+++ /dev/null
-/*
- * 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::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 (biomfile != "") { mothurOut("biom=" + biomfile); 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 (biomfile != "") { 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 = "";
- biomfile = "";
- processors = "1";
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "clearCurrentFiles");
- exit(1);
- }
-}
-/*********************************************************************************************/
-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) || (__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 {
-
- #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
-
- out << output;
- logger() << 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
-
- out << endl;
- logger() << endl;
-
- #ifdef USE_MPI
- }
- #endif
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "MothurOutEndLine");
- exit(1);
- }
-}
-/*********************************************************************************************/
-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
- 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) || (__linux__) || (__unix__) || (__unix)
-
- 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())) { ;}
- 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);
- }
-
-}
-/***********************************************************************/
-
-bool MothurOut::dirCheck(string& dirName){
- try {
-
- string tag = "";
- #ifdef USE_MPI
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- tag = toString(pid);
- #endif
-
- //add / to name if needed
- string lastChar = dirName.substr(dirName.length()-1);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if (lastChar != "/") { dirName += "/"; }
- #else
- if (lastChar != "\\") { dirName += "\\"; }
- #endif
-
- //test to make sure directory exists
- dirName = getFullPathName(dirName);
- string outTemp = dirName + tag + "temp";
- ofstream out;
- out.open(outTemp.c_str(), ios::trunc);
- if(!out) {
- mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine();
- }else{
- out.close();
- mothurRemove(outTemp);
- return true;
- }
-
- return false;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "dirCheck");
- 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 = "";
-
- 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<string> 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<string> 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(!input.eof()){
- 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<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
- try {
- vector<unsigned long long> 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<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
- try {
- filename = getFullPathName(filename);
-
- vector<unsigned long long> 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<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
- try{
- vector<unsigned long long> 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<string>& files) {
- try{
-
- vector<unsigned long long> 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<string, string>& 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 nameMap.size();
-
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "readNames");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-int MothurOut::readNames(string namefile, map<string, vector<string> >& 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<string> temp;
- splitAtComma(secondCol, temp);
-
- nameMap[firstCol] = temp;
- }
- in.close();
-
- return nameMap.size();
-
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "readNames");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-map<string, int> MothurOut::readNames(string namefile) {
- try {
-
- map<string, int> nameMap;
-
- //open input file
- ifstream in;
- openInputFile(namefile, in);
-
- while (!in.eof()) {
- if (control_pressed) { break; }
-
- string firstCol, secondCol;
- in >> firstCol; gobble(in);
- in >> 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<seqPriorityNode>& nameVector, map<string, string>& 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<string, string>::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<names.size();i++){
- if(names[i] == ','){
- count++;
- }
- }
- }
-
- return count;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "getNumNames");
- exit(1);
- }
-}
-/***********************************************************************/
-
-int MothurOut::getNumChar(string line, char c){
- try {
- int count = 0;
-
- if(line != ""){
- for(int i=0;i<line.size();i++){
- if(line[i] == c){
- count++;
- }
- }
- }
-
- return count;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "getNumChar");
- exit(1);
- }
-}
-/***********************************************************************/
-int MothurOut::mothurRemove(string filename){
- try {
- filename = getFullPathName(filename);
- int error = remove(filename.c_str());
- //if (error != 0) {
- // if (errno != ENOENT) { //ENOENT == file does not exist
- // string message = "Error deleting file " + filename;
- // perror(message.c_str());
- // }
- //}
- return error;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "mothurRemove");
- exit(1);
- }
-}
-/***********************************************************************/
-bool MothurOut::mothurConvert(string item, int& num){
- try {
- bool error = false;
-
- if (isNumeric1(item)) {
- convert(item, num);
- }else {
- num = 0;
- error = true;
- mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
- commandInputsConvertError = true;
- }
-
- return error;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "mothurConvert");
- exit(1);
- }
-}
-/***********************************************************************/
-bool MothurOut::isNumeric1(string stringToCheck){
- try {
- bool numeric = false;
-
- if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
-
- return numeric;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "isNumeric1");
- exit(1);
- }
-
-}
-/***********************************************************************/
-bool MothurOut::mothurConvert(string item, float& num){
- try {
- bool error = false;
-
- if (isNumeric1(item)) {
- convert(item, num);
- }else {
- num = 0;
- error = true;
- mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
- commandInputsConvertError = true;
- }
-
- return error;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "mothurConvert");
- exit(1);
- }
-}
-/***********************************************************************/
-bool MothurOut::mothurConvert(string item, double& num){
- try {
- bool error = false;
-
- if (isNumeric1(item)) {
- convert(item, num);
- }else {
- num = 0;
- error = true;
- mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
- commandInputsConvertError = true;
- }
-
- return error;
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "mothurConvert");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-vector<vector<double> > MothurOut::binomial(int maxOrder){
- try {
- vector<vector<double> > 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<char, int> 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<char>(file),istreambuf_iterator<char>(), '>');
- 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<string>& container, char symbol) {
- try {
- string individual = "";
- int estimLength = estim.size();
- for(int i=0;i<estimLength;i++){
- if(estim[i] == symbol){
- container.push_back(individual);
- individual = "";
- }
- else{
- individual += estim[i];
- }
- }
- container.push_back(individual);
-
- }
- 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<string>& container) {
- try {
- string individual = "";
- int estimLength = estim.size();
- for(int i=0;i<estimLength;i++){
- if(estim[i] == '-'){
- container.push_back(individual);
- individual = "";
- }
- else{
- individual += estim[i];
- }
- }
- container.push_back(individual);
-
-
- /* string individual;
-
- 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());
- container.push_back(individual);
- }
- }
- //get last one
- container.push_back(estim); */
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtDash");
- exit(1);
- }
-}
-
-/***********************************************************************/
-//This function parses the label options and puts them in a set
-void MothurOut::splitAtDash(string& estim, set<string>& container) {
- try {
- string individual = "";
- int estimLength = estim.size();
- for(int i=0;i<estimLength;i++){
- if(estim[i] == '-'){
- container.insert(individual);
- individual = "";
- }
- else{
- individual += estim[i];
- }
- }
- container.insert(individual);
-
- // string individual;
-
- // 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());
- // container.insert(individual);
- // }
- // }
- //get last one
- // container.insert(estim);
-
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtDash");
- exit(1);
- }
-}
-/***********************************************************************/
-//This function parses the line options and puts them in a set
-void MothurOut::splitAtDash(string& estim, set<int>& 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<string>& container) {
- try {
- string individual = "";
- int estimLength = estim.size();
- for(int i=0;i<estimLength;i++){
- if(estim[i] == ','){
- container.push_back(individual);
- individual = "";
- }
- else{
- individual += estim[i];
- }
- }
- container.push_back(individual);
-
-
-
-
-// string individual;
-//
-// 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 comma at end of string
-// estim = estim.substr(estim.find_first_of(',')+1, estim.length());
-// container.push_back(individual);
-// }
-// }
-// //get last one
-// container.push_back(estim);
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtComma");
- exit(1);
- }
-}
-/***********************************************************************/
-//This function splits up the various option parameters
-void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
- try {
- prefix = suffix.substr(0,suffix.find_first_of(c));
- if ((suffix.find_first_of(c)+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
- suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
- string space = " ";
- while(suffix.at(0) == ' ')
- suffix = suffix.substr(1, suffix.length());
- }
-
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtComma");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-//This function splits up the various option parameters
-void MothurOut::splitAtComma(string& prefix, string& suffix){
- try {
- prefix = suffix.substr(0,suffix.find_first_of(','));
- if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
- suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
- string space = " ";
- while(suffix.at(0) == ' ')
- suffix = suffix.substr(1, suffix.length());
- }
-
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtComma");
- exit(1);
- }
-}
-/***********************************************************************/
-
-//This function separates the key value from the option value i.e. dist=96_...
-void MothurOut::splitAtEquals(string& key, string& value){
- try {
- if(value.find_first_of('=') != -1){
- key = value.substr(0,value.find_first_of('='));
- if ((value.find_first_of('=')+1) <= value.length()) {
- value = value.substr(value.find_first_of('=')+1, value.length());
- }
- }else{
- key = value;
- value = 1;
- }
- }
- catch(exception& e) {
- errorOut(e, "MothurOut", "splitAtEquals");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-bool MothurOut::inUsersGroups(string groupname, vector<string> 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<string> groupnames, vector<string> 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<string>& userLabels, string errorOff) {
- try {
-
- set<string>::iterator it;
- vector<float> orderFloat;
- map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
- map<string, float>::iterator it2;
- float labelFloat;
- bool smaller = false;
-
- //unique is the smallest line
- if (label == "unique") { return false; }
- else {
- 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<string> versionVector;
- splitAtChar(version, versionVector, '.');
-
- //check file version
- vector<string> 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);
- }
-}
-/**************************************************************************************************/
-
-
-
-
-
projects / mothur.git / blobdiff