try {
globaldata = GlobalData::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;
}
}
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";
+ 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);
- }
}
/*****************************************************************/
}
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";
+ 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";
+ 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() {
}
}
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";
+ 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) {
}
}
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";
+ 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";
+ 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";
+ 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";
+ 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);
- }
}
/**************************************************************************************************/
}
}
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";
+ 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);
- }
}
/**************************************************************************************************/
}
}
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";
+ 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";
+ 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) {
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";
+ 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) {
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";
+ 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";
- exit(1);
- }
}
/*****************************************************************/
void Tree::printForBoot(ostream& out) {
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";
+ errorOut(e, "Tree", "printForBoot");
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);
- }
}
/*****************************************************************/
int root = findRoot();
//filename = getRootName(globaldata->getTreeFile()) + "newick";
filename = f;
+
openOutputFile(filename, out);
printBranch(root, out, "branch");
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";
+ 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);
- }
}
/*****************************************************************/
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";
+ 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);
- }
}
/*****************************************************************/
}
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";
+ 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) {
+ 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) {
+ errorOut(e, "Tree", "readTreeString");
+ exit(1);
+ }
+}
+
+/*******************************************************/
+/*******************************************************/
projects / mothur.git / blobdiff