X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=c89d580d64f6c69a6afedada448143ae114453a3;hb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;hp=8bf216a39ce9b6d8492e1e2ec10dedc70d46843e;hpb=a86aff4f80701bf0d436f02c0095920114e1cba2;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 8bf216a..c89d580 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -1,5 +1,5 @@ /* - * m->mothurOut.cpp + * mothurOut.cpp * Mothur * * Created by westcott on 2/25/10. @@ -9,6 +9,7 @@ #include "mothurout.h" + /******************************************************/ MothurOut* MothurOut::getInstance() { if( _uniqueInstance == 0) { @@ -17,6 +18,103 @@ MothurOut* MothurOut::getInstance() { return _uniqueInstance; } /*********************************************************************************************/ +void MothurOut::printCurrentFiles() { + try { + if (accnosfile != "") { mothurOut("accnos=" + accnosfile); mothurOutEndLine(); } + if (columnfile != "") { mothurOut("column=" + columnfile); mothurOutEndLine(); } + if (designfile != "") { mothurOut("design=" + designfile); mothurOutEndLine(); } + if (fastafile != "") { mothurOut("fasta=" + fastafile); mothurOutEndLine(); } + if (groupfile != "") { mothurOut("group=" + groupfile); mothurOutEndLine(); } + if (listfile != "") { mothurOut("list=" + listfile); mothurOutEndLine(); } + if (namefile != "") { mothurOut("name=" + namefile); mothurOutEndLine(); } + if (oligosfile != "") { mothurOut("oligos=" + oligosfile); mothurOutEndLine(); } + if (orderfile != "") { mothurOut("order=" + orderfile); mothurOutEndLine(); } + if (ordergroupfile != "") { mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine(); } + if (phylipfile != "") { mothurOut("phylip=" + phylipfile); mothurOutEndLine(); } + if (qualfile != "") { mothurOut("qfile=" + qualfile); mothurOutEndLine(); } + if (rabundfile != "") { mothurOut("rabund=" + rabundfile); mothurOutEndLine(); } + if (relabundfile != "") { mothurOut("relabund=" + relabundfile); mothurOutEndLine(); } + if (sabundfile != "") { mothurOut("sabund=" + sabundfile); mothurOutEndLine(); } + if (sfffile != "") { mothurOut("sff=" + sfffile); mothurOutEndLine(); } + if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); } + if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); } + if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); } + if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); } + if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); } + + } + catch(exception& e) { + errorOut(e, "MothurOut", "printCurrentFiles"); + exit(1); + } +} +/*********************************************************************************************/ +bool MothurOut::hasCurrentFiles() { + try { + bool hasCurrent = false; + + if (accnosfile != "") { return true; } + if (columnfile != "") { return true; } + if (designfile != "") { return true; } + if (fastafile != "") { return true; } + if (groupfile != "") { return true; } + if (listfile != "") { return true; } + if (namefile != "") { return true; } + if (oligosfile != "") { return true; } + if (orderfile != "") { return true; } + if (ordergroupfile != "") { return true; } + if (phylipfile != "") { return true; } + if (qualfile != "") { return true; } + if (rabundfile != "") { return true; } + if (relabundfile != "") { return true; } + if (sabundfile != "") { return true; } + if (sfffile != "") { return true; } + if (sharedfile != "") { return true; } + if (taxonomyfile != "") { return true; } + if (treefile != "") { return true; } + if (flowfile != "") { return true; } + if (processors != "1") { return true; } + + return hasCurrent; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "hasCurrentFiles"); + exit(1); + } +} + +/*********************************************************************************************/ +void MothurOut::clearCurrentFiles() { + try { + phylipfile = ""; + columnfile = ""; + listfile = ""; + rabundfile = ""; + sabundfile = ""; + namefile = ""; + groupfile = ""; + designfile = ""; + orderfile = ""; + treefile = ""; + sharedfile = ""; + ordergroupfile = ""; + relabundfile = ""; + fastafile = ""; + qualfile = ""; + sfffile = ""; + oligosfile = ""; + accnosfile = ""; + taxonomyfile = ""; + flowfile = ""; + processors = "1"; + } + catch(exception& e) { + errorOut(e, "MothurOut", "clearCurrentFiles"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::setFileName(string filename) { try { logFileName = filename; @@ -40,6 +138,36 @@ void MothurOut::setFileName(string filename) { } } /*********************************************************************************************/ +void MothurOut::setDefaultPath(string pathname) { + try { + + //add / to name if needed + string lastChar = pathname.substr(pathname.length()-1); + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if (lastChar != "/") { pathname += "/"; } + #else + if (lastChar != "\\") { pathname += "\\"; } + #endif + + defaultPath = pathname; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "setDefaultPath"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::setOutputDir(string pathname) { + try { + outputDir = pathname; + } + catch(exception& e) { + errorOut(e, "MothurOut", "setOutputDir"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::closeLog() { try { @@ -84,8 +212,8 @@ void MothurOut::mothurOut(string output) { if (pid == 0) { //only one process should output to screen #endif - cout << output; out << output; + logger() << output; #ifdef USE_MPI } @@ -106,8 +234,8 @@ void MothurOut::mothurOutEndLine() { if (pid == 0) { //only one process should output to screen #endif - cout << endl; out << endl; + logger() << endl; #ifdef USE_MPI } @@ -119,6 +247,55 @@ void MothurOut::mothurOutEndLine() { } } /*********************************************************************************************/ +void MothurOut::mothurOut(string output, ofstream& outputFile) { + try { + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen +#endif + + + out << output; + outputFile << output; + logger() << output; + +#ifdef USE_MPI + } +#endif + + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOut"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::mothurOutEndLine(ofstream& outputFile) { + try { +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen +#endif + + out << endl; + outputFile << endl; + logger() << endl; + +#ifdef USE_MPI + } +#endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutEndLine"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::mothurOutJustToLog(string output) { try { #ifdef USE_MPI @@ -141,10 +318,10 @@ void MothurOut::mothurOutJustToLog(string output) { } /*********************************************************************************************/ void MothurOut::errorOut(exception& e, string object, string function) { - double vm, rss; - mem_usage(vm, rss); + //double vm, rss; + //mem_usage(vm, rss); - mothurOut("Error: "); + 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(); @@ -157,7 +334,7 @@ void MothurOut::errorOut(exception& e, string object, string function) { // // On failure, returns 0.0, 0.0 int MothurOut::mem_usage(double& vm_usage, double& resident_set) { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) vm_usage = 0.0; resident_set = 0.0; @@ -232,7 +409,1772 @@ int MothurOut::mem_usage(double& vm_usage, double& resident_set) { #endif } -/*********************************************************************************************/ + + +/***********************************************************************/ +int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){ + try { + fileName = getFullPathName(fileName); + + fileHandle.open(fileName.c_str(), ios::app); + if(!fileHandle) { + mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine(); + return 1; + } + else { + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openOutputFileAppend"); + exit(1); + } +} +/***********************************************************************/ +void MothurOut::gobble(istream& f){ + try { + + char d; + while(isspace(d=f.get())) { ;} + if(!f.eof()) { f.putback(d); } + } + catch(exception& e) { + errorOut(e, "MothurOut", "gobble"); + exit(1); + } +} +/***********************************************************************/ +void MothurOut::gobble(istringstream& f){ + try { + char d; + while(isspace(d=f.get())) {;} + if(!f.eof()) { f.putback(d); } + } + catch(exception& e) { + errorOut(e, "MothurOut", "gobble"); + exit(1); + } +} + +/***********************************************************************/ + +string MothurOut::getline(istringstream& 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) { + errorOut(e, "MothurOut", "getline"); + exit(1); + } +} +/***********************************************************************/ + +string MothurOut::getline(ifstream& fileHandle) { + try { + + string line = ""; + + while (fileHandle) { + //get next character + char c = fileHandle.get(); + + //are you at the end of the line + if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; } + else { line += c; } + } + + return line; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "getline"); + exit(1); + } +} +/***********************************************************************/ + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#ifdef USE_COMPRESSION +inline bool endsWith(string s, const char * suffix){ + size_t suffixLength = strlen(suffix); + return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0; +} +#endif +#endif + +string MothurOut::getRootName(string longName){ + try { + + string rootName = longName; + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#ifdef USE_COMPRESSION + if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) { + int pos = rootName.find_last_of('.'); + rootName = rootName.substr(0, pos); + cerr << "shortening " << longName << " to " << rootName << "\n"; + } +#endif +#endif + if(rootName.find_last_of(".") != rootName.npos){ + int pos = rootName.find_last_of('.')+1; + rootName = rootName.substr(0, pos); + } + + return rootName; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getRootName"); + exit(1); + } +} +/***********************************************************************/ + +string MothurOut::getSimpleName(string longName){ + try { + string simpleName = longName; + + size_t found; + found=longName.find_last_of("/\\"); + + if(found != longName.npos){ + simpleName = longName.substr(found+1); + } + + return simpleName; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getSimpleName"); + exit(1); + } +} + +/***********************************************************************/ + +int MothurOut::getRandomIndex(int highest){ + try { + + int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0)); + + return random; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getRandomIndex"); + exit(1); + } + +} +/**********************************************************************/ + +string MothurOut::getPathName(string longName){ + try { + string rootPathName = longName; + + if(longName.find_last_of("/\\") != longName.npos){ + int pos = longName.find_last_of("/\\")+1; + rootPathName = longName.substr(0, pos); + } + + return rootPathName; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getPathName"); + exit(1); + } + +} +/***********************************************************************/ + +string MothurOut::hasPath(string longName){ + try { + string path = ""; + + size_t found; + found=longName.find_last_of("~/\\"); + + if(found != longName.npos){ + path = longName.substr(0, found+1); + } + + return path; + } + catch(exception& e) { + errorOut(e, "MothurOut", "hasPath"); + exit(1); + } +} + +/***********************************************************************/ + +string MothurOut::getExtension(string longName){ + try { + string extension = longName; + + if(longName.find_last_of('.') != longName.npos){ + int pos = longName.find_last_of('.'); + extension = longName.substr(pos, longName.length()); + } + + return extension; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getExtension"); + exit(1); + } +} +/***********************************************************************/ +bool MothurOut::isBlank(string fileName){ + try { + + fileName = getFullPathName(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; } + fileHandle.close(); + } + return false; + } + catch(exception& e) { + errorOut(e, "MothurOut", "isBlank"); + exit(1); + } +} +/***********************************************************************/ + +string MothurOut::getFullPathName(string fileName){ + try{ + + string path = hasPath(fileName); + string newFileName; + int pos; + + if (path == "") { return fileName; } //its a simple name + else { //we need to complete the pathname + // ex. ../../../filename + // cwd = /user/work/desktop + + string cwd; + //get current working directory + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + + if (path.find("~") != -1) { //go to home directory + string homeDir; + + char *homepath = NULL; + homepath = getenv ("HOME"); + if ( homepath != NULL) { homeDir = homepath; } + else { homeDir = ""; } + + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + if (path.rfind("./") == string::npos) { 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; + + char *cwdpath = NULL; + cwdpath = getcwd(NULL, 0); // or _getcwd + if ( cwdpath != NULL) { cwd = cwdpath; } + else { cwd = ""; } + + + //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('/') != string::npos) { + 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; + + while((pos = path.rfind("./")) != string::npos) { //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 { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } + } + + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "/" + newFileName; + } + + newFileName = "/" + newFileName; + return newFileName; + } + #else + if (path.find("~") != string::npos) { //go to home directory + string homeDir = getenv ("HOMEPATH"); + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + if (path.rfind(".\\") == string::npos) { 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; + + while((pos = path.rfind(".\\")) != string::npos) { //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 { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } + } + + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "\\" + newFileName; + } + + return newFileName; + } + + #endif + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "getFullPathName"); + exit(1); + } +} +/***********************************************************************/ + +int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ + try { + //get full path name + string completeFileName = getFullPathName(fileName); +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#ifdef USE_COMPRESSION + // check for gzipped or bzipped file + if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { + string tempName = string(tmpnam(0)); + mkfifo(tempName.c_str(), 0666); + int fork_result = fork(); + if (fork_result < 0) { + cerr << "Error forking.\n"; + exit(1); + } else if (fork_result == 0) { + string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName; + cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; + system(command.c_str()); + cerr << "Done decompressing " << completeFileName << "\n"; + mothurRemove(tempName); + exit(EXIT_SUCCESS); + } else { + cerr << "waiting on child process " << fork_result << "\n"; + completeFileName = tempName; + } + } +#endif +#endif + fileHandle.open(completeFileName.c_str()); + if(!fileHandle) { + //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine(); + return 1; + }else { + //check for blank file + gobble(fileHandle); + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openInputFile - no Error"); + exit(1); + } +} +/***********************************************************************/ + +int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ + try { + + //get full path name + string completeFileName = getFullPathName(fileName); +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#ifdef USE_COMPRESSION + // check for gzipped or bzipped file + if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { + string tempName = string(tmpnam(0)); + mkfifo(tempName.c_str(), 0666); + int fork_result = fork(); + if (fork_result < 0) { + cerr << "Error forking.\n"; + exit(1); + } else if (fork_result == 0) { + string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName; + cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; + system(command.c_str()); + cerr << "Done decompressing " << completeFileName << "\n"; + mothurRemove(tempName); + exit(EXIT_SUCCESS); + } else { + cerr << "waiting on child process " << fork_result << "\n"; + completeFileName = tempName; + } + } +#endif +#endif + + fileHandle.open(completeFileName.c_str()); + if(!fileHandle) { + mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine(); + return 1; + } + else { + //check for blank file + gobble(fileHandle); + if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine(); } + + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openInputFile"); + exit(1); + } +} +/***********************************************************************/ + +int MothurOut::renameFile(string oldName, string newName){ + try { + ifstream inTest; + int exist = openInputFile(newName, inTest, ""); + inTest.close(); + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if (exist == 0) { //you could open it so you want to delete it + string command = "rm " + newName; + system(command.c_str()); + } + + string command = "mv " + oldName + " " + newName; + system(command.c_str()); + #else + mothurRemove(newName); + int renameOk = rename(oldName.c_str(), newName.c_str()); + #endif + return 0; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "renameFile"); + exit(1); + } +} + +/***********************************************************************/ + +int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ + try { + + string completeFileName = getFullPathName(fileName); +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#ifdef USE_COMPRESSION + // check for gzipped file + if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { + string tempName = string(tmpnam(0)); + mkfifo(tempName.c_str(), 0666); + cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; + int fork_result = fork(); + if (fork_result < 0) { + cerr << "Error forking.\n"; + exit(1); + } else if (fork_result == 0) { + string command = string(endsWith(completeFileName, ".gz") ? "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName; + system(command.c_str()); + exit(0); + } else { + completeFileName = tempName; + } + } +#endif +#endif + fileHandle.open(completeFileName.c_str(), ios::trunc); + if(!fileHandle) { + mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine(); + return 1; + } + else { + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openOutputFile"); + exit(1); + } + +} + +/**************************************************************************************************/ +int MothurOut::appendFiles(string temp, string filename) { + try{ + ofstream output; + ifstream input; + + //open output file in append mode + openOutputFileAppend(filename, output); + int ableToOpen = openInputFile(temp, input, "no error"); + //int ableToOpen = openInputFile(temp, input); + + int numLines = 0; + if (ableToOpen == 0) { //you opened it + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; if (c == '\n') {numLines++;} } + } + input.close(); + } + + output.close(); + + return numLines; + } + catch(exception& e) { + errorOut(e, "MothurOut", "appendFiles"); + exit(1); + } +} + +/**************************************************************************************************/ +string MothurOut::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) || (__linux__) || (__unix__) || (__unix) + string command = "sort -n -k +3 " + distFile + " -o " + outfile; + system(command.c_str()); + #else //you are stuck with my best attempt... + //windows sort does not have a way to specify a column, only a character in the line + //since we cannot assume that the distance will always be at the the same character location on each line + //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back. + + //read in file line by file and put distance first + string tempDistFile = distFile + ".temp"; + ifstream input; + ofstream output; + openInputFile(distFile, input); + openOutputFile(tempDistFile, output); + + string firstName, secondName; + float dist; + while (input) { + input >> firstName >> secondName >> dist; + output << dist << '\t' << firstName << '\t' << secondName << endl; + gobble(input); + } + input.close(); + output.close(); + + + //sort using windows sort + string tempOutfile = outfile + ".temp"; + string command = "sort " + tempDistFile + " /O " + tempOutfile; + system(command.c_str()); + + //read in sorted file and put distance at end again + ifstream input2; + openInputFile(tempOutfile, input2); + openOutputFile(outfile, output); + + while (input2) { + input2 >> dist >> firstName >> secondName; + output << firstName << '\t' << secondName << '\t' << dist << endl; + gobble(input2); + } + input2.close(); + output.close(); + + //remove temp files + mothurRemove(tempDistFile); + mothurRemove(tempOutfile); + #endif + + return outfile; + } + catch(exception& e) { + errorOut(e, "MothurOut", "sortFile"); + exit(1); + } +} +/**************************************************************************************************/ +vector MothurOut::setFilePosFasta(string filename, int& num) { + try { + vector positions; + ifstream inFASTA; + //openInputFile(filename, inFASTA); + inFASTA.open(filename.c_str(), ios::binary); + + string input; + unsigned long long count = 0; + while(!inFASTA.eof()){ + //input = getline(inFASTA); + //cout << input << '\t' << inFASTA.tellg() << endl; + //if (input.length() != 0) { + // if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); cout << (pos - input.length() - 1) << endl; } + //} + //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions + char c = inFASTA.get(); count++; + if (c == '>') { + positions.push_back(count-1); + //cout << count << endl; + } + } + 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); + }*/ + + unsigned long long size = positions[(positions.size()-1)]; + ifstream in; + openInputFile(filename, in); + + in.seekg(size); + + while(in.get()){ + if(in.eof()) { break; } + else { size++; } + } + in.close(); + + positions.push_back(size); + positions[0] = 0; + + return positions; + } + catch(exception& e) { + errorOut(e, "MothurOut", "setFilePosFasta"); + exit(1); + } +} +/**************************************************************************************************/ +vector MothurOut::setFilePosEachLine(string filename, int& num) { + try { + filename = getFullPathName(filename); + + vector positions; + ifstream in; + //openInputFile(filename, in); + in.open(filename.c_str(), ios::binary); + + string input; + unsigned long long count = 0; + positions.push_back(0); + + while(!in.eof()){ + //unsigned long long lastpos = in.tellg(); + //input = getline(in); + //if (input.length() != 0) { + //unsigned long long pos = in.tellg(); + //if (pos != -1) { positions.push_back(pos - input.length() - 1); } + //else { positions.push_back(lastpos); } + //} + //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions + + + //getline counting reads + char d = in.get(); count++; + while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) { + //get next character + d = in.get(); + count++; + } + + if (!in.eof()) { + d=in.get(); count++; + while(isspace(d) && (d != in.eof())) { d=in.get(); count++;} + } + positions.push_back(count-1); + //cout << count-1 << endl; + } + in.close(); + + num = positions.size()-1; + + FILE * pFile; + unsigned long 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[(positions.size()-1)] = size; + + return positions; + } + catch(exception& e) { + errorOut(e, "MothurOut", "setFilePosEachLine"); + exit(1); + } +} +/**************************************************************************************************/ + +vector MothurOut::divideFile(string filename, int& proc) { + try{ + vector filePos; + filePos.push_back(0); + + FILE * pFile; + unsigned long long size; + + filename = getFullPathName(filename); + + //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); + } + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + + //estimate file breaks + unsigned long long chunkSize = 0; + chunkSize = size / proc; + + //file to small to divide by processors + if (chunkSize == 0) { proc = 1; filePos.push_back(size); return filePos; } + + //for each process seekg to closest file break and search for next '>' char. make that the filebreak + for (int i = 0; i < proc; i++) { + unsigned long long spot = (i+1) * chunkSize; + + ifstream in; + openInputFile(filename, in); + in.seekg(spot); + + //look for next '>' + unsigned long long newSpot = spot; + while (!in.eof()) { + char c = in.get(); + + if (c == '>') { in.putback(c); newSpot = in.tellg(); break; } + else if (int(c) == -1) { break; } + + } + + //there was not another sequence before the end of the file + unsigned long long sanityPos = in.tellg(); + + if (sanityPos == -1) { break; } + else { filePos.push_back(newSpot); } + + in.close(); + } + + //save end pos + filePos.push_back(size); + + //sanity check filePos + for (int i = 0; i < (filePos.size()-1); i++) { + if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; } + } + + proc = (filePos.size() - 1); +#else + mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine(); + proc=1; + filePos.push_back(size); +#endif + return filePos; + } + catch(exception& e) { + errorOut(e, "MothurOut", "divideFile"); + exit(1); + } +} +/**************************************************************************************************/ +int MothurOut::divideFile(string filename, int& proc, vector& files) { + try{ + + vector filePos = divideFile(filename, proc); + + for (int i = 0; i < (filePos.size()-1); i++) { + + //read file chunk + ifstream in; + openInputFile(filename, in); + in.seekg(filePos[i]); + unsigned long long size = filePos[(i+1)] - filePos[i]; + char* chunk = new char[size]; + in.read(chunk, size); + in.close(); + + //open new file + string fileChunkName = filename + "." + toString(i) + ".tmp"; + ofstream out; + openOutputFile(fileChunkName, out); + + out << chunk << endl; + out.close(); + delete[] chunk; + + //save name + files.push_back(fileChunkName); + } + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "divideFile"); + exit(1); + } +} +/***********************************************************************/ + +bool MothurOut::isTrue(string f){ + try { + + for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); } + + if ((f == "TRUE") || (f == "T")) { return true; } + else { return false; } + } + catch(exception& e) { + errorOut(e, "MothurOut", "isTrue"); + exit(1); + } +} + +/***********************************************************************/ + +float MothurOut::roundDist(float dist, int precision){ + try { + return int(dist * precision + 0.5)/float(precision); + } + catch(exception& e) { + errorOut(e, "MothurOut", "roundDist"); + exit(1); + } +} +/***********************************************************************/ + +float MothurOut::ceilDist(float dist, int precision){ + try { + return int(ceil(dist * precision))/float(precision); + } + catch(exception& e) { + errorOut(e, "MothurOut", "ceilDist"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map& nameMap) { + try { + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + nameMap[firstCol] = secondCol; + } + in.close(); + + return 0; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map >& nameMap) { + try { + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + vector temp; + splitAtComma(secondCol, temp); + + nameMap[firstCol] = temp; + } + in.close(); + + return 0; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ +map MothurOut::readNames(string namefile) { + try { + + map nameMap; + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + int num = getNumNames(secondCol); + + nameMap[firstCol] = num; + } + in.close(); + + return nameMap; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, vector& nameVector, map& fastamap) { + try { + int error = 0; + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + int num = getNumNames(secondCol); + + map::iterator it = fastamap.find(firstCol); + if (it == fastamap.end()) { + error = 1; + mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine(); + }else { + seqPriorityNode temp(num, it->second, firstCol); + nameVector.push_back(temp); + } + } + in.close(); + + return error; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} + +/***********************************************************************/ + +int MothurOut::getNumNames(string names){ + try { + int count = 0; + + if(names != ""){ + count = 1; + for(int i=0;i > MothurOut::binomial(int maxOrder){ + try { + vector > binomial(maxOrder+1); + + for(int i=0;i<=maxOrder;i++){ + binomial[i].resize(maxOrder+1); + binomial[i][0]=1; + binomial[0][i]=0; + } + binomial[0][0]=1; + + binomial[1][0]=1; + binomial[1][1]=1; + + for(int i=2;i<=maxOrder;i++){ + binomial[1][i]=0; + } + + for(int i=2;i<=maxOrder;i++){ + for(int j=1;j<=maxOrder;j++){ + if(i==j){ binomial[i][j]=1; } + if(j>i) { binomial[i][j]=0; } + else { binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j]; } + } + } + + return binomial; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "binomial"); + exit(1); + } +} +/**************************************************************************************************/ +unsigned int MothurOut::fromBase36(string base36){ + try { + unsigned int num = 0; + + map converts; + converts['A'] = 0; + converts['a'] = 0; + converts['B'] = 1; + converts['b'] = 1; + converts['C'] = 2; + converts['c'] = 2; + converts['D'] = 3; + converts['d'] = 3; + converts['E'] = 4; + converts['e'] = 4; + converts['F'] = 5; + converts['f'] = 5; + converts['G'] = 6; + converts['g'] = 6; + converts['H'] = 7; + converts['h'] = 7; + converts['I'] = 8; + converts['i'] = 8; + converts['J'] = 9; + converts['j'] = 9; + converts['K'] = 10; + converts['k'] = 10; + converts['L'] = 11; + converts['l'] = 11; + converts['M'] = 12; + converts['m'] = 12; + converts['N'] = 13; + converts['n'] = 13; + converts['O'] = 14; + converts['o'] = 14; + converts['P'] = 15; + converts['p'] = 15; + converts['Q'] = 16; + converts['q'] = 16; + converts['R'] = 17; + converts['r'] = 17; + converts['S'] = 18; + converts['s'] = 18; + converts['T'] = 19; + converts['t'] = 19; + converts['U'] = 20; + converts['u'] = 20; + converts['V'] = 21; + converts['v'] = 21; + converts['W'] = 22; + converts['w'] = 22; + converts['X'] = 23; + converts['x'] = 23; + converts['Y'] = 24; + converts['y'] = 24; + converts['Z'] = 25; + converts['z'] = 25; + converts['0'] = 26; + converts['1'] = 27; + converts['2'] = 28; + converts['3'] = 29; + converts['4'] = 30; + converts['5'] = 31; + converts['6'] = 32; + converts['7'] = 33; + converts['8'] = 34; + converts['9'] = 35; + + int i = 0; + while (i < base36.length()) { + char c = base36[i]; + num = 36 * num + converts[c]; + i++; + } + + return num; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "fromBase36"); + exit(1); + } +} +/***********************************************************************/ + +int MothurOut::factorial(int num){ + try { + int total = 1; + + for (int i = 1; i <= num; i++) { + total *= i; + } + + return total; + } + catch(exception& e) { + errorOut(e, "MothurOut", "factorial"); + exit(1); + } +} +/***********************************************************************/ + +int MothurOut::getNumSeqs(ifstream& file){ + try { + int numSeqs = count(istreambuf_iterator(file),istreambuf_iterator(), '>'); + file.seekg(0); + return numSeqs; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getNumSeqs"); + exit(1); + } +} +/***********************************************************************/ +void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){ + try { + string input; + numSeqs = 0; + while(!file.eof()){ + input = getline(file); + if (input.length() != 0) { + if(input[0] == '>'){ numSeqs++; } + } + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "getNumSeqs"); + exit(1); + } +} +/***********************************************************************/ + +//This function parses the estimator options and puts them in a vector +void MothurOut::splitAtChar(string& estim, vector& container, char symbol) { + try { + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container) { + try { + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container) { + try { + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container) { + try { + string individual; + int lineNum; + + while (estim.find_first_of('-') != -1) { + individual = estim.substr(0,estim.find_first_of('-')); + if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string + estim = estim.substr(estim.find_first_of('-')+1, estim.length()); + convert(individual, lineNum); //convert the string to int + container.insert(lineNum); + } + } + //get last one + convert(estim, lineNum); //convert the string to int + container.insert(lineNum); + } + catch(exception& e) { + errorOut(e, "MothurOut", "splitAtDash"); + exit(1); + } +} +/***********************************************************************/ +//This function parses the a string and puts peices in a vector +void MothurOut::splitAtComma(string& estim, vector& container) { + try { + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i Groups) { + try { + for (int i = 0; i < Groups.size(); i++) { + if (groupname == Groups[i]) { return true; } + } + return false; + } + catch(exception& e) { + errorOut(e, "MothurOut", "inUsersGroups"); + exit(1); + } +} +/**************************************************************************************************/ +//returns true if any of the strings in first vector are in second vector +bool MothurOut::inUsersGroups(vector groupnames, vector Groups) { + try { + + for (int i = 0; i < groupnames.size(); i++) { + if (inUsersGroups(groupnames[i], Groups)) { return true; } + } + return false; + } + catch(exception& e) { + errorOut(e, "MothurOut", "inUsersGroups"); + 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. +bool MothurOut::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 { + 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();) { + + float temp; + if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){ + convert(*it, temp); + orderFloat.push_back(temp); + userMap[*it] = temp; + it++; + }else if (*it == "unique") { + orderFloat.push_back(-1.0); + userMap["unique"] = -1.0; + it++; + }else { + if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); } + userLabels.erase(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, "MothurOut", "anyLabelsToProcess"); + exit(1); + } +} + +/**************************************************************************************************/ +bool MothurOut::checkReleaseVersion(ifstream& file, string version) { + try { + + bool good = true; + + string line = getline(file); + + //before we added this check + if (line[0] != '#') { good = false; } + else { + //rip off # + line = line.substr(1); + + vector versionVector; + splitAtChar(version, versionVector, '.'); + + //check file version + vector linesVector; + splitAtChar(line, linesVector, '.'); + + if (versionVector.size() != linesVector.size()) { good = false; } + else { + for (int j = 0; j < versionVector.size(); j++) { + int num1, num2; + convert(versionVector[j], num1); + convert(linesVector[j], num2); + + //if mothurs version is newer than this files version, then we want to remake it + if (num1 > num2) { good = false; break; } + } + } + + } + + if (!good) { file.close(); } + else { file.seekg(0); } + + return good; + } + catch(exception& e) { + errorOut(e, "MothurOut", "checkReleaseVersion"); + exit(1); + } +} +/**************************************************************************************************/ +bool MothurOut::isContainingOnlyDigits(string input) { + try{ + + //are you a digit in ascii code + for (int i = 0;i < input.length(); i++){ + if( input[i]>47 && input[i]<58){} + else { return false; } + } + + return true; + } + catch(exception& e) { + errorOut(e, "MothurOut", "isContainingOnlyDigits"); + exit(1); + } +} +/**************************************************************************************************/ +int MothurOut::removeConfidences(string& tax) { + try { + + string taxon; + string newTax = ""; + + while (tax.find_first_of(';') != -1) { + + if (control_pressed) { return 0; } + + //get taxon + taxon = tax.substr(0,tax.find_first_of(';')); + + int pos = taxon.find_last_of('('); + if (pos != -1) { + //is it a number? + int pos2 = taxon.find_last_of(')'); + if (pos2 != -1) { + string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1))); + if (isNumeric1(confidenceScore)) { + taxon = taxon.substr(0, pos); //rip off confidence + } + } + } + taxon += ";"; + + tax = tax.substr(tax.find_first_of(';')+1, tax.length()); + newTax += taxon; + } + + tax = newTax; + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "removeConfidences"); + exit(1); + } +} +/**************************************************************************************************/