X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=114f545aa26eb326f078b6ab7e1b18e024ecdcb5;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=9866753329374dc768433488a7d4943555bb1b77;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp index 9866753..114f545 100644 --- a/pairwiseseqscommand.cpp +++ b/pairwiseseqscommand.cpp @@ -99,6 +99,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -141,48 +142,65 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { //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 = 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]; } - } - - int ableToOpen; - ifstream in; - - 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() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; + bool ignore = false; + if (fastaFileNames[i] == "current") { + fastaFileNames[i] = m->getFastaFile(); + if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - //if you can't open it, try output location - if (ableToOpen == 1) { - if (m->getOutputDir() != "") { //default path is set - string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; - } - } + if (!ignore) { - in.close(); + if (inputDir != "") { + 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]; } + } + + int ableToOpen; + ifstream in; - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - fastaFileNames.erase(fastaFileNames.begin()+i); - i--; + 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() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + //if you can't open it, try output location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + }else { + m->setFastaFile(fastaFileNames[i]); + } } } @@ -194,23 +212,23 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { // ...at some point should added some additional type checking... string temp; temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; } - convert(temp, match); + m->mothurConvert(temp, match); temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; } - convert(temp, misMatch); + m->mothurConvert(temp, misMatch); temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; } - convert(temp, gapOpen); + m->mothurConvert(temp, gapOpen); temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; } - convert(temp, gapExtend); + m->mothurConvert(temp, gapExtend); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; } countends = m->isTrue(temp); @@ -294,14 +312,14 @@ int PairwiseSeqsCommand::execute(){ if (output == "lt") { //does the user want lower triangle phylip formatted file outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist"; - remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile); + m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); }else if (output == "column") { //user wants column format outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist"; outputTypes["column"].push_back(outputFile); - remove(outputFile.c_str()); + m->mothurRemove(outputFile); }else { //assume square outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist"; - remove(outputFile.c_str()); + m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); } @@ -339,11 +357,11 @@ int PairwiseSeqsCommand::execute(){ driverMPI(start, end, outMPI, cutoff); - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; } //wait on chidren for(int i = 1; i < processors; i++) { - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; } char buf[5]; MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); @@ -352,7 +370,7 @@ int PairwiseSeqsCommand::execute(){ //do your part driverMPI(start, end, outMPI, cutoff); - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; } char buf[5]; strcpy(buf, "done"); @@ -367,12 +385,12 @@ int PairwiseSeqsCommand::execute(){ //do your part string outputMyPart; - unsigned long int mySize; + unsigned long long mySize; if (output != "square"){ driverMPI(start, end, outputFile, mySize); } else { driverMPI(start, end, outputFile, mySize, output); } - if (m->control_pressed) { outputTypes.clear(); remove(outputFile.c_str()); delete distCalculator; return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); delete distCalculator; return 0; } int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; // MPI_File outMPI; @@ -385,9 +403,9 @@ int PairwiseSeqsCommand::execute(){ //wait on chidren for(int b = 1; b < processors; b++) { - unsigned long int fileSize; + unsigned long long fileSize; - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; } MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); @@ -413,7 +431,7 @@ int PairwiseSeqsCommand::execute(){ MPI_File_close(&outMPI); }else { //you are a child process //do your part - unsigned long int size; + unsigned long long size; if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); } else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); } @@ -454,7 +472,7 @@ int PairwiseSeqsCommand::execute(){ #endif #endif - if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; } #ifdef USE_MPI MPI_Comm_rank(MPI_COMM_WORLD, &pid); @@ -482,7 +500,7 @@ int PairwiseSeqsCommand::execute(){ m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; } } delete distCalculator; @@ -553,7 +571,7 @@ void PairwiseSeqsCommand::createProcesses(string filename) { //append and remove temp files for (int i=0;iappendFiles((filename + toString(processIDS[i]) + ".temp"), filename); - remove((filename + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((filename + toString(processIDS[i]) + ".temp")); } #endif } @@ -764,7 +782,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, } /**************************************************************************************************/ /////// need to fix to work with calcs and sequencedb -int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){ +int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){ try { MPI_Status status; @@ -840,7 +858,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi } /**************************************************************************************************/ /////// need to fix to work with calcs and sequencedb -int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){ +int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){ try { MPI_Status status;