X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=61b39514e43b79bc146eb3e37ed4dc8d41017a62;hb=ccf2fedbb600a362777a11501bb56c9c7746068e;hp=9dcdc80e761f1483059297dbcd996a0a06b43e5b;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 9dcdc80..61b3951 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -40,6 +40,7 @@ void MothurOut::printCurrentFiles() { 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(); } } @@ -73,6 +74,7 @@ bool MothurOut::hasCurrentFiles() { if (taxonomyfile != "") { return true; } if (treefile != "") { return true; } if (flowfile != "") { return true; } + if (biomfile != "") { return true; } if (processors != "1") { return true; } return hasCurrent; @@ -107,6 +109,7 @@ void MothurOut::clearCurrentFiles() { accnosfile = ""; taxonomyfile = ""; flowfile = ""; + biomfile = ""; processors = "1"; } catch(exception& e) { @@ -143,7 +146,7 @@ void MothurOut::setDefaultPath(string pathname) { //add / to name if needed string lastChar = pathname.substr(pathname.length()-1); - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if (lastChar != "/") { pathname += "/"; } #else if (lastChar != "\\") { pathname += "\\"; } @@ -212,8 +215,8 @@ void MothurOut::mothurOut(string output) { if (pid == 0) { //only one process should output to screen #endif - cout << output; out << output; + logger() << output; #ifdef USE_MPI } @@ -234,8 +237,8 @@ void MothurOut::mothurOutEndLine() { if (pid == 0) { //only one process should output to screen #endif - cout << endl; out << endl; + logger() << endl; #ifdef USE_MPI } @@ -257,13 +260,15 @@ void MothurOut::mothurOut(string output, ofstream& outputFile) { if (pid == 0) { //only one process should output to screen #endif - cout << output; + out << output; outputFile << output; + logger() << output; #ifdef USE_MPI } #endif + } catch(exception& e) { errorOut(e, "MothurOut", "MothurOut"); @@ -280,9 +285,9 @@ void MothurOut::mothurOutEndLine(ofstream& outputFile) { if (pid == 0) { //only one process should output to screen #endif - cout << endl; out << endl; outputFile << endl; + logger() << endl; #ifdef USE_MPI } @@ -332,7 +337,7 @@ void MothurOut::errorOut(exception& e, string object, string function) { // // On failure, returns 0.0, 0.0 int MothurOut::mem_usage(double& vm_usage, double& resident_set) { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) vm_usage = 0.0; resident_set = 0.0; @@ -504,7 +509,7 @@ string MothurOut::getline(ifstream& fileHandle) { } /***********************************************************************/ -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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); @@ -518,7 +523,7 @@ string MothurOut::getRootName(string longName){ string rootName = longName; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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('.'); @@ -596,6 +601,48 @@ string MothurOut::getPathName(string longName){ } /***********************************************************************/ +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 = ""; @@ -619,7 +666,7 @@ string MothurOut::hasPath(string longName){ string MothurOut::getExtension(string longName){ try { - string extension = longName; + string extension = ""; if(longName.find_last_of('.') != longName.npos){ int pos = longName.find_last_of('.'); @@ -673,7 +720,7 @@ string MothurOut::getFullPathName(string fileName){ string cwd; //get current working directory - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if (path.find("~") != -1) { //go to home directory string homeDir; @@ -726,7 +773,7 @@ string MothurOut::getFullPathName(string fileName){ }else if (path[(pos-1)] == '/') { //you want the current working dir ./ path = path.substr(0, pos); }else if (pos == 1) { break; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } } for (int i = index; i >= 0; i--) { @@ -772,7 +819,7 @@ string MothurOut::getFullPathName(string fileName){ }else if (path[(pos-1)] == '\\') { //you want the current working dir ./ path = path.substr(0, pos); }else if (pos == 1) { break; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } } for (int i = index; i >= 0; i--) { @@ -796,7 +843,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ try { //get full path name string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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")) { @@ -842,7 +889,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ //get full path name string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#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")) { @@ -893,7 +940,7 @@ int MothurOut::renameFile(string oldName, string newName){ int exist = openInputFile(newName, inTest, ""); inTest.close(); - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #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()); @@ -920,7 +967,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ try { string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION // check for gzipped file if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { @@ -970,7 +1017,8 @@ int MothurOut::appendFiles(string temp, string filename) { int numLines = 0; if (ableToOpen == 0) { //you opened it - while(char c = input.get()){ + while(!input.eof()){ + char c = input.get(); if(input.eof()) { break; } else { output << c; if (c == '\n') {numLines++;} } } @@ -996,7 +1044,7 @@ string MothurOut::sortFile(string distFile, string outputDir){ //if you can, use the unix sort since its been optimized for years - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #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... @@ -1151,7 +1199,7 @@ vector MothurOut::setFilePosEachLine(string filename, int& n while(isspace(d) && (d != in.eof())) { d=in.get(); count++;} } positions.push_back(count-1); - cout << count-1 << endl; + //cout << count-1 << endl; } in.close(); @@ -1199,7 +1247,7 @@ vector MothurOut::divideFile(string filename, int& proc) { fclose (pFile); } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //estimate file breaks unsigned long long chunkSize = 0; @@ -1349,7 +1397,7 @@ int MothurOut::readNames(string namefile, map& nameMap) { } in.close(); - return 0; + return nameMap.size(); } catch(exception& e) { @@ -1378,7 +1426,7 @@ int MothurOut::readNames(string namefile, map >& nameMap) } in.close(); - return 0; + return nameMap.size(); } catch(exception& e) { @@ -1400,7 +1448,8 @@ map MothurOut::readNames(string namefile) { if (control_pressed) { break; } string firstCol, secondCol; - in >> firstCol >> secondCol; gobble(in); + in >> firstCol; gobble(in); + in >> secondCol; gobble(in); int num = getNumNames(secondCol); @@ -1880,6 +1929,26 @@ void MothurOut::splitAtDash(string& estim, set& container) { exit(1); } } +/***********************************************************************/ +string MothurOut::makeList(vector& names) { + try { + string list = ""; + + if (names.size() == 0) { return list; } + + for (int i = 0; i < names.size()-1; i++) { list += names[i] + ","; } + + //get last name + list += names[names.size()-1]; + + return list; + } + catch(exception& e) { + errorOut(e, "MothurOut", "makeList"); + exit(1); + } +} + /***********************************************************************/ //This function parses the a string and puts peices in a vector void MothurOut::splitAtComma(string& estim, vector& container) { @@ -1917,6 +1986,25 @@ void MothurOut::splitAtComma(string& estim, vector& container) { 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 @@ -2152,7 +2240,7 @@ int MothurOut::removeConfidences(string& tax) { int pos2 = taxon.find_last_of(')'); if (pos2 != -1) { string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1))); - if (isContainingOnlyDigits(confidenceScore)) { + if (isNumeric1(confidenceScore)) { taxon = taxon.substr(0, pos); //rip off confidence } }