char c;
if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
{
- cout << "'" << s << "' is unable to be converted into an integer.\n";
+ cout << "unable to be converted into an integer.\n" << endl;
return false;
}
return true;
return output.str();
}
+/***********************************************************************/
+
+inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
+
+ fileHandle.open(fileName.c_str(), ios::app);
+ if(!fileHandle) {
+ cerr << "Error: Could not open " << fileName << endl;
+ return 1;
+ }
+ else {
+ return 0;
+ }
+
+}
+
+
+/**************************************************************************************************/
+
+inline void mothurOut(string message) {
+ try{
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ cout << message;
+ out << message;
+
+ out.close();
+ }
+ catch(exception& e) {
+ cout << "Error in mothur class mothurOut" << endl;
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+inline void mothurOut(string message, string precision) {
+ try{
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ cout << precision << message;
+ out << precision << message;
+
+ out.close();
+ }
+ catch(exception& e) {
+ cout << "Error in mothur class mothurOut" << endl;
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+inline void mothurOutEndLine() {
+ try {
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ cout << endl;
+ out << endl;
+
+ out.close();
+ }
+ catch(exception& e) {
+ cout << "error in mothur mothurOutEndLine" << endl;
+ exit(1);
+ }
+}
+
+
+/**************************************************************************************************/
+
+inline void errorOut(exception& e, string object, string function) {
+
+ mothurOut("Error: ");
+ mothurOut(toString(e.what()));
+ mothurOut(" has occurred in the " + object + " class function " + function + "Please contact Pat Schloss at pschloss@microbio.umass.edu, and be sure to include the mothur.logFile with your inquiry.");
+ mothurOutEndLine();
+
+}
+
/***********************************************************************/
}
}
-/***********************************************************************/
-
-inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
-
- fileHandle.open(fileName.c_str(), ios::app);
- if(!fileHandle) {
- cerr << "Error: Could not open " << fileName << endl;
- return 1;
- }
- else {
- return 0;
- }
-
-}
-
/***********************************************************************/
container.push_back(estim);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtDash");
exit(1);
}
-
}
/***********************************************************************/
container.insert(estim);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtDash");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/***********************************************************************/
//This function parses the line options and puts them in a set
container.insert(lineNum);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtDash");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/***********************************************************************/
//This function parses the a string and puts peices in a vector
container.push_back(estim);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtComma");
exit(1);
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtComma");
exit(1);
}
-
}
/***********************************************************************/
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "splitAtEquals");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/
return false;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "inUsersGroups");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/**************************************************************************************************/
+
+inline void mothurOutJustToLog(string message) {
+ try {
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ out << message;
+
+ out.close();
+ }
+ catch(exception& e) {
+ errorOut(e, "mothur", "mothurOutJustToLog");
+ exit(1);
+ }
+}
+
+
+/**************************************************************************************************/
+
+inline void mothurOut(float num) {
+ try {
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ cout << num;
+ out << num;
+
+ out.close();
+ }
+ catch(exception& e) {
+ cout << "Error in mothur class mothurOut float" << endl;
+ exit(1);
+ }
+}
+/***********************************************************************/
+inline void mothurOut(double value) {
+ try {
+ ofstream out;
+ string logFileName = "mothur.logFile";
+ openOutputFileAppend(logFileName, out);
+
+ cout << value;
+ out << value;
+
+ out.close();
+ }
+ catch(exception& e) {
+ cout << "Error in mothur class mothurOut double" << endl;
exit(1);
}
}
orderFloat.push_back(-1.0);
userMap["unique"] = -1.0;
}else {
- if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
+ if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
userLabels.erase(*it);
it--;
}
if (orderFloat[i] < labelFloat) {
smaller = true;
if (orderFloat[i] == -1) {
- if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
+ if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
userLabels.erase("unique");
}
else {
- if (errorOff == "") { cout << "Your file does not include the label "; }
+ if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
string s = "";
for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
if (it2->second == orderFloat[i]) {
break;
}
}
- if (errorOff == "") { cout << s << ". I will use the next smallest distance. " << endl; }
+ if (errorOff == "") { mothurOut(s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
}
//since they are sorted once you find a bigger one stop looking
}else { break; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "mothur", "anyLabelsToProcess");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the mothur class function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/
projects / mothur.git / blobdiff