X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=2404a84f08672c2178bd3e0a33946124348a72a7;hb=a8367302932de9be5434e77f6e5829d7609e2aec;hp=8190152b8be3c15ee0a3559b93d846174d6c992d;hpb=e057ab99eca7d45544c83ca6665a042b934b661b;p=mothur.git diff --git a/mothur.h b/mothur.h index 8190152..2404a84 100644 --- a/mothur.h +++ b/mothur.h @@ -47,6 +47,9 @@ #include #include +#ifdef USE_MPI + #include "mpi.h" +#endif /***********************************************************************/ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -58,8 +61,6 @@ #include #endif - //#include - //#include #else #include //allows unbuffered screen capture from stdin #include //get cwd @@ -193,12 +194,11 @@ 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 +240,6 @@ 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){ @@ -322,6 +254,13 @@ inline float roundDist(float dist, int precision){ return int(dist * precision + 0.5)/float(precision); +} +/***********************************************************************/ + +inline float ceilDist(float dist, int precision){ + + return int(ceil(dist * precision))/float(precision); + } /***********************************************************************/ @@ -447,7 +386,7 @@ inline string hasPath(string longName){ string path = ""; size_t found; - found=longName.find_last_of("/\\"); + found=longName.find_last_of("~/\\"); if(found != longName.npos){ path = longName.substr(0, found+1); @@ -475,7 +414,7 @@ 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 @@ -488,6 +427,7 @@ inline bool isBlank(string fileName){ inline string getFullPathName(string fileName){ try{ + string path = hasPath(fileName); string newFileName; int pos; @@ -500,99 +440,111 @@ inline string getFullPathName(string fileName){ string cwd; //get current working directory #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - 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 = new char[1024]; + if (path.find("~") != -1) { //go to home directory + string homeDir = getenv ("HOME"); + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + 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 = new char[1024]; - size_t size; - cwdpath=getcwd(cwdpath,size); - - cwd = cwdpath; - - //rip off first '/' - string simpleCWD; - if (cwd.length() > 0) { simpleCWD = cwd.substr(1); } + size_t size; + cwdpath=getcwd(cwdpath,size); - //break apart the current working directory - vector dirs; - while (simpleCWD.find_first_of('/') != -1) { - string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/')); - simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length()); - dirs.push_back(dir); - } - //get last one // ex. ../../../filename = /user/work/desktop/filename - dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop + cwd = cwdpath; + + //rip off first '/' + string simpleCWD; + if (cwd.length() > 0) { simpleCWD = cwd.substr(1); } + + //break apart the current working directory + vector dirs; + while (simpleCWD.find_first_of('/') != -1) { + string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/')); + simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length()); + dirs.push_back(dir); + } + //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; - 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); - index--; - if (index == 0) { break; } - }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; } - } - - for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "/" + newFileName; - } + while((pos = path.rfind("./")) != -1) { //while you don't have a complete path + if (pos == 0) { break; //you are at the end + }else if (path[(pos-1)] == '.') { //you want your parent directory ../ + path = path.substr(0, pos-1); + index--; + if (index == 0) { break; } + }else if (path[(pos-1)] == '/') { //you want the current working dir ./ + path = path.substr(0, pos); + }else if (pos == 1) { break; //you are at the end + }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + } - newFileName = "/" + newFileName; - return newFileName; + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "/" + newFileName; + } + newFileName = "/" + newFileName; + return newFileName; + } #else - 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 = NULL; - cwdpath = getcwd(NULL, 0); // or _getcwd - if ( cwdpath != NULL) { cwd = cwdpath; } - else { cwd = ""; } - - //break apart the current working directory - vector dirs; - while (cwd.find_first_of('\\') != -1) { - string dir = cwd.substr(0,cwd.find_first_of('\\')); - cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length()); - dirs.push_back(dir); - - } - //get last one - dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop - - int index = dirs.size()-1; + if (path.find("~") != -1) { //go to home directory + string homeDir = getenv ("HOMEPATH"); + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + 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 = NULL; + cwdpath = getcwd(NULL, 0); // or _getcwd + if ( cwdpath != NULL) { cwd = cwdpath; } + else { cwd = ""; } - 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); - index--; - if (index == 0) { break; } - }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; } - } + //break apart the current working directory + vector dirs; + while (cwd.find_first_of('\\') != -1) { + string dir = cwd.substr(0,cwd.find_first_of('\\')); + cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length()); + dirs.push_back(dir); - for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "\\" + newFileName; - } + } + //get last one + dirs.push_back(cwd); //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 (pos == 0) { break; //you are at the end + }else if (path[(pos-1)] == '.') { //you want your parent directory ../ + path = path.substr(0, pos-1); + index--; + if (index == 0) { break; } + }else if (path[(pos-1)] == '\\') { //you want the current working dir ./ + path = path.substr(0, pos); + }else if (pos == 1) { break; //you are at the end + }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + } - return newFileName; + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "\\" + newFileName; + } + + return newFileName; + } #endif } } catch(exception& e) { - errorOut(e, "getFullPathName", "getFullPathName"); + 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); - } - - + } } /***********************************************************************/ @@ -613,18 +565,19 @@ 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 0; } @@ -656,12 +609,12 @@ 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 { @@ -679,6 +632,19 @@ inline int getNumSeqs(ifstream& file){ return numSeqs; } +/***********************************************************************/ +inline void getNumSeqs(ifstream& file, int& numSeqs){ + + string input; + numSeqs = 0; + while(!file.eof()){ + input = getline(file); + if (input.length() != 0) { + if(input[0] == '>'){ numSeqs++; } + } + } +} + /***********************************************************************/ inline bool inVector(string member, vector group){ @@ -707,9 +673,9 @@ 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); - } + } } /***********************************************************************/ @@ -729,9 +695,9 @@ 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 @@ -753,9 +719,9 @@ 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 @@ -774,9 +740,9 @@ 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); - } + } } /***********************************************************************/ @@ -793,9 +759,9 @@ 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); - } + } } /***********************************************************************/ @@ -813,9 +779,9 @@ 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); - } + } } /**************************************************************************************************/ @@ -827,72 +793,32 @@ inline bool inUsersGroups(string groupname, vector Groups) { return false; } catch(exception& e) { - errorOut(e, "mothur", "inUsersGroups"); + 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 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) { +//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 << num; - out << num; - 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 float" << 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); - } + } } -/***********************************************************************/ -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 @@ -902,7 +828,13 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err //unique is the smallest line if (label == "unique") { return false; } - else { convert(label, labelFloat); } + else { + if (convertTestFloat(label, labelFloat)) { + convert(label, labelFloat); + }else { //cant convert + return false; + } + } //go through users set and make them floats for(it = userLabels.begin(); it != userLabels.end(); ++it) { @@ -916,7 +848,7 @@ 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--; } @@ -934,11 +866,11 @@ 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]) { @@ -948,7 +880,7 @@ 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; } @@ -958,9 +890,9 @@ 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); - } + } } /**************************************************************************************************/ @@ -971,26 +903,31 @@ inline void appendFiles(string temp, string filename) { //open output file in append mode openOutputFileAppend(filename, output); - openInputFile(temp, input); + int ableToOpen = openInputFile(temp, input, "no error"); - while(char c = input.get()){ - if(input.eof()) { break; } - else { output << c; } + if (ableToOpen == 0) { //you opened it + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } + input.close(); } - input.close(); 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); - } + } } /**************************************************************************************************/ -inline string sortFile(string distFile){ +inline string sortFile(string distFile, string outputDir){ try { + + //if (outputDir == "") { outputDir += hasPath(distFile); } string outfile = getRootName(distFile) + "sorted.dist"; + //if you can, use the unix sort since its been optimized for years #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -1045,10 +982,94 @@ 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); - } + } +} +/**************************************************************************************************/ +inline vector setFilePosFasta(string filename, int& num) { + + vector positions; + ifstream inFASTA; + openInputFile(filename, inFASTA); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); gobble(inFASTA); + if (input.length() != 0) { + if(input[0] == '>'){ long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } + } + inFASTA.close(); + + num = positions.size(); + + /*FILE * pFile; + long size; + + //get num bytes in file + pFile = fopen (filename.c_str(),"rb"); + if (pFile==NULL) perror ("Error opening file"); + else{ + fseek (pFile, 0, SEEK_END); + size=ftell (pFile); + fclose (pFile); + }*/ + + long size = positions[(positions.size()-1)]; + ifstream in; + openInputFile(filename, in); + + in.seekg(size); + + while(char c = in.get()){ + if(in.eof()) { break; } + else { size++; } + } + in.close(); + + positions.push_back(size); + + return positions; } +/**************************************************************************************************/ +inline vector setFilePosEachLine(string filename, int& num) { + + vector positions; + ifstream in; + openInputFile(filename, in); + + string input; + while(!in.eof()){ + long lastpos = in.tellg(); + input = getline(in); gobble(in); + if (input.length() != 0) { + long pos = in.tellg(); + if (pos != -1) { positions.push_back(pos - input.length() - 1); } + else { positions.push_back(lastpos); } + } + } + in.close(); + + num = positions.size(); + + FILE * pFile; + long size; + + //get num bytes in file + pFile = fopen (filename.c_str(),"rb"); + if (pFile==NULL) perror ("Error opening file"); + else{ + fseek (pFile, 0, SEEK_END); + size=ftell (pFile); + fclose (pFile); + } + + positions.push_back(size); + + return positions; +} + /**************************************************************************************************/ #endif