/*****************************************************************/
Tree::Tree() {
try {
-
globaldata = GlobalData::getInstance();
- numLeaves = globaldata->gTreemap->getNumSeqs();
+
+ numLeaves = globaldata->Treenames.size();
numNodes = 2*numLeaves - 1;
tree.resize(numNodes);
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]));
+ tree[i].setName(globaldata->Treenames[i]);
+ tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[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;
+ tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+ tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
//Treemap knows name, group and index to speed up search
- globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+ globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
}
/*****************************************************************/
-void Tree::resetTree(){
-try {
- numLeaves = globaldata->gTreemap->getNumSeqs();
- numNodes = 2*numLeaves - 1;
-
- tree.resize(numNodes);
-
- //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]));
- //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("");
- tree[i].setGroup("");
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
+Tree::~Tree() {}
/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
try {
int lc = tree[i].getLChild();
int rc = tree[i].getRChild();
-cout << i << lc << rc << endl;
+
//set parsimony groups to left child
map<string,int> parsimony = tree[lc].pGroups;
for(it=parsimony.begin();it!=parsimony.end();it++){
if(it->second == 1){
parsimony.erase(it->first);
- it--;
+// it--;
}
}
//set one remaining groups to 1
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) {
exit(1);
}
}
+/*****************************************************************/
+void Tree::print(ostream& out) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, "branch");
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::printForBoot(ostream& out) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, "boot");
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/*****************************************************************/
// This prints out the tree in Newick form.
filename = f;
openOutputFile(filename, out);
- printBranch(root);
+ printBranch(root, out, "branch");
// you are at the end of the tree
out << ";" << endl;
for (int i = 0; i < numNodes; i++) {
//you found the root
if (tree[i].getParent() == -1) { return i; }
+ //cout << "i = " << i << endl;
+ //cout << "i's parent = " << tree[i].getParent() << endl;
}
return -1;
}
}
/*****************************************************************/
-void Tree::printBranch(int node) {
+void Tree::printBranch(int node, ostream& out, string mode) {
try {
// you are not a leaf
if (tree[node].getLChild() != -1) {
out << "(";
- printBranch(tree[node].getLChild());
+ printBranch(tree[node].getLChild(), out, mode);
out << ",";
- printBranch(tree[node].getRChild());
+ printBranch(tree[node].getRChild(), out, mode);
out << ")";
+ if (mode == "branch") {
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ //if there is a label then print it
+ if (tree[node].getLabel() != -1) {
+ out << tree[node].getLabel();
+ }
+ }
}else { //you are a leaf
- out << tree[node].getGroup() << ":" << tree[node].getBranchLength();
+ out << tree[node].getGroup();
+ if (mode == "branch") {
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ //if there is a label then print it
+ if (tree[node].getLabel() != -1) {
+ out << tree[node].getLabel();
+ }
+ }
}
}