X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=16a9844b70799c1334e95aabc20c6557688bdaaf;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=fdaa06362db6ecda7054fe4ff9b21442487c19d4;hpb=6777912b79eb6d011163da47f3ada09d1a9293c1;p=mothur.git diff --git a/mothur.h b/mothur.h index fdaa063..16a9844 100644 --- a/mothur.h +++ b/mothur.h @@ -58,8 +58,6 @@ #include #endif - //#include - //#include #else #include //allows unbuffered screen capture from stdin #include //get cwd @@ -193,12 +191,11 @@ string toString(const T&x, int i){ 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 { @@ -240,74 +237,6 @@ inline string getline(ifstream& fileHandle) { } } -/**************************************************************************************************/ - -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){ @@ -475,7 +404,7 @@ inline bool isBlank(string fileName){ 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 @@ -487,6 +416,7 @@ inline bool isBlank(string fileName){ /***********************************************************************/ inline string getFullPathName(string fileName){ + try{ string path = hasPath(fileName); string newFileName; @@ -503,11 +433,13 @@ inline string getFullPathName(string fileName){ if (path.rfind("./") == -1) { return fileName; } //already complete name else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name - char* cwdpath; + char* cwdpath = new char[1024]; + size_t size; cwdpath=getcwd(cwdpath,size); - cwd = cwdpath; + cwd = cwdpath; + //rip off first '/' string simpleCWD; if (cwd.length() > 0) { simpleCWD = cwd.substr(1); } @@ -521,9 +453,10 @@ inline string getFullPathName(string fileName){ } //get last one // ex. ../../../filename = /user/work/desktop/filename dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop - + + int index = dirs.size()-1; - + while((pos = path.rfind("./")) != -1) { //while you don't have a complete path if (path[(pos-1)] == '.') { //you want your parent directory ../ path = path.substr(0, pos-1); @@ -532,7 +465,7 @@ inline string getFullPathName(string fileName){ }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--) { @@ -572,7 +505,7 @@ inline string getFullPathName(string fileName){ }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--) { @@ -583,7 +516,11 @@ inline string getFullPathName(string fileName){ #endif } - + } + catch(exception& e) { + 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); + } } /***********************************************************************/ @@ -604,18 +541,19 @@ inline int openInputFile(string fileName, ifstream& fileHandle, string m){ /***********************************************************************/ 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; } @@ -639,7 +577,7 @@ inline int renameFile(string oldName, string newName){ system(command.c_str()); #else remove(newName.c_str()); - renameOk = rename(oldName.c_str(), newName.c_str()); + int renameOk = rename(oldName.c_str(), newName.c_str()); #endif return 0; } @@ -647,12 +585,12 @@ inline int renameFile(string oldName, string newName){ /***********************************************************************/ 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 { @@ -698,9 +636,9 @@ inline void splitAtDash(string& estim, vector& container) { 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); - } + } } /***********************************************************************/ @@ -720,9 +658,9 @@ inline void splitAtDash(string& estim, set& container) { 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 @@ -744,9 +682,9 @@ inline void splitAtDash(string& estim, set& container) { 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 @@ -765,9 +703,9 @@ inline void splitAtComma(string& estim, vector& container) { 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); - } + } } /***********************************************************************/ @@ -784,9 +722,9 @@ inline void splitAtComma(string& prefix, string& suffix){ } 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); - } + } } /***********************************************************************/ @@ -804,9 +742,9 @@ inline void splitAtEquals(string& key, string& value){ } } 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); - } + } } /**************************************************************************************************/ @@ -818,72 +756,32 @@ inline bool inUsersGroups(string groupname, vector Groups) { return false; } catch(exception& e) { - errorOut(e, "mothur", "inUsersGroups"); - exit(1); - } -} - -/**************************************************************************************************/ - -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"); + 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 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) { +//returns true if any of the strings in first vector are in second vector +inline bool inUsersGroups(vector groupnames, vector Groups) { 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& userLabels, string errorOff) { try { + set::iterator it; vector orderFloat; map userMap; //the conversion process removes trailing 0's which we need to put back @@ -907,7 +805,7 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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--; } @@ -925,11 +823,11 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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]) { @@ -939,7 +837,7 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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; } @@ -949,9 +847,9 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err } 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); - } + } } /**************************************************************************************************/ @@ -973,9 +871,9 @@ inline void appendFiles(string temp, string filename) { 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); - } + } } /**************************************************************************************************/ @@ -1036,9 +934,9 @@ inline string sortFile(string distFile){ 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