Tree::Tree() {
try {
globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
+ if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; }
+//for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; }
numLeaves = globaldata->Treenames.size();
numNodes = 2*numLeaves - 1;
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->Treenames[i]);
- tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+ vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+ tree[i].setGroup(tempGroups);
//set pcount and pGroup for groupname to 1.
tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
- tree[i].setGroup("");
+ vector<string> tempGroups;
+ tree[i].setGroup(tempGroups);
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "Tree");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
Tree::~Tree() {}
/*****************************************************************/
+void Tree::addNamesToCounts() {
+ try {
+ //ex. seq1 seq2,seq3,se4
+ // seq1 = pasture
+ // seq2 = forest
+ // seq4 = pasture
+ // seq3 = ocean
+
+ //before this function seq1.pcount = pasture -> 1
+ //after seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
+
+ //before this function seq1.pgroups = pasture -> 1
+ //after seq1.pgroups = pasture -> 1 since that is the dominant group
+
+
+ //go through each leaf and update its pcounts and pgroups
+ for (int i = 0; i < numLeaves; i++) {
+
+ string name = tree[i].getName();
+
+ map<string, string>::iterator itNames = globaldata->names.find(name);
+
+ if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else {
+ vector<string> dupNames;
+ splitAtComma(globaldata->names[name], dupNames);
+
+ map<string, int>::iterator itCounts;
+ int maxPars = 1;
+ for (int j = 0; j < dupNames.size(); j++) {
+
+ if (dupNames[j] != name) {//you already added yourself in the constructor
+ string group = globaldata->gTreemap->getGroup(dupNames[j]);
+
+ //update pcounts
+ itCounts = tree[i].pcount.find(group);
+ if (itCounts == tree[i].pcount.end()) { //new group, add it
+ tree[i].pcount[group] = 1;
+ }else {
+ tree[i].pcount[group]++;
+ }
+
+ //update pgroups
+ itCounts = tree[i].pGroups.find(group);
+ if (itCounts == tree[i].pGroups.end()) { //new group, add it
+ tree[i].pGroups[group] = 1;
+ }else {
+ tree[i].pGroups[group]++;
+ }
+
+ //keep highest group
+ if(tree[i].pGroups[group] > maxPars){
+ maxPars = tree[i].pGroups[group];
+ }
+ }//end if
+ }//end for
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //update groups to reflect all the groups this node represents
+ vector<string> nodeGroups;
+ map<string, int>::iterator itGroups;
+ for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+ nodeGroups.push_back(itGroups->first);
+ }
+ tree[i].setGroup(nodeGroups);
+
+ }//end else
+ }//end for
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "addNamesToCounts");
+ exit(1);
+ }
+}
+/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
//Treemap knows name, group and index to speed up search
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "getIndex");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
globaldata->gTreemap->setIndex(searchName, index);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "setIndex");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
-void Tree::assembleTree() {
+int Tree::assembleTree() {
try {
+
+ //if user has given a names file we want to include that info in the pgroups and pcount info.
+ if(globaldata->names.size() != 0) { addNamesToCounts(); }
+
//build the pGroups in non leaf nodes to be used in the parsimony calcs.
for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
tree[i].pGroups = (mergeGroups(i));
tree[i].pcount = (mergeGcounts(i));
}
+
+ return 0;
}
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";
+ m->errorOut(e, "Tree", "assembleTree");
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) {
//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";
+ m->errorOut(e, "Tree", "getCopy");
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
// 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++){
+ for(it=parsimony.begin();it!=parsimony.end();){
if(it->second == 1){
- parsimony.erase(it->first);
-// it--;
- }
+ parsimony.erase(it++);
+ }else { 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
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";
+ m->errorOut(e, "Tree", "mergeGroups");
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);
- }
}
/*****************************************************************/
//returns a map with a groupname and the number of times that group was seen in the children
int rc = tree[i].getRChild();
//loop through nodes groups removing the ones the user doesn't want
- for (it = tree[lc].pGroups.begin(); it != tree[lc].pGroups.end(); it++) {
- if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); }
+ for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
+ if (inUsersGroups(it->first, g) != true) {
+ tree[lc].pGroups.erase(it++);
+ }else { it++; }
}
-
+
//loop through nodes groups removing the ones the user doesn't want
- for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) {
- if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
+ if (inUsersGroups(it->first, g) != true) {
+ tree[rc].pGroups.erase(it++);
+ }else { it++; }
}
//set parsimony groups to left child
// 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++){
+ for(it=parsimony.begin();it!=parsimony.end();){
if(it->second == 1){
- parsimony.erase(it->first);
- }
+ parsimony.erase(it++);
+ }else { it++; }
}
+
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";
+ m->errorOut(e, "Tree", "mergeUserGroups");
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);
- }
}
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";
+ m->errorOut(e, "Tree", "mergeGcounts");
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);
- }
}
/**************************************************************************************************/
tree[z].pGroups = (tree[i].pGroups);
tree[i].pGroups = (lib_hold);
- string zgroup = tree[z].getGroup();
+ vector<string> zgroup = tree[z].getGroup();
tree[z].setGroup(tree[i].getGroup());
tree[i].setGroup(zgroup);
}
}
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";
+ m->errorOut(e, "Tree", "randomLabels");
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::randomLabels(string groupA, string groupB) {
try {
}
}
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";
+ m->errorOut(e, "Tree", "randomLabels");
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() {
}
}
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";
+ m->errorOut(e, "Tree", "randomBlengths");
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(vector<string> g) {
}
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
- randomLabels(groupA, groupB);
+
+ vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+ randomLabels(temp);
assembleTree();
}
escape = 1;
}
}
-
+
tree[i].setChildren(rnd_index1,rnd_index2);
tree[i].setParent(-1);
tree[rnd_index1].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";
+ m->errorOut(e, "Tree", "randomTopology");
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);
- }
}
/*****************************************************************/
void Tree::print(ostream& out) {
try {
int root = findRoot();
- printBranch(root, out);
+ 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";
+ m->errorOut(e, "Tree", "print");
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";
+}
+/*****************************************************************/
+void Tree::printForBoot(ostream& out) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, "boot");
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "printForBoot");
exit(1);
- }
+ }
}
+
/*****************************************************************/
// This prints out the tree in Newick form.
void Tree::createNewickFile(string f) {
int root = findRoot();
//filename = getRootName(globaldata->getTreeFile()) + "newick";
filename = f;
+
openOutputFile(filename, out);
- printBranch(root, out);
+ printBranch(root, out, "branch");
// you are at the end of the tree
out << ";" << endl;
out.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "createNewickFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
try {
for (int i = 0; i < numNodes; i++) {
//you found the root
- if (tree[i].getParent() == -1) { return i; }
+ if (tree[i].getParent() == -1) { return i; }
+ //cout << "i = " << i << endl;
+ //cout << "i's parent = " << tree[i].getParent() << endl;
}
return -1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "findRoot");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
-void Tree::printBranch(int node, ostream& out) {
+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(), out);
+ printBranch(tree[node].getLChild(), out, mode);
out << ",";
- printBranch(tree[node].getRChild(), out);
+ printBranch(tree[node].getRChild(), out, mode);
out << ")";
- //if there is a branch length then print it
- if (tree[node].getBranchLength() != -1) {
- out << ":" << tree[node].getBranchLength();
+ 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();
- //if there is a branch length then print it
- if (tree[node].getBranchLength() != -1) {
- out << ":" << tree[node].getBranchLength();
+ string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+
+ out << leafGroup;
+ 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();
+ }
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Tree", "printBranch");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/*****************************************************************/
}
/*****************************************************************/
+//this code is a mess and should be rethought...-slw
+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;
+ int done = 1;
+
+ //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();
+ }
+
+ done = readTreeString(filehandle);
+ if (done == 0) { break; }
+ }
+ //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;
+
+ //if there 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.
+ done = readTreeString(filehandle);
+
+ break;
+ }
+
+ if (done == 0) { 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
+ }
+ }
+ filehandle.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "parseTreeFile");
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+int Tree::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //, k
+
+ while((c = filehandle.peek()) != ';') {
+//k = c;
+//cout << " at beginning of while " << k << endl;
+ if(c == ')') {
+ //to pass over labels in trees
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
+ }
+ if(c == ';') { return 0; }
+ if(c == -1) { return 0; }
+ //if you 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();
+//k = c;
+ //cout << " here after get " << k << endl;
+ if(c == ';') { return 0; }
+ if(c == ')') { filehandle.putback(c); }
+ //k = c;
+//cout << k << endl;
+
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "readTreeString");
+ exit(1);
+ }
+}
+
+/*******************************************************/
+/*******************************************************/
projects / mothur.git / blobdiff