlengths() {
+ try {
+ for(int i=numNodes-1;i>=0;i--){
+ int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ float bl_hold = tree[z].getBranchLength();
+ tree[z].setBranchLength(tree[i].getBranchLength());
+ tree[i].setBranchLength(bl_hold);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree() {
+ randomLabels();
+ assembleTree();
+}
+
+/*************************************************************************************************/
+//for now it's just random topology but may become random labels as well later that why this is such a simple function now...
+void Tree::assembleRandomTree() {
+ randomTopology();
+ assembleTree();
+}
+/**************************************************************************************************/
+
+void Tree::randomTopology() {
+ try {
+ for(int i=0;i<numNodes;i++){
+ tree[i].setParent(-1);
+ }
+ for(int i=numLeaves;i<numNodes;i++){
+ tree[i].setChildren(-1, -1);
+ }
+
+ for(int i=numLeaves;i<numNodes;i++){
+ int escape =0;
+ int rnd_index1, rnd_index2;
+ while(escape == 0){
+ rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(tree[rnd_index1].getParent() == -1){escape = 1;}
+ }
+
+ escape = 0;
+ while(escape == 0){
+ rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
+ escape = 1;
+ }
+ }
+
+ tree[i].setChildren(rnd_index1,rnd_index2);
+ tree[i].setParent(-1);
+ tree[rnd_index1].setParent(i);
+ tree[rnd_index2].setParent(i);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/*****************************************************************/
// This prints out the tree in Newick form.
projects / mothur.git / blobdiff