X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=54cf25d891e4528b1a6c1f08bc350a58b8aeb9e6;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=5c5fd373a32cbb233fb9a76dd81de87c54cb80eb;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 5c5fd37..54cf25d 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -9,6 +9,7 @@ #include "mothurout.h" + /******************************************************/ MothurOut* MothurOut::getInstance() { if( _uniqueInstance == 0) { @@ -60,6 +61,16 @@ void MothurOut::setDefaultPath(string pathname) { } } /*********************************************************************************************/ +void MothurOut::setOutputDir(string pathname) { + try { + outputDir = pathname; + } + catch(exception& e) { + errorOut(e, "MothurOut", "setOutputDir"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::closeLog() { try { @@ -257,6 +268,8 @@ int MothurOut::mem_usage(double& vm_usage, double& resident_set) { /***********************************************************************/ 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(); @@ -274,8 +287,9 @@ int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){ /***********************************************************************/ void MothurOut::gobble(istream& f){ try { + char d; - while(isspace(d=f.get())) {;} + while(isspace(d=f.get())) { ;} f.putback(d); } catch(exception& e) { @@ -346,14 +360,32 @@ string MothurOut::getline(ifstream& fileHandle) { } /***********************************************************************/ +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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(longName.find_last_of(".") != longName.npos){ - int pos = longName.find_last_of('.')+1; - rootName = longName.substr(0, pos); + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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; @@ -445,6 +477,9 @@ string MothurOut::getExtension(string longName){ /***********************************************************************/ bool MothurOut::isBlank(string fileName){ try { + + fileName = getFullPathName(fileName); + ifstream fileHandle; fileHandle.open(fileName.c_str()); if(!fileHandle) { @@ -454,6 +489,7 @@ bool MothurOut::isBlank(string fileName){ //check for blank file gobble(fileHandle); if (fileHandle.eof()) { fileHandle.close(); return true; } + fileHandle.close(); } return false; } @@ -481,19 +517,29 @@ string MothurOut::getFullPathName(string fileName){ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if (path.find("~") != -1) { //go to home directory - string homeDir = getenv ("HOME"); + 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("./") == -1) { return fileName; } //already complete name + 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]; + //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 = ""; } - size_t size; - cwdpath=getcwd(cwdpath,size); - - cwd = cwdpath; //rip off first '/' string simpleCWD; @@ -501,7 +547,7 @@ string MothurOut::getFullPathName(string fileName){ //break apart the current working directory vector dirs; - while (simpleCWD.find_first_of('/') != -1) { + 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); @@ -512,7 +558,7 @@ string MothurOut::getFullPathName(string fileName){ int index = dirs.size()-1; - while((pos = path.rfind("./")) != -1) { //while you don't have a complete path + 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); @@ -532,12 +578,12 @@ string MothurOut::getFullPathName(string fileName){ return newFileName; } #else - if (path.find("~") != -1) { //go to home directory + 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(".\\") == -1) { return fileName; } //already complete name + 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; @@ -558,7 +604,7 @@ string MothurOut::getFullPathName(string fileName){ int index = dirs.size()-1; - while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path + 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); @@ -591,9 +637,33 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ try { //get full path name string completeFileName = getFullPathName(fileName); - +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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"; + remove(tempName.c_str()); + 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 @@ -610,8 +680,33 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ try { + //get full path name string completeFileName = getFullPathName(fileName); +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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"; + remove(tempName.c_str()); + exit(EXIT_SUCCESS); + } else { + cerr << "waiting on child process " << fork_result << "\n"; + completeFileName = tempName; + } + } +#endif +#endif fileHandle.open(completeFileName.c_str()); if(!fileHandle) { @@ -666,7 +761,27 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ try { string completeFileName = getFullPathName(fileName); - +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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(); @@ -692,6 +807,7 @@ void MothurOut::appendFiles(string temp, string filename) { //open output file in append mode openOutputFileAppend(filename, output); int ableToOpen = openInputFile(temp, input, "no error"); + //int ableToOpen = openInputFile(temp, input); if (ableToOpen == 0) { //you opened it while(char c = input.get()){ @@ -829,7 +945,8 @@ vector MothurOut::setFilePosFasta(string filename, int& num) /**************************************************************************************************/ vector MothurOut::setFilePosEachLine(string filename, int& num) { try { - + filename = getFullPathName(filename); + vector positions; ifstream in; openInputFile(filename, in); @@ -851,7 +968,7 @@ vector MothurOut::setFilePosEachLine(string filename, int& nu FILE * pFile; unsigned long int size; - + //get num bytes in file pFile = fopen (filename.c_str(),"rb"); if (pFile==NULL) perror ("Error opening file"); @@ -881,6 +998,8 @@ vector MothurOut::divideFile(string filename, int& proc) { FILE * pFile; unsigned long int size; + filename = getFullPathName(filename); + //get num bytes in file pFile = fopen (filename.c_str(),"rb"); if (pFile==NULL) perror ("Error opening file"); @@ -893,7 +1012,7 @@ vector MothurOut::divideFile(string filename, int& proc) { //estimate file breaks unsigned long int chunkSize = 0; chunkSize = size / proc; - + //file to small to divide by processors if (chunkSize == 0) { proc = 1; filePos.push_back(size); return filePos; } @@ -911,18 +1030,19 @@ vector MothurOut::divideFile(string filename, int& proc) { char c = in.get(); if (c == '>') { in.putback(c); newSpot = in.tellg(); break; } } - + //there was not another sequence before the end of the file unsigned long int sanityPos = in.tellg(); - if (sanityPos = -1) { break; } - else { filePos.push_back(newSpot); } + + 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--; } @@ -1036,7 +1156,90 @@ vector > MothurOut::binomial(int maxOrder){ exit(1); } } - +/**************************************************************************************************/ +unsigned int MothurOut::fromBase36(string base36){ + try { + unsigned int num = 0; + + map converts; + converts['A'] = 0; + converts['a'] = 0; + converts['B'] = 1; + converts['b'] = 1; + converts['C'] = 2; + converts['c'] = 2; + converts['D'] = 3; + converts['d'] = 3; + converts['E'] = 4; + converts['e'] = 4; + converts['F'] = 5; + converts['f'] = 5; + converts['G'] = 6; + converts['g'] = 6; + converts['H'] = 7; + converts['h'] = 7; + converts['I'] = 8; + converts['i'] = 8; + converts['J'] = 9; + converts['j'] = 9; + converts['K'] = 10; + converts['k'] = 10; + converts['L'] = 11; + converts['l'] = 11; + converts['M'] = 12; + converts['m'] = 12; + converts['N'] = 13; + converts['n'] = 13; + converts['O'] = 14; + converts['o'] = 14; + converts['P'] = 15; + converts['p'] = 15; + converts['Q'] = 16; + converts['q'] = 16; + converts['R'] = 17; + converts['r'] = 17; + converts['S'] = 18; + converts['s'] = 18; + converts['T'] = 19; + converts['t'] = 19; + converts['U'] = 20; + converts['u'] = 20; + converts['V'] = 21; + converts['v'] = 21; + converts['W'] = 22; + converts['w'] = 22; + converts['X'] = 23; + converts['x'] = 23; + converts['Y'] = 24; + converts['y'] = 24; + converts['Z'] = 25; + converts['z'] = 25; + converts['0'] = 26; + converts['1'] = 27; + converts['2'] = 28; + converts['3'] = 29; + converts['4'] = 30; + converts['5'] = 31; + converts['6'] = 32; + converts['7'] = 33; + converts['8'] = 34; + converts['9'] = 35; + + int i = 0; + while (i < base36.length()) { + char c = base36[i]; + num = 36 * num + converts[c]; + i++; + } + + return num; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "fromBase36"); + exit(1); + } +} /***********************************************************************/ int MothurOut::factorial(int num){ @@ -1089,17 +1292,19 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){ //This function parses the estimator options and puts them in a vector void MothurOut::splitAtChar(string& estim, vector& container, char symbol) { try { - string individual; - - while (estim.find_first_of(symbol) != -1) { - individual = estim.substr(0,estim.find_first_of(symbol)); - if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string - estim = estim.substr(estim.find_first_of(symbol)+1, estim.length()); + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container, char symbo //This function parses the estimator options and puts them in a vector void MothurOut::splitAtDash(string& estim, vector& container) { try { - string individual; + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container) { } } //get last one - container.push_back(estim); + container.push_back(estim); */ } catch(exception& e) { errorOut(e, "MothurOut", "splitAtDash"); @@ -1134,17 +1353,31 @@ void MothurOut::splitAtDash(string& estim, vector& container) { //This function parses the label options and puts them in a set void MothurOut::splitAtDash(string& estim, set& container) { try { - 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()); + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container) { //This function parses the a string and puts peices in a vector void MothurOut::splitAtComma(string& estim, vector& container) { try { - 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()); + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& userLabels, string } //go through users set and make them floats - for(it = userLabels.begin(); it != userLabels.end(); ++it) { + 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 == "") { cout << *it << " is not a valid label." << endl; } - userLabels.erase(*it); - it--; + if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); } + userLabels.erase(it++); } } @@ -1319,11 +1569,11 @@ bool MothurOut::anyLabelsToProcess(string label, set& userLabels, string if (orderFloat[i] < labelFloat) { smaller = true; if (orderFloat[i] == -1) { - if (errorOff == "") { cout << "Your file does not include the label unique." << endl; } + if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); } userLabels.erase("unique"); } else { - if (errorOff == "") { cout << "Your file does not include the label " << endl; } + 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]) { @@ -1333,7 +1583,7 @@ bool MothurOut::anyLabelsToProcess(string label, set& userLabels, string break; } } - if (errorOff == "") {cout << s << ". I will use the next smallest distance. " << endl; } + 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; } @@ -1393,6 +1643,7 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) { exit(1); } } + /**************************************************************************************************/