X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=b30ee3ca630c91fea01343c9d873e709e027a4fb;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=88a18ed452314c38c5d2cf6909ea44db465d61af;hpb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 88a18ed..b30ee3c 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 { @@ -276,8 +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) { @@ -348,14 +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; @@ -486,19 +516,29 @@ 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; @@ -506,7 +546,7 @@ 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); @@ -517,7 +557,7 @@ 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); @@ -537,12 +577,12 @@ 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; @@ -563,7 +603,7 @@ 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); @@ -596,9 +636,33 @@ 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 @@ -615,8 +679,33 @@ 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) { @@ -671,7 +760,27 @@ 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(); @@ -697,6 +806,7 @@ 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()){ @@ -901,7 +1011,7 @@ 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; } @@ -919,7 +1029,7 @@ 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(); @@ -1098,7 +1208,20 @@ 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; + string individual = ""; + int estimLength = estim.size(); + for(int i=0;i& container, char symbo } } //get last one - container.push_back(estim); + container.push_back(estim); */ } catch(exception& e) { errorOut(e, "MothurOut", "splitAtChar"); @@ -1343,20 +1466,21 @@ bool MothurOut::anyLabelsToProcess(string label, set& 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++); } } @@ -1372,11 +1496,11 @@ 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]) { @@ -1386,7 +1510,7 @@ 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; } @@ -1446,6 +1570,7 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) { exit(1); } } + /**************************************************************************************************/