X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=c8761b9bd51ea60fed4e9f5bc1636a8b0afb1987;hb=2c5386dc0cb6a0e42e8d7256bd6fb18ab66e4480;hp=de6f438d81f7fcd62e111d97a02e87d63aad1e66;hpb=b45e6f3d505a212cebad5ca22e2611b1466bca48;p=mothur.git diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp index de6f438..c8761b9 100644 --- a/chimeracheckcommand.cpp +++ b/chimeracheckcommand.cpp @@ -41,7 +41,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { it = parameters.find("template"); //user has given a template file if(it != parameters.end()){ - string path = hasPath(it->second); + string path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["template"] = inputDir + it->second; } } @@ -51,12 +51,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { fastafile = validParameter.validFile(parameters, "fasta", false); if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(fastafile, fastaFileNames); + m->splitAtDash(fastafile, fastaFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < fastaFileNames.size(); i++) { if (inputDir != "") { - string path = hasPath(fastaFileNames[i]); + string path = m->hasPath(fastaFileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } } @@ -64,14 +64,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { int ableToOpen; ifstream in; - ableToOpen = openInputFile(fastaFileNames[i], in, "noerror"); + ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); //if you can't open it, try default location if (ableToOpen == 1) { if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ableToOpen = m->openInputFile(tryPath, in, "noerror"); fastaFileNames[i] = tryPath; } } @@ -99,12 +99,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { namefile = validParameter.validFile(parameters, "name", false); if (namefile == "not found") { namefile = ""; } else { - splitAtDash(namefile, nameFileNames); + m->splitAtDash(namefile, nameFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < nameFileNames.size(); i++) { if (inputDir != "") { - string path = hasPath(nameFileNames[i]); + string path = m->hasPath(nameFileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } } @@ -112,14 +112,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { int ableToOpen; ifstream in; - ableToOpen = openInputFile(nameFileNames[i], in, "noerror"); + ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror"); //if you can't open it, try default location if (ableToOpen == 1) { if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + getSimpleName(nameFileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]); m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ableToOpen = m->openInputFile(tryPath, in, "noerror"); nameFileNames[i] = tryPath; } } @@ -150,7 +150,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { convert(temp, ksize); temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } - svg = isTrue(temp); + svg = m->isTrue(temp); if (nameFileNames.size() != 0) { svg = true; } temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } @@ -217,7 +217,8 @@ int ChimeraCheckCommand::execute(){ if (m->control_pressed) { delete chimera; return 0; } - string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; outputNames.push_back(outputFileName); #ifdef USE_MPI @@ -248,7 +249,7 @@ int ChimeraCheckCommand::execute(){ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int j = 1; j < processors; j++) { @@ -299,7 +300,7 @@ int ChimeraCheckCommand::execute(){ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastaFileNames[i], processors); + vector positions = m->divideFile(fastaFileNames[i], processors); for (int s = 0; s < (positions.size()-1); s++) { lines.push_back(new linePair(positions[s], positions[(s+1)])); @@ -321,7 +322,7 @@ int ChimeraCheckCommand::execute(){ //append output files for(int j=1;jappendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName); remove((outputFileName + toString(processIDS[j]) + ".temp").c_str()); } @@ -365,12 +366,12 @@ int ChimeraCheckCommand::execute(){ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){ try { ofstream out; - openOutputFile(outputFName, out); + m->openOutputFile(outputFName, out); ofstream out2; ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); inFASTA.seekg(filePos->start); @@ -381,7 +382,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi if (m->control_pressed) { return 1; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file //find chimeras @@ -394,8 +395,12 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi } delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + #else + if (inFASTA.eof()) { break; } + #endif //report progress if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } @@ -437,7 +442,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File istringstream iss (tempBuf,istringstream::in); delete buf4; - Sequence* candidateSeq = new Sequence(iss); gobble(iss); + Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file //find chimeras @@ -484,7 +489,7 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) //pass numSeqs to parent ofstream out; string tempFile = outputFileName + toString(getpid()) + ".num.temp"; - openOutputFile(tempFile, out); + m->openOutputFile(tempFile, out); out << num << endl; out.close(); @@ -501,7 +506,7 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) for (int i = 0; i < processIDS.size(); i++) { ifstream in; string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp"; - openInputFile(tempFile, in); + m->openInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } in.close(); remove(tempFile.c_str()); }