return output.str();
}
/***********************************************************************/
-
inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
fileHandle.open(fileName.c_str(), ios::app);
if(!fileHandle) {
- cout << "Error: Could not open " << fileName << endl;
+ cout << "Error: Could not open " << fileName << endl;
return 1;
}
else {
}
}
-/**************************************************************************************************/
-
-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 mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
- mothurOutEndLine();
-
-}
-
/***********************************************************************/
inline bool isTrue(string f){
ifstream fileHandle;
fileHandle.open(fileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ cout << "Error: Could not open " << fileName << endl;
return false;
}else {
//check for blank file
inline string getFullPathName(string fileName){
try{
+
string path = hasPath(fileName);
string newFileName;
int pos;
}else if (path[(pos-1)] == '/') { //you want the current working dir ./
path = path.substr(0, pos);
}else if (pos == 1) { break;
- }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
}
for (int i = index; i >= 0; i--) {
}else if (path[(pos-1)] == '\\') { //you want the current working dir ./
path = path.substr(0, pos);
}else if (pos == 1) { break;
- }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
}
for (int i = index; i >= 0; i--) {
}
}
catch(exception& e) {
- errorOut(e, "getFullPathName", "getFullPathName");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function getFullPathName. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
-
-
+ }
}
/***********************************************************************/
/***********************************************************************/
inline int openInputFile(string fileName, ifstream& fileHandle){
+
//get full path name
string completeFileName = getFullPathName(fileName);
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
+ cout << "Error: Could not open " << completeFileName << endl;
return 1;
}
else {
//check for blank file
gobble(fileHandle);
- if (fileHandle.eof()) { mothurOut(completeFileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
+ if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; return 1; }
return 0;
}
/***********************************************************************/
inline int openOutputFile(string fileName, ofstream& fileHandle){
-
+
string completeFileName = getFullPathName(fileName);
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
- mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
+ cout << "Error: Could not open " << completeFileName << endl;
return 1;
}
else {
container.push_back(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
container.insert(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
//This function parses the line options and puts them in a set
container.insert(lineNum);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
//This function parses the a string and puts peices in a vector
container.push_back(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
}
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtEquals");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtEquals. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
return false;
}
catch(exception& e) {
- errorOut(e, "mothur", "inUsersGroups");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
-
/**************************************************************************************************/
-
-inline void mothurOutJustToLog(string message) {
+//returns true if any of the strings in first vector are in second vector
+inline bool inUsersGroups(vector<string> groupnames, vector<string> Groups) {
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();
+ for (int i = 0; i < groupnames.size(); i++) {
+ if (inUsersGroups(groupnames[i], Groups)) { return true; }
+ }
+ return false;
}
catch(exception& e) {
- cout << "Error in mothur class mothurOut double" << endl;
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
-
/***********************************************************************/
//this function determines if the user has given us labels that are smaller than the given label.
//if so then it returns true so that the calling function can run the previous valid distance.
//it's a "smart" distance function. It also checks for invalid labels.
inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
try {
+
set<string>::iterator it;
vector<float> orderFloat;
map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
orderFloat.push_back(-1.0);
userMap["unique"] = -1.0;
}else {
- if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
+ if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
userLabels.erase(*it);
it--;
}
if (orderFloat[i] < labelFloat) {
smaller = true;
if (orderFloat[i] == -1) {
- if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
+ if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
userLabels.erase("unique");
}
else {
- if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
+ if (errorOff == "") { cout << "Your file does not include the label " << endl; }
string s = "";
for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
if (it2->second == orderFloat[i]) {
break;
}
}
- if (errorOff == "") { mothurOut(s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
+ if (errorOff == "") {cout << s << ". I will use the next smallest distance. " << endl; }
}
//since they are sorted once you find a bigger one stop looking
}else { break; }
}
catch(exception& e) {
- errorOut(e, "mothur", "anyLabelsToProcess");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function anyLabelsToProcess. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
output.close();
}
catch(exception& e) {
- errorOut(e, "mothur", "appendFiles");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function appendFiles. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
return outfile;
}
catch(exception& e) {
- errorOut(e, "mothur", "sortFile");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function sortfile. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff