X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=a56a6217a8c136e1fcb9f3f3078c5418547220fa;hb=75962c819c16814e5c2340d99af1aa62e564dc20;hp=27b36ce5ff83dceadeb77e84045caef94d5168c9;hpb=73fb1fe84d565ea9a0ff793de990546b177310c8;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 27b36ce..a56a621 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -18,6 +18,103 @@ MothurOut* MothurOut::getInstance() { 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; @@ -150,6 +247,53 @@ void MothurOut::mothurOutEndLine() { } } /*********************************************************************************************/ +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 + + cout << output; + out << output; + outputFile << 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 + + cout << endl; + out << endl; + outputFile << endl; + +#ifdef USE_MPI + } +#endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutEndLine"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::mothurOutJustToLog(string output) { try { #ifdef USE_MPI @@ -341,12 +485,12 @@ string MothurOut::getline(ifstream& fileHandle) { string line = ""; - while (!fileHandle.eof()) { + while (fileHandle) { //get next character char c = fileHandle.get(); //are you at the end of the line - if ((c == '\n') || (c == '\r') || (c == '\f')){ break; } + if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; } else { line += c; } } @@ -1057,7 +1201,43 @@ vector MothurOut::divideFile(string filename, int& proc) { exit(1); } } - +/**************************************************************************************************/ +int MothurOut::divideFile(string filename, int& proc, vector& files) { + try{ + + vector 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 int 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){ @@ -1096,6 +1276,99 @@ float MothurOut::ceilDist(float dist, int precision){ exit(1); } } +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map& 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); + } +} + +/**********************************************************************************************************************/ +map MothurOut::readNames(string namefile) { + try { + + map 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& nameVector, map& 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::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); + } +} /***********************************************************************/ @@ -1643,7 +1916,23 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) { 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); + } +} /**************************************************************************************************/