X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=c5afe86a79a9e92c789735ea3b1be3d33accf66a;hb=952a85d59a12e664f5efa6d01681be189e4fff9c;hp=f07f343b05d91148c64ebccc79b7d165bf51c8f7;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git diff --git a/mothur.h b/mothur.h index f07f343..c5afe86 100644 --- a/mothur.h +++ b/mothur.h @@ -1,7 +1,6 @@ #ifndef MOTHUR_H #define MOTHUR_H -using namespace std; /* @@ -41,7 +40,28 @@ using namespace std; #include #include -typedef unsigned long long ull; +//misc +#include +#include +#include + + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #include + #include +#endif + +using namespace std; + +#define exp(x) (exp((double) x)) +#define sqrt(x) (sqrt((double) x)) +#define log10(x) (log10((double) x)) +#define log2(x) (log10(x)/log10(2)) +#define isnan(x) ((x) != (x)) +#define isinf(x) (fabs(x) == std::numeric_limits::infinity()) + + +typedef unsigned long ull; struct IntNode { int lvalue; @@ -51,7 +71,13 @@ struct IntNode { IntNode* left; IntNode* right; }; - + +struct ThreadNode { + int* pid; + IntNode* left; + IntNode* right; +}; + /***********************************************************************/ // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2 @@ -71,6 +97,7 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){ if (!(i >> x) || (failIfLeftoverChars && i.get(c))) throw BadConversion(s); } + //********************************************************************************************************************** template @@ -92,7 +119,7 @@ inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){ 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; @@ -128,6 +155,114 @@ 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; + return 1; + } + else { + return 0; + } + +} +/***********************************************************************/ + +inline string getline(ifstream& fileHandle) { + try { + + string line = ""; + + while (!fileHandle.eof()) { + //get next character + char c = fileHandle.get(); + + //are you at the end of the line + if ((c == '\n') || (c == '\r') || (c == '\f')){ break; } + else { line += c; } + } + + return line; + + } + catch(exception& e) { + cout << "Error in mothur function getline" << endl; + exit(1); + } +} + +/**************************************************************************************************/ + +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@umich.edu, and be sure to include the mothur.logFile with your inquiry."); + mothurOutEndLine(); + +} + + /***********************************************************************/ @@ -139,6 +274,13 @@ inline void gobble(istream& f){ f.putback(d); } +/***********************************************************************/ + +inline bool isTrue(string f){ + + if ((f == "TRUE") || (f == "T") || (f == "true") || (f == "t")) { return true; } + else { return false; } +} /***********************************************************************/ @@ -224,6 +366,7 @@ inline string getSimpleName(string longName){ return simpleName; } + /***********************************************************************/ inline int factorial(int num){ @@ -277,7 +420,7 @@ inline int openInputFile(string fileName, ifstream& fileHandle){ fileHandle.open(fileName.c_str()); if(!fileHandle) { - cerr << "Error: Could not open " << fileName << endl; + mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); return 1; } else { @@ -292,21 +435,7 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){ fileHandle.open(fileName.c_str(), ios::trunc); if(!fileHandle) { - cerr << "Error: Could not open " << fileName << endl; - return 1; - } - else { - return 0; - } - -} -/***********************************************************************/ - -inline int openOutputFileAppend(string fileName, ofstream& fileHandle){ - - fileHandle.open(fileName.c_str(), ios::app); - if(!fileHandle) { - cerr << "Error: Could not open " << fileName << endl; + mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); return 1; } else { @@ -315,7 +444,6 @@ inline int openOutputFileAppend(string fileName, ofstream& fileHandle){ } - /***********************************************************************/ inline int getNumSeqs(ifstream& file){ @@ -344,14 +472,9 @@ inline void splitAtDash(string& estim, vector& container) { 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); } - } /***********************************************************************/ @@ -371,14 +494,9 @@ inline void splitAtDash(string& estim, set& container) { 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 @@ -400,14 +518,9 @@ inline void splitAtDash(string& estim, set& container) { 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 @@ -426,11 +539,7 @@ inline void splitAtComma(string& estim, vector& container) { 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); } } @@ -449,14 +558,9 @@ inline void splitAtComma(string& prefix, string& suffix){ } 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); } - } /***********************************************************************/ @@ -474,14 +578,9 @@ inline void splitAtEquals(string& key, string& value){ } } 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"; - 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"; + errorOut(e, "mothur", "splitAtEquals"); exit(1); } - } /**************************************************************************************************/ @@ -493,11 +592,62 @@ inline bool inUsersGroups(string groupname, vector Groups) { 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); } } @@ -531,7 +681,7 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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--; } @@ -549,11 +699,11 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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]) { @@ -563,7 +713,7 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err 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; } @@ -573,14 +723,9 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err } 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"; - 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"; + errorOut(e, "mothur", "anyLabelsToProcess"); exit(1); } - } /**************************************************************************************************/