X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=23b9f189c992f97e2e9a47823cacce62db363696;hb=f5023c911c377e5320c5110c78af98dd8841ef58;hp=07bb971347d974066ab5449614172c5e68d4c2a6;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git diff --git a/mothur.h b/mothur.h index 07bb971..23b9f18 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 +71,21 @@ struct IntNode { IntNode* left; IntNode* right; }; - + +struct ThreadNode { + int* pid; + IntNode* left; + IntNode* right; +}; + +/************************************************************/ +struct clusterNode { + int numSeq; + int parent; + int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node + clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {}; +}; + /***********************************************************************/ // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2 @@ -71,6 +105,7 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){ if (!(i >> x) || (failIfLeftoverChars && i.get(c))) throw BadConversion(s); } + //********************************************************************************************************************** template @@ -92,7 +127,7 @@ 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; @@ -128,8 +163,20 @@ 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 void gobble(istream& f){ @@ -142,6 +189,110 @@ inline void gobble(istream& f){ /***********************************************************************/ +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 mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry."); + mothurOutEndLine(); + +} + + + + +/***********************************************************************/ + +inline bool isTrue(string f){ + + if ((f == "TRUE") || (f == "T") || (f == "true") || (f == "t")) { return true; } + else { return false; } +} + +/***********************************************************************/ + inline float roundDist(float dist, int precision){ return int(dist * precision + 0.5)/float(precision); @@ -224,6 +375,7 @@ inline string getSimpleName(string longName){ return simpleName; } + /***********************************************************************/ inline int factorial(int num){ @@ -249,7 +401,7 @@ inline string getPathName(string longName){ string rootPathName = longName; - if(longName.find_last_of("/") != longName.npos){ + if(longName.find_last_of('/') != longName.npos){ int pos = longName.find_last_of('/')+1; rootPathName = longName.substr(0, pos); } @@ -259,14 +411,32 @@ inline string getPathName(string longName){ /***********************************************************************/ +inline string getExtension(string longName){ + + string extension = longName; + + if(longName.find_last_of('.') != longName.npos){ + int pos = longName.find_last_of('.'); + extension = longName.substr(pos, longName.length()); + } + + return extension; +} + +/***********************************************************************/ + 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 { + //check for blank file + gobble(fileHandle); + if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; } + return 0; } @@ -278,7 +448,7 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){ fileHandle.open(fileName.c_str(), ios::trunc); if(!fileHandle) { - cerr << "Error: Could not open " << fileName << endl; + mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); return 1; } else { @@ -286,22 +456,17 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){ } } + /***********************************************************************/ -inline int openOutputFileAppend(string fileName, ofstream& fileHandle){ +inline int getNumSeqs(ifstream& file){ - fileHandle.open(fileName.c_str(), ios::app); - if(!fileHandle) { - cerr << "Error: Could not open " << fileName << endl; - return 1; - } - else { - return 0; - } + int numSeqs = count(istreambuf_iterator(file),istreambuf_iterator(), '>'); + file.seekg(0); + return numSeqs; } - /***********************************************************************/ //This function parses the estimator options and puts them in a vector @@ -320,14 +485,9 @@ 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"; + 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); - } - } /***********************************************************************/ @@ -347,14 +507,9 @@ 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"; - 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); } - } /***********************************************************************/ //This function parses the line options and puts them in a set @@ -376,14 +531,9 @@ 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"; - 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); } - } /***********************************************************************/ //This function parses the a string and puts peices in a vector @@ -402,11 +552,7 @@ 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); } } @@ -425,14 +571,9 @@ 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); } - } /***********************************************************************/ @@ -450,14 +591,9 @@ 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); } - } /**************************************************************************************************/ @@ -469,11 +605,62 @@ 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); + } +} + +/**************************************************************************************************/ + +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); } - 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 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); } } @@ -507,7 +694,7 @@ 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--; } @@ -525,11 +712,11 @@ 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]) { @@ -539,7 +726,7 @@ 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; } @@ -549,14 +736,9 @@ 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"; + 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); - } - } /**************************************************************************************************/