X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=78ccf1105795ec6dd018ae5820c5ceca2110c505;hb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e;hp=8ad1645a57a5345a7f48ca8236d83963d8700afc;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10;p=mothur.git diff --git a/mothur.h b/mothur.h index 8ad1645..78ccf11 100644 --- a/mothur.h +++ b/mothur.h @@ -1,7 +1,6 @@ #ifndef MOTHUR_H #define MOTHUR_H -using namespace std; /* @@ -15,12 +14,14 @@ using namespace std; /* This file contains all the standard incudes we use in the project as well as some common utilities. */ +//#include //io libraries #include #include #include #include +#include //exception #include @@ -40,7 +41,33 @@ using namespace std; #include #include -typedef unsigned long long ull; +//misc +#include +#include +#include +#include +#include + +/***********************************************************************/ + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #include + #include +#else + #include //allows unbuffered screen capture from stdin +#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; @@ -49,8 +76,25 @@ struct IntNode { int rcoef; IntNode* left; IntNode* right; -}; + IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {}; + IntNode() {}; +}; + +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 @@ -70,6 +114,20 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){ if (!(i >> x) || (failIfLeftoverChars && i.get(c))) throw BadConversion(s); } + +//********************************************************************************************************************** + +template +inline bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){ + istringstream i(s); + char c; + if (!(i >> x) || (failIfLeftoverChars && i.get(c))) + { + return false; + } + return true; +} + //********************************************************************************************************************** template @@ -78,7 +136,7 @@ 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; @@ -114,8 +172,20 @@ 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){ @@ -128,6 +198,107 @@ 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); @@ -210,6 +381,7 @@ inline string getSimpleName(string longName){ return simpleName; } + /***********************************************************************/ inline int factorial(int num){ @@ -221,6 +393,13 @@ inline int factorial(int num){ return total; } +/************************************************************************************************** + +double min(double x, double y) +{ + if(x(file),istreambuf_iterator(), '>'); + file.seekg(0); + return numSeqs; + +} +/***********************************************************************/ + +inline bool inVector(string member, vector group){ + + for (int i = 0; i < group.size(); i++) { + if (group[i] == member) { return true; } + } + + return false; +} + +/***********************************************************************/ + //This function parses the estimator options and puts them in a vector inline void splitAtDash(string& estim, vector& container) { try { @@ -284,14 +515,9 @@ 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); - } - } /***********************************************************************/ @@ -311,14 +537,9 @@ 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 @@ -340,14 +561,9 @@ 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 @@ -366,11 +582,7 @@ 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); } } @@ -389,14 +601,9 @@ 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"; + errorOut(e, "mothur", "splitAtComma"); 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"; - exit(1); - } - } /***********************************************************************/ @@ -414,14 +621,9 @@ 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"; + 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); - } - } /**************************************************************************************************/ @@ -433,17 +635,142 @@ 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); + } +} +/***********************************************************************/ +//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 + map::iterator it2; + float labelFloat; + bool smaller = false; + + //unique is the smallest line + if (label == "unique") { return false; } + else { convert(label, labelFloat); } + + //go through users set and make them floats + for(it = userLabels.begin(); it != userLabels.end(); ++it) { + + float temp; + if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){ + convert(*it, temp); + orderFloat.push_back(temp); + userMap[*it] = temp; + }else if (*it == "unique") { + orderFloat.push_back(-1.0); + userMap["unique"] = -1.0; + }else { + if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); } + userLabels.erase(*it); + it--; + } + } + + //sort order + sort(orderFloat.begin(), orderFloat.end()); + + /*************************************************/ + //is this label bigger than any of the users labels + /*************************************************/ + + //loop through order until you find a label greater than label + for (int i = 0; i < orderFloat.size(); i++) { + if (orderFloat[i] < labelFloat) { + smaller = true; + if (orderFloat[i] == -1) { + if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); } + userLabels.erase("unique"); + } + else { + 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]) { + s = it2->first; + //remove small labels + userLabels.erase(s); + break; + } + } + 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; } + } + + return smaller; + + } + catch(exception& e) { + errorOut(e, "mothur", "anyLabelsToProcess"); + exit(1); + } +} + +/**************************************************************************************************/ #endif