X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=88a18ed452314c38c5d2cf6909ea44db465d61af;hb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;hp=95b523e8a4a71056c782ae8319568eead3240fde;hpb=4dbf93479b205ec5d72663e5b01611000266bc13;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 95b523e..88a18ed 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -1,241 +1,1454 @@ -/* - * m->mothurOut.cpp - * Mothur - * - * Created by westcott on 2/25/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "mothurout.h" - -/******************************************************/ -MothurOut* MothurOut::getInstance() { - if( _uniqueInstance == 0) { - _uniqueInstance = new MothurOut(); - } - return _uniqueInstance; -} -/*********************************************************************************************/ -void MothurOut::setFileName(string filename) { - try { - logFileName = filename; - - #ifdef USE_MPI - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - - if (pid == 0) { //only one process should output to screen - #endif - - openOutputFile(filename, out); - - #ifdef USE_MPI - } - #endif - } - catch(exception& e) { - errorOut(e, "MothurOut", "setFileName"); - exit(1); - } -} -/*********************************************************************************************/ -void MothurOut::closeLog() { - 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.close(); - - #ifdef USE_MPI - } - #endif - } - catch(exception& e) { - errorOut(e, "MothurOut", "closeLog"); - exit(1); - } -} - -/*********************************************************************************************/ -MothurOut::~MothurOut() { - try { - _uniqueInstance = 0; - - } - catch(exception& e) { - errorOut(e, "MothurOut", "MothurOut"); - exit(1); - } -} -/*********************************************************************************************/ -void MothurOut::mothurOut(string output) { - try { - - #ifdef USE_MPI - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - - if (pid == 0) { //only one process should output to screen - #endif - - cout << output; - out << output; - - #ifdef USE_MPI - } - #endif - } - catch(exception& e) { - errorOut(e, "MothurOut", "MothurOut"); - exit(1); - } -} -/*********************************************************************************************/ -void MothurOut::mothurOutEndLine() { - try { - #ifdef USE_MPI - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - - if (pid == 0) { //only one process should output to screen - #endif - - cout << endl; - out << endl; - - #ifdef USE_MPI - } - #endif - } - catch(exception& e) { - errorOut(e, "MothurOut", "MothurOutEndLine"); - exit(1); - } -} -/*********************************************************************************************/ -void MothurOut::mothurOutJustToLog(string output) { - 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; - - #ifdef USE_MPI - } - #endif - } - catch(exception& e) { - errorOut(e, "MothurOut", "MothurOutJustToLog"); - exit(1); - } -} -/*********************************************************************************************/ -void MothurOut::errorOut(exception& e, string object, string function) { - double vm, rss; - mem_usage(vm, rss); - - 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(); -} -/*********************************************************************************************/ -//The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c -// process_mem_usage(double &, double &) - takes two doubles by reference, -// attempts to read the system-dependent data for a process' virtual memory -// size and resident set size, and return the results in KB. -// -// On failure, returns 0.0, 0.0 -int MothurOut::mem_usage(double& vm_usage, double& resident_set) { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - - vm_usage = 0.0; - resident_set = 0.0; - - // 'file' stat seems to give the most reliable results - // - ifstream stat_stream("/proc/self/stat",ios_base::in); - - // dummy vars for leading entries in stat that we don't care about - // - string pid, comm, state, ppid, pgrp, session, tty_nr; - string tpgid, flags, minflt, cminflt, majflt, cmajflt; - string utime, stime, cutime, cstime, priority, nice; - string O, itrealvalue, starttime; - - // the two fields we want - // - unsigned long vsize; - long rss; - - stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr - >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt - >> utime >> stime >> cutime >> cstime >> priority >> nice - >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest - - long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages - vm_usage = vsize / 1024.0; - resident_set = rss * page_size_kb; - - mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n"); - return 0; - - #else -/* //windows memory usage - // Get the list of process identifiers. - DWORD aProcesses[1024], cbNeeded, cProcesses; - - if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; } - - // Calculate how many process identifiers were returned. - cProcesses = cbNeeded / sizeof(DWORD); - - // Print the memory usage for each process - for (int i = 0; i < cProcesses; i++ ) { - DWORD processID = aProcesses[i]; - - PROCESS_MEMORY_COUNTERS pmc; - - HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID); - - // Print the process identifier. - printf( "\nProcess ID: %u\n", processID); - - if (NULL != hProcess) { - - if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) { - printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount ); - printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize ); - printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize ); - printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage ); - printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage ); - printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage ); - printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage ); - printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage ); - printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage ); - } - CloseHandle(hProcess); - } - } -*/ - return 0; - - #endif -} -/*********************************************************************************************/ - - - - - - +/* + * mothurOut.cpp + * Mothur + * + * Created by westcott on 2/25/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "mothurout.h" + +/******************************************************/ +MothurOut* MothurOut::getInstance() { + if( _uniqueInstance == 0) { + _uniqueInstance = new MothurOut(); + } + return _uniqueInstance; +} +/*********************************************************************************************/ +void MothurOut::setFileName(string filename) { + try { + logFileName = filename; + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen + #endif + + openOutputFile(filename, out); + + #ifdef USE_MPI + } + #endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "setFileName"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::setDefaultPath(string pathname) { + try { + + //add / to name if needed + string lastChar = pathname.substr(pathname.length()-1); + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if (lastChar != "/") { pathname += "/"; } + #else + if (lastChar != "\\") { pathname += "\\"; } + #endif + + defaultPath = pathname; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "setDefaultPath"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::closeLog() { + 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.close(); + + #ifdef USE_MPI + } + #endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "closeLog"); + exit(1); + } +} + +/*********************************************************************************************/ +MothurOut::~MothurOut() { + try { + _uniqueInstance = 0; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOut"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::mothurOut(string output) { + try { + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen + #endif + + cout << output; + out << output; + + #ifdef USE_MPI + } + #endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOut"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::mothurOutEndLine() { + try { + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen + #endif + + cout << endl; + out << endl; + + #ifdef USE_MPI + } + #endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutEndLine"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::mothurOutJustToLog(string output) { + 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; + + #ifdef USE_MPI + } + #endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutJustToLog"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::errorOut(exception& e, string object, string function) { + //double vm, rss; + //mem_usage(vm, rss); + + 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(); +} +/*********************************************************************************************/ +//The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c +// process_mem_usage(double &, double &) - takes two doubles by reference, +// attempts to read the system-dependent data for a process' virtual memory +// size and resident set size, and return the results in KB. +// +// On failure, returns 0.0, 0.0 +int MothurOut::mem_usage(double& vm_usage, double& resident_set) { + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + + vm_usage = 0.0; + resident_set = 0.0; + + // 'file' stat seems to give the most reliable results + // + ifstream stat_stream("/proc/self/stat",ios_base::in); + + // dummy vars for leading entries in stat that we don't care about + // + string pid, comm, state, ppid, pgrp, session, tty_nr; + string tpgid, flags, minflt, cminflt, majflt, cmajflt; + string utime, stime, cutime, cstime, priority, nice; + string O, itrealvalue, starttime; + + // the two fields we want + // + unsigned long vsize; + long rss; + + stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr + >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt + >> utime >> stime >> cutime >> cstime >> priority >> nice + >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest + + long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages + vm_usage = vsize / 1024.0; + resident_set = rss * page_size_kb; + + mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n"); + return 0; + + #else +/* //windows memory usage + // Get the list of process identifiers. + DWORD aProcesses[1024], cbNeeded, cProcesses; + + if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; } + + // Calculate how many process identifiers were returned. + cProcesses = cbNeeded / sizeof(DWORD); + + // Print the memory usage for each process + for (int i = 0; i < cProcesses; i++ ) { + DWORD processID = aProcesses[i]; + + PROCESS_MEMORY_COUNTERS pmc; + + HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID); + + // Print the process identifier. + printf( "\nProcess ID: %u\n", processID); + + if (NULL != hProcess) { + + if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) { + printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount ); + printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize ); + printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize ); + printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage ); + printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage ); + printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage ); + printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage ); + printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage ); + printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage ); + } + CloseHandle(hProcess); + } + } +*/ + return 0; + + #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())) {;} + 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())) {;} + 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.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::getRootName(string longName){ + try { + + string rootName = longName; + + if(longName.find_last_of(".") != longName.npos){ + int pos = longName.find_last_of('.')+1; + rootName = longName.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); + } +} + +/***********************************************************************/ + +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; } + } + 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) + + 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); } + + //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; + + 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; } + } + + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "/" + newFileName; + } + + newFileName = "/" + newFileName; + return newFileName; + } + #else + 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 = ""; } + + //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(".\\")) != -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; } + } + + 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); + + fileHandle.open(completeFileName.c_str()); + if(!fileHandle) { + 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); + + 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, ""); + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if (exist == 0) { //you could open it so you want to delete it + inTest.close(); + string command = "rm " + newName; + system(command.c_str()); + } + + string command = "mv " + oldName + " " + newName; + system(command.c_str()); + #else + remove(newName.c_str()); + 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); + + 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); + } + +} + +/**************************************************************************************************/ +void 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"); + + if (ableToOpen == 0) { //you opened it + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } + input.close(); + } + + output.close(); + } + 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) + 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 + remove(tempDistFile.c_str()); + remove(tempOutfile.c_str()); + #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); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); + if (input.length() != 0) { + if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } + gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions + } + 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 int 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; + } + 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); + + string input; + while(!in.eof()){ + unsigned long int lastpos = in.tellg(); + input = getline(in); + if (input.length() != 0) { + unsigned long int 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 + } + in.close(); + + num = positions.size(); + + FILE * pFile; + unsigned long int 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; + } + 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 int 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); + } + + //estimate file breaks + unsigned long int 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 int spot = (i+1) * chunkSize; + + ifstream in; + openInputFile(filename, in); + in.seekg(spot); + + //look for next '>' + unsigned long int newSpot = spot; + while (!in.eof()) { + char c = in.get(); + if (c == '>') { in.putback(c); newSpot = in.tellg(); break; } + } + + //there was not another sequence before the end of the file + unsigned long int 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); + + return filePos; + } + 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::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); + } +} + +/***********************************************************************/ + +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; + + while (estim.find_first_of(symbol) != -1) { + individual = estim.substr(0,estim.find_first_of(symbol)); + if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string + estim = estim.substr(estim.find_first_of(symbol)+1, estim.length()); + container.push_back(individual); + } + } + //get last one + container.push_back(estim); + } + catch(exception& e) { + errorOut(e, "MothurOut", "splitAtChar"); + exit(1); + } +} + +/***********************************************************************/ + +//This function parses the estimator options and puts them in a vector +void MothurOut::splitAtDash(string& estim, vector& 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(); ++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 == "") { cout << *it << " is not a valid label." << endl; } + 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 == "") { cout << "Your file does not include the label unique." << endl; } + userLabels.erase("unique"); + } + else { + 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]) { + s = it2->first; + //remove small labels + userLabels.erase(s); + break; + } + } + 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; } + } + + 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); + } +} +/**************************************************************************************************/ + + + + +