}
}
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
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
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) {
}
}
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);
- }
}
/*****************************************************************/
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);
- }
}
/*****************************************************************/
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) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "Tree", "parseTreeFile");
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
+ string name;// k;
while((c = filehandle.peek()) != ';') {
- //ifyou are a name
+//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 == ';') { break; }
+ //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;
+ //k = c;
//cout << k << endl;
while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
name += c;
c = filehandle.get();
- // k = c;
+ //k = c;
//cout << " in name while " << 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;
+ //k = c;
//cout << " in branch while " << k << endl;
}
filehandle.putback(c);
}
+
c = filehandle.get();
if(c == ';') { break; }
- // k = c;
+ if(c == ')') { filehandle.putback(c); }
+ // 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";
+ errorOut(e, "Tree", "readTreeString");
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);
- }
}
/*******************************************************/