#ifndef MOTHUR_H
#define MOTHUR_H
-using namespace std;
/*
/* This file contains all the standard incudes we use in the project as well as some common utilities. */
+//#include <cstddef>
//io libraries
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
+#include <signal.h>
//exception
#include <stdexcept>
#include <math.h>
#include <algorithm>
-typedef unsigned long long ull;
+//misc
+#include <cerrno>
+#include <ctime>
+#include <limits>
+#include <readline/readline.h>
+#include <readline/history.h>
+
+/***********************************************************************/
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #include <sys/wait.h>
+ #include <unistd.h>
+#else
+ #include <conio.h> //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<double>::infinity())
+
+
+typedef unsigned long ull;
struct IntNode {
int lvalue;
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
if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
throw BadConversion(s);
}
+
+//**********************************************************************************************************************
+
+template<typename T>
+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<typename T>
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;
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){
/***********************************************************************/
+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);
return simpleName;
}
+
/***********************************************************************/
inline int factorial(int num){
return total;
}
+/**************************************************************************************************
+
+double min(double x, double y)
+{
+ if(x<y){ return x; }
+ else { return y; }
+}
/***********************************************************************/
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);
}
/***********************************************************************/
+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 bool isBlank(string fileName){
+
+ ifstream fileHandle;
+ fileHandle.open(fileName.c_str());
+ if(!fileHandle) {
+ mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ return false;
+ }else {
+ //check for blank file
+ gobble(fileHandle);
+ if (fileHandle.eof()) { fileHandle.close(); return true; }
+ }
+ return false;
+}
+/***********************************************************************/
+
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;
}
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 {
/***********************************************************************/
+inline int getNumSeqs(ifstream& file){
+
+ int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
+ file.seekg(0);
+ return numSeqs;
+
+}
+/***********************************************************************/
+
+inline bool inVector(string member, vector<string> 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<string>& container) {
try {
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);
- }
-
}
/***********************************************************************/
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
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
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);
}
}
}
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);
- }
-
}
/***********************************************************************/
}
}
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);
- }
-
}
/**************************************************************************************************/
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<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
+ map<string, float>::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
projects / mothur.git / blobdiff