/*****************************************************************/
Tree::Tree() {
try {
-
globaldata = GlobalData::getInstance();
- numLeaves = globaldata->gTreemap->getNumSeqs();
+
+ if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; }
+
+ 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)) {
}
}
+/*****************************************************************/
+Tree::~Tree() {}
/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
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.
int root = findRoot();
//filename = getRootName(globaldata->getTreeFile()) + "newick";
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();
+ }
+ }
}
}
/*****************************************************************/
+void Tree::parseTreeFile() {
+
+ //only takes names from the first tree and assumes that all trees use the same names.
+ try {
+ string filename = globaldata->getTreeFile();
+ ifstream filehandle;
+ openInputFile(filename, filehandle);
+ int c, comment;
+ comment = 0;
+
+ //ifyou are not a nexus file
+ if((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != ';') {
+ while ((c = filehandle.peek()) != ';') {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ readTreeString(filehandle);
+ }
+ //ifyou are a nexus file
+ }else if((c = filehandle.peek()) == '#') {
+ string holder = "";
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+
+ //ifthere is no translate then you must read tree string otherwise use translate to get names
+ if(holder == "tree" && comment != 1){
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
+
+ if(c == EOF) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+ readTreeString(filehandle);
+ break;
+ }
+ }
+
+ //use nexus translation rather than parsing tree to save time
+ if((holder == "translate") || (holder == "Translate")) {
+
+ string number, name, h;
+ h = ""; // so it enters the loop the first time
+ while((h != ";") && (number != ";")) {
+ filehandle >> number;
+ filehandle >> name;
+
+ //c = , until done with translation then c = ;
+ h = name.substr(name.length()-1, name.length());
+ name.erase(name.end()-1); //erase the comma
+ globaldata->Treenames.push_back(number);
+ }
+ if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+void Tree::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //k
+
+ while((c = filehandle.peek()) != ';') {
+ //ifyou are a name
+ if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+ name = "";
+ c = filehandle.get();
+ // k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ // k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
+ globaldata->Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
+ }
+
+ if(c == ':') { //read until you reach the end of the branch length
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ // k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
+ }
+ c = filehandle.get();
+ if(c == ';') { break; }
+ // k = c;
+//cout << k << endl;
+
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/*******************************************************/
+
+/*******************************************************/
projects / mothur.git / blobdiff