/*
- * m->mothurOut.cpp
+ * mothurOut.cpp
* Mothur
*
* Created by westcott on 2/25/10.
#include "mothurout.h"
+
/******************************************************/
MothurOut* MothurOut::getInstance() {
if( _uniqueInstance == 0) {
return _uniqueInstance;
}
/*********************************************************************************************/
+void MothurOut::printCurrentFiles() {
+ try {
+ if (accnosfile != "") { mothurOut("accnos=" + accnosfile); mothurOutEndLine(); }
+ if (columnfile != "") { mothurOut("column=" + columnfile); mothurOutEndLine(); }
+ if (designfile != "") { mothurOut("design=" + designfile); mothurOutEndLine(); }
+ if (fastafile != "") { mothurOut("fasta=" + fastafile); mothurOutEndLine(); }
+ if (groupfile != "") { mothurOut("group=" + groupfile); mothurOutEndLine(); }
+ if (listfile != "") { mothurOut("list=" + listfile); mothurOutEndLine(); }
+ if (namefile != "") { mothurOut("name=" + namefile); mothurOutEndLine(); }
+ if (oligosfile != "") { mothurOut("oligos=" + oligosfile); mothurOutEndLine(); }
+ if (orderfile != "") { mothurOut("order=" + orderfile); mothurOutEndLine(); }
+ if (ordergroupfile != "") { mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine(); }
+ if (phylipfile != "") { mothurOut("phylip=" + phylipfile); mothurOutEndLine(); }
+ if (qualfile != "") { mothurOut("qfile=" + qualfile); mothurOutEndLine(); }
+ if (rabundfile != "") { mothurOut("rabund=" + rabundfile); mothurOutEndLine(); }
+ if (relabundfile != "") { mothurOut("relabund=" + relabundfile); mothurOutEndLine(); }
+ if (sabundfile != "") { mothurOut("sabund=" + sabundfile); mothurOutEndLine(); }
+ if (sfffile != "") { mothurOut("sff=" + sfffile); mothurOutEndLine(); }
+ if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); }
+ if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
+ if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
+ if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
+ if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "printCurrentFiles");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+bool MothurOut::hasCurrentFiles() {
+ try {
+ bool hasCurrent = false;
+
+ if (accnosfile != "") { return true; }
+ if (columnfile != "") { return true; }
+ if (designfile != "") { return true; }
+ if (fastafile != "") { return true; }
+ if (groupfile != "") { return true; }
+ if (listfile != "") { return true; }
+ if (namefile != "") { return true; }
+ if (oligosfile != "") { return true; }
+ if (orderfile != "") { return true; }
+ if (ordergroupfile != "") { return true; }
+ if (phylipfile != "") { return true; }
+ if (qualfile != "") { return true; }
+ if (rabundfile != "") { return true; }
+ if (relabundfile != "") { return true; }
+ if (sabundfile != "") { return true; }
+ if (sfffile != "") { return true; }
+ if (sharedfile != "") { return true; }
+ if (taxonomyfile != "") { return true; }
+ if (treefile != "") { return true; }
+ if (flowfile != "") { return true; }
+ if (processors != "1") { return true; }
+
+ return hasCurrent;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "hasCurrentFiles");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************/
+void MothurOut::clearCurrentFiles() {
+ try {
+ phylipfile = "";
+ columnfile = "";
+ listfile = "";
+ rabundfile = "";
+ sabundfile = "";
+ namefile = "";
+ groupfile = "";
+ designfile = "";
+ orderfile = "";
+ treefile = "";
+ sharedfile = "";
+ ordergroupfile = "";
+ relabundfile = "";
+ fastafile = "";
+ qualfile = "";
+ sfffile = "";
+ oligosfile = "";
+ accnosfile = "";
+ taxonomyfile = "";
+ flowfile = "";
+ processors = "1";
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "clearCurrentFiles");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::setFileName(string filename) {
try {
logFileName = filename;
+
+ #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;
- out.close();
+
}
catch(exception& e) {
errorOut(e, "MothurOut", "MothurOut");
exit(1);
}
}
-
/*********************************************************************************************/
void MothurOut::mothurOut(string output) {
try {
-
- cout << output;
+
+ #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");
/*********************************************************************************************/
void MothurOut::mothurOutEndLine() {
try {
- cout << endl;
+ #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");
/*********************************************************************************************/
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");
}
/*********************************************************************************************/
void MothurOut::errorOut(exception& e, string object, string function) {
- mothurOut("Error: ");
+ //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);
+ }
+
+}
+/***********************************************************************/
+
+string MothurOut::hasPath(string longName){
+ try {
+ string path = "";
+
+ size_t found;
+ found=longName.find_last_of("~/\\");
+
+ if(found != longName.npos){
+ path = longName.substr(0, found+1);
+ }
+
+ return path;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "hasPath");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+string MothurOut::getExtension(string longName){
+ try {
+ string extension = longName;
+
+ if(longName.find_last_of('.') != longName.npos){
+ int pos = longName.find_last_of('.');
+ extension = longName.substr(pos, longName.length());
+ }
+
+ return extension;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getExtension");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::isBlank(string fileName){
+ try {
+
+ fileName = getFullPathName(fileName);
+
+ ifstream fileHandle;
+ fileHandle.open(fileName.c_str());
+ if(!fileHandle) {
+ mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
+ return false;
+ }else {
+ //check for blank file
+ gobble(fileHandle);
+ if (fileHandle.eof()) { fileHandle.close(); return true; }
+ fileHandle.close();
+ }
+ return false;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isBlank");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+string MothurOut::getFullPathName(string fileName){
+ try{
+
+ string path = hasPath(fileName);
+ string newFileName;
+ int pos;
+
+ if (path == "") { return fileName; } //its a simple name
+ else { //we need to complete the pathname
+ // ex. ../../../filename
+ // cwd = /user/work/desktop
+
+ string cwd;
+ //get current working directory
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir;
+
+ char *homepath = NULL;
+ homepath = getenv ("HOME");
+ if ( homepath != NULL) { homeDir = homepath; }
+ else { homeDir = ""; }
+
+ newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+ return newFileName;
+ }else { //find path
+ if (path.rfind("./") == string::npos) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
+
+ //char* cwdpath = new char[1024];
+ //size_t size;
+ //cwdpath=getcwd(cwdpath,size);
+ //cwd = cwdpath;
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
+
+
+ //rip off first '/'
+ string simpleCWD;
+ if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+
+ //break apart the current working directory
+ vector<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(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 0;
+
+ }
+ 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 0;
+
+ }
+ 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 >> 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::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