List of usage examples for java.lang Exception Exception
public Exception(Throwable cause)
From source file:BrokerFrame.java
/** * @param args the command line arguments *///from w w w. j a va2 s . c om public static void main(String args[]) throws Exception { /* Set the Nimbus look and feel */ //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) "> /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel. * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html */ try { for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) { if ("Nimbus".equals(info.getName())) { javax.swing.UIManager.setLookAndFeel(info.getClassName()); break; } } } catch (ClassNotFoundException ex) { java.util.logging.Logger.getLogger(BrokerFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (InstantiationException ex) { java.util.logging.Logger.getLogger(BrokerFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (IllegalAccessException ex) { java.util.logging.Logger.getLogger(BrokerFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (javax.swing.UnsupportedLookAndFeelException ex) { java.util.logging.Logger.getLogger(BrokerFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } //</editor-fold> String ola = new String(); ola = "olajjhgjhhjkhjkhjhkjhjhgg"; RSA rs = new RSA(); rs.generateKeys(); System.out.println((RSA.privKey).toString()); byte[] signature = rs.encrypt(ola, RSA.privKey); String sig = new Base64().encodeAsString(signature); byte[] byt = new Base64().decode(sig); System.out.println(sig); try { rs.verifySignature(ola.getBytes(), signature); } catch (Exception e) { throw new Exception(e); } /* Create and display the form */ java.awt.EventQueue.invokeLater(new Runnable() { public void run() { new BrokerFrame().setVisible(true); } }); }
From source file:edu.msu.cme.rdp.readseq.utils.RmDupSeqs.java
public static void main(String[] args) throws Exception { String inFile;/*from w w w . j a va2s.c o m*/ String outFile; int length = 0; boolean debug = false; boolean removeDuplicates = false; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("duplicates")) { removeDuplicates = true; } if (line.hasOption("min_seq_length")) { length = Integer.parseInt(line.getOptionValue("min_seq_length")); } if (line.hasOption("infile")) { inFile = line.getOptionValue("infile"); } else { throw new Exception("infile is required"); } if (line.hasOption("outfile")) { outFile = line.getOptionValue("outfile"); } else { throw new Exception("outfile is required"); } if (line.hasOption("debug")) { debug = true; } } catch (Exception e) { new HelpFormatter().printHelp(120, "RmRedundantSeqs [options]", "", options, ""); System.err.println("ERROR: " + e.getMessage()); return; } if (!removeDuplicates) { filterByLength(inFile, outFile, length); } else { filterDuplicates(inFile, outFile, length, debug); } }
From source file:edu.msu.cme.rdp.probematch.cli.SliceToPrimer.java
public static void main(String[] args) throws Exception { //args = "--fedit-dist 4 --redit-dist=4 -k --max-length=400 --min-length=280 -o java_sliced_edit4.fasta TGCGAYCCSAARGCBGACTC ATSGCCATCATYTCRCCGGA /scratch/fishjord/tae_kwon_primer_match/all_genomes.fasta".split(" "); PatternBitMask64[] fprimers;/*w ww. j av a 2s.c om*/ String[] fprimerStrs, rprimerStrs; PatternBitMask64[] rprimers; FastaWriter seqOut; PrintStream statsOut; int fEdit = 3; int rEdit = 3; int minLength = Integer.MIN_VALUE; int maxLength = Integer.MAX_VALUE; boolean allowAmbiguities = true; boolean keepPrimers = false; SequenceReader inSeqs; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("edit-dist")) { fEdit = rEdit = Integer.parseInt(line.getOptionValue("edit-dist")); if (line.hasOption("redit-dist") || line.hasOption("fedit-dist")) { throw new Exception("edit-dist, [fedit-dist, redit-dist] are mutually exclusive"); } } if (line.hasOption("fedit-dist")) { fEdit = Integer.parseInt(line.getOptionValue("fedit-dist")); } if (line.hasOption("no-ambiguities")) { allowAmbiguities = false; } if (line.hasOption("keep-primers")) { keepPrimers = true; } if (line.hasOption("redit-dist")) { rEdit = Integer.parseInt(line.getOptionValue("redit-dist")); } if (line.hasOption("seq-out")) { seqOut = new FastaWriter(new File(line.getOptionValue("seq-out"))); } else { throw new Exception("Must specify seq-out"); } if (line.hasOption("stats-out")) { statsOut = new PrintStream(new File(line.getOptionValue("stats-out"))); } else { statsOut = System.out; } if (line.hasOption("min-length")) { minLength = Integer.parseInt(line.getOptionValue("min-length")); } if (line.hasOption("max-length")) { maxLength = Integer.parseInt(line.getOptionValue("max-length")); } args = line.getArgs(); if (args.length != 3) { throw new Exception("Unexpected number of command line arguments"); } fprimers = translateStringPrimers(args[0].split(","), allowAmbiguities, false); fprimerStrs = args[0].split(","); rprimers = translateStringPrimers(args[1].split(","), allowAmbiguities, true); rprimerStrs = args[1].split(","); inSeqs = new SequenceReader(new File(args[2])); } catch (Exception e) { new HelpFormatter().printHelp("SliceToPrimer [options] <f,p,r,i,m,e,r> <r,p,r,i,m,e,r> <in_seq_file>", options); System.err.println("ERROR: " + e.getMessage()); return; } Sequence seq; statsOut.println( "orig_seqid\tsliced_seqid\tfprimer\tstart\tend\tscore\trprimer\tstart\tend\tscore\tlength"); ScoringMatrix sccoringMatrix = ScoringMatrix.getDefaultNuclMatrix(); DPMAligner[] faligners = new DPMAligner[fprimers.length]; for (int index = 0; index < faligners.length; index++) { faligners[index] = new DPMAligner(fprimerStrs[index], Integer.MAX_VALUE); } try { while ((seq = inSeqs.readNextSequence()) != null) { Set<PrimerMatch> fprimerMatches = new HashSet(); Set<PrimerMatch> rprimerMatches = new HashSet(); for (int index = 0; index < fprimers.length; index++) { PatternBitMask64 primer = fprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, fEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; fprimerMatches.add(match); } } for (int index = 0; index < rprimers.length; index++) { PatternBitMask64 primer = rprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, rEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; rprimerMatches.add(match); } } if (fprimerMatches.isEmpty() || rprimerMatches.isEmpty()) { statsOut.println(seq.getSeqName() + "\tEither/or no forward/reverse primer hits"); continue; } for (PrimerMatch fmatch : fprimerMatches) { PrimerMatch bestReverse = null; int bestScore = Integer.MAX_VALUE; for (PrimerMatch rmatch : rprimerMatches) { if (rmatch.start > fmatch.end && rmatch.start - fmatch.end < bestScore) { bestReverse = rmatch; bestScore = rmatch.start - fmatch.end; } } if (bestReverse == null) { statsOut.println(seq.getSeqName() + "\tNo reverse primer before " + fmatch.end); continue; } String slicedSeq = null; if (keepPrimers) { slicedSeq = seq.getSeqString().substring(fmatch.start, bestReverse.end); } else { slicedSeq = seq.getSeqString().substring(fmatch.end, bestReverse.start); } String seqid = seq.getSeqName() + "_" + fmatch.primerIndex + "_" + fmatch.start; if (slicedSeq.length() > minLength && slicedSeq.length() < maxLength) { seqOut.writeSeq(seqid, "", slicedSeq); } DPMAlignment seqs = faligners[fmatch.primerIndex] .align(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(">" + seqid); System.err.println(fprimerStrs[fmatch.primerIndex]); System.err.println(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(); System.err.println(seqs.getAlignedMatchFragment()); System.err.println(seqs.getAlignedProbe()); System.err.println(); statsOut.println(seq.getSeqName() + "\t" + seqid + "\t" + fmatch.primerIndex + "\t" + fmatch.start + "\t" + fmatch.end + "\t" + fmatch.score + "\t" + bestReverse.primerIndex + "\t" + bestReverse.start + "\t" + bestReverse.end + "\t" + bestReverse.score + "\t" + slicedSeq.length()); } } } catch (Exception e) { e.printStackTrace(); } finally { statsOut.close(); seqOut.close(); } }
From source file:edu.msu.cme.rdp.readseq.writers.StkWriter.java
public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("r", "removeref", false, "is set, do not write the GC reference sequences to output"); options.addOption("h", "header", true, "the header of the output file in case a differenet stk version, default is " + STK_HEADER); String header = STK_HEADER;//from w w w . j av a 2 s .c o m boolean removeRef = false; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("removeref")) { removeRef = true; } if (line.hasOption("header")) { header = line.getOptionValue("header"); } args = line.getArgs(); if (args.length < 2) { throw new Exception("Need input and output files"); } } catch (Exception e) { new HelpFormatter().printHelp("USAGE: to-stk <input-file> <out-file>", options); System.err.println("ERROR: " + e.getMessage()); System.exit(1); return; } SequenceReader reader = new SequenceReader(new File(args[0])); PrintStream out = new PrintStream(new File(args[1])); StkWriter writer = new StkWriter(reader, out, header); reader = new SequenceReader(new File(args[0])); Sequence seq; while ((seq = reader.readNextSequence()) != null) { if (seq.getSeqName().startsWith("#") && removeRef) { continue; } writer.writeSeq(seq); } writer.writeEndOfBlock(); writer.close(); reader.close(); }
From source file:com.tiempometa.thingmagic.ReadTest.java
public static void main(String argv[]) { // Program setup Reader r = null;//from w w w . ja v a 2 s . c om int nextarg = 0; boolean trace = false; if (argv.length < 1) usage(); if (argv[nextarg].equals("-v")) { trace = true; nextarg++; } // Create Reader object, connecting to physical device try { TagReadData[] tagReads; String uri = argv[nextarg]; System.out.println("Creating reader with " + uri); r = Reader.create(uri); System.out.println("Setting trace..."); // if (trace) { // setTrace(r, new String[] { "on" }); // } System.out.println("Connecting..."); r.connect(); System.out.println("Connected!"); if (Reader.Region.UNSPEC == (Reader.Region) r.paramGet("/reader/region/id")) { Reader.Region[] supportedRegions = (Reader.Region[]) r .paramGet(TMConstants.TMR_PARAM_REGION_SUPPORTEDREGIONS); if (supportedRegions.length < 1) { throw new Exception("Reader doesn't support any regions"); } else { r.paramSet("/reader/region/id", supportedRegions[0]); } } r.addReadListener(new TagReadListener()); int count = 0; while (runMe) { // Read tags tagReads = r.read(500); // Print tag reads Long password = null; Long killword = null; for (TagReadData tr : tagReads) { p(tr.toString()); try { String accessCode = readAccess(tr, r); password = Long.parseLong(accessCode, 16); p("Password " + password); p("--" + Long.toHexString(password)); accessCode = readKill(tr, r); killword = Long.parseLong(accessCode, 16); p("Killword " + killword); p("--" + Long.toHexString(killword)); // if (password == 0) { p("Setting password"); password = 0xAFCC01ACl; short[] access = new short[2]; access[1] = (short) 0x01AC; access[0] = (short) 0xAFCC; p("Setting password to "); for (short word : access) { System.out.printf("%04X", word); } p("\n"); writeAccess(access, tr, r); // } // if (killword == 0) { p("Setting killword"); killword = 0xADD001ACl; access = new short[2]; access[1] = (short) 0x01AC; access[0] = (short) 0xADD0; p("Setting killword to "); for (short word : access) { System.out.printf("%04X", word); } p("\n"); writeKill(access, tr, r); // } if (count < 10) { p("Waiting to lock " + (10 - count)); } else if (count == 10) { p("Locking..." + password.intValue()); p("--" + Long.toHexString(password)); lockTag(password.intValue(), new LockAction(LockAction.KILL_LOCK), tr, r); p("Locked kill"); lockTag(password.intValue(), new LockAction(LockAction.ACCESS_LOCK), tr, r); p("Locked access"); } else { p("Done with this tag"); } count++; } catch (ReaderException e) { System.out.println("Exception : " + e.getMessage()); killword = 0xADD001ACl; password = 0xAFCC01ACl; if (count < 20) { p("Waiting to unlock " + (20 - count)); } else if (count == 20) { p("Unlocking..."); p("Password :" + password.intValue()); p("--" + Integer.toHexString(password.intValue())); lockTag(password.intValue(), new LockAction(LockAction.ACCESS_UNLOCK), tr, r); p("Unlocked access"); lockTag(password.intValue(), new LockAction(LockAction.KILL_UNLOCK), tr, r); p("Unlocked kill"); p("***Unlocked"); p("Locking..."); p("Password :" + password.intValue()); lockTag(password.intValue(), new LockAction(LockAction.KILL_LOCK), tr, r); p("Locked kill"); lockTag(password.intValue(), new LockAction(LockAction.ACCESS_LOCK), tr, r); p("Locked access"); } else if (count == 30) { p("Killing"); p("Unlocking access"); lockTag(password.intValue(), new LockAction(LockAction.KILL_UNLOCK), tr, r); p("Issuing kill command"); killTag(killword.intValue(), tr, r); } else { p("Waiting to kill"); } count++; } } } // Shut down reader r.destroy(); } catch (ReaderException re) { System.out.println("Reader Exception : " + re.getMessage()); } catch (Exception re) { System.out.println("Exception : " + re.getLocalizedMessage()); System.out.println("Exception : " + re.getMessage()); } finally { r.destroy(); } }
From source file:edu.cmu.lti.oaqa.knn4qa.apps.QueryGenNMSLIB.java
public static void main(String[] args) { Options options = new Options(); options.addOption(CommonParams.QUERY_FILE_PARAM, null, true, CommonParams.QUERY_FILE_DESC); options.addOption(CommonParams.MEMINDEX_PARAM, null, true, CommonParams.MEMINDEX_DESC); options.addOption(CommonParams.KNN_QUERIES_PARAM, null, true, CommonParams.KNN_QUERIES_DESC); options.addOption(CommonParams.NMSLIB_FIELDS_PARAM, null, true, CommonParams.NMSLIB_FIELDS_DESC); options.addOption(CommonParams.MAX_NUM_QUERY_PARAM, null, true, CommonParams.MAX_NUM_QUERY_DESC); options.addOption(CommonParams.SEL_PROB_PARAM, null, true, CommonParams.SEL_PROB_DESC); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); BufferedWriter knnQueries = null; int maxNumQuery = Integer.MAX_VALUE; Float selProb = null;/* www . j av a 2s . c om*/ try { CommandLine cmd = parser.parse(options, args); String queryFile = null; if (cmd.hasOption(CommonParams.QUERY_FILE_PARAM)) { queryFile = cmd.getOptionValue(CommonParams.QUERY_FILE_PARAM); } else { Usage("Specify 'query file'", options); } String knnQueriesFile = cmd.getOptionValue(CommonParams.KNN_QUERIES_PARAM); if (null == knnQueriesFile) Usage("Specify '" + CommonParams.KNN_QUERIES_DESC + "'", options); String tmpn = cmd.getOptionValue(CommonParams.MAX_NUM_QUERY_PARAM); if (tmpn != null) { try { maxNumQuery = Integer.parseInt(tmpn); } catch (NumberFormatException e) { Usage("Maximum number of queries isn't integer: '" + tmpn + "'", options); } } String tmps = cmd.getOptionValue(CommonParams.NMSLIB_FIELDS_PARAM); if (null == tmps) Usage("Specify '" + CommonParams.NMSLIB_FIELDS_DESC + "'", options); String nmslibFieldList[] = tmps.split(","); knnQueries = new BufferedWriter(new FileWriter(knnQueriesFile)); knnQueries.write("isQueryFile=1"); knnQueries.newLine(); knnQueries.newLine(); String memIndexPref = cmd.getOptionValue(CommonParams.MEMINDEX_PARAM); if (null == memIndexPref) { Usage("Specify '" + CommonParams.MEMINDEX_DESC + "'", options); } String tmpf = cmd.getOptionValue(CommonParams.SEL_PROB_PARAM); if (tmpf != null) { try { selProb = Float.parseFloat(tmpf); } catch (NumberFormatException e) { Usage("A selection probability isn't a number in the range (0,1)'" + tmpf + "'", options); } if (selProb < Float.MIN_NORMAL || selProb + Float.MIN_NORMAL >= 1) Usage("A selection probability isn't a number in the range (0,1)'" + tmpf + "'", options); } BufferedReader inpText = new BufferedReader( new InputStreamReader(CompressUtils.createInputStream(queryFile))); String docText = XmlHelper.readNextXMLIndexEntry(inpText); NmslibQueryGenerator queryGen = new NmslibQueryGenerator(nmslibFieldList, memIndexPref); Random rnd = new Random(); for (int docNum = 1; docNum <= maxNumQuery && docText != null; ++docNum, docText = XmlHelper.readNextXMLIndexEntry(inpText)) { if (selProb != null) { if (rnd.nextFloat() > selProb) continue; } Map<String, String> docFields = null; try { docFields = XmlHelper.parseXMLIndexEntry(docText); String queryObjStr = queryGen.getStrObjForKNNService(docFields); knnQueries.append(queryObjStr); knnQueries.newLine(); } catch (SAXException e) { System.err.println("Parsing error, offending DOC:" + NL + docText + " doc # " + docNum); throw new Exception("Parsing error."); } } knnQueries.close(); } catch (ParseException e) { Usage("Cannot parse arguments", options); if (null != knnQueries) try { knnQueries.close(); } catch (IOException e1) { e1.printStackTrace(); } } catch (Exception e) { System.err.println("Terminating due to an exception: " + e); try { if (knnQueries != null) knnQueries.close(); } catch (IOException e1) { e1.printStackTrace(); } System.exit(1); } System.out.println("Terminated successfully!"); }
From source file:eu.annocultor.converter.Analyser.java
static public void main(String... args) throws Exception { // Handling command line parameters with Apache Commons CLI Options options = new Options(); options.addOption(OptionBuilder.withArgName(OPT_FN).hasArg().isRequired() .withDescription("XML file name to be analysed").withValueSeparator(',').create(OPT_FN)); options.addOption(OptionBuilder.withArgName(OPT_MAX_VALUE_SIZE).hasArg().withDescription( "Maximal size when values are counted separately. Longer values are counted altogether. Reasonable values are 100, 300, etc.") .create(OPT_MAX_VALUE_SIZE)); options.addOption(OptionBuilder.withArgName(OPT_VALUES).hasArg().withDescription( "Maximal number of most frequent values displayed in the report. Reasonable values are 10, 25, 50") .create(OPT_VALUES));/* w ww .j a v a 2 s . c om*/ // now lets parse the input CommandLineParser parser = new BasicParser(); CommandLine cmd; try { cmd = parser.parse(options, Utils.getCommandLineFromANNOCULTOR_ARGS(args)); } catch (ParseException pe) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("analyse", options); return; } MAX_VALUE_SIZE = Integer.parseInt(cmd.getOptionValue(OPT_MAX_VALUE_SIZE, Integer.toString(MAX_VALUE_SIZE))); MAX_VALUES = Integer.parseInt(cmd.getOptionValue(OPT_VALUES, Integer.toString(MAX_VALUES))); Analyser analyser = new Analyser(new EnvironmentImpl()); // undo: /* analyser.task.setSrcFiles(new File("."), cmd.getOptionValue(OPT_FN)); if (analyser.task.getSrcFiles().size() > 1) { analyser.task.mergeSourceFiles(); } if (analyser.task.getSrcFiles().size() == 0) { throw new Exception("No files to analyze, pattern " + cmd.getOptionValue(OPT_FN)); } File trg = new File(analyser.task.getSrcFiles().get(0).getParentFile(), "rdf"); if (!trg.exists()) trg.mkdir(); System.out.println("[Analysis] Analysing files " + cmd.getOptionValue(OPT_FN) + ", writing analysis to " + trg.getCanonicalPath() + ", max value length (long values are aggregated into one 'long value' value) " + MAX_VALUE_SIZE + ", number most fequently used values per field shown in report " + MAX_VALUES); */ if (true) throw new Exception("unimplemented"); System.exit(analyser.run()); }
From source file:edu.msu.cme.rdp.kmer.KmerFilter.java
public static void main(String[] args) throws Exception { final KmerTrie kmerTrie; final SeqReader queryReader; final SequenceType querySeqType; final File queryFile; final KmerStartsWriter out; final boolean translQuery; final int wordSize; final int translTable; final boolean alignedSeqs; final List<String> refLabels = new ArrayList(); final int maxThreads; try {/*from w w w.j a v a2s . c o m*/ CommandLine cmdLine = new PosixParser().parse(options, args); args = cmdLine.getArgs(); if (args.length < 3) { throw new Exception("Unexpected number of arguments"); } if (cmdLine.hasOption("out")) { out = new KmerStartsWriter(cmdLine.getOptionValue("out")); } else { out = new KmerStartsWriter(System.out); } if (cmdLine.hasOption("aligned")) { alignedSeqs = true; } else { alignedSeqs = false; } if (cmdLine.hasOption("transl-table")) { translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table")); } else { translTable = 11; } if (cmdLine.hasOption("threads")) { maxThreads = Integer.valueOf(cmdLine.getOptionValue("threads")); } else { maxThreads = Runtime.getRuntime().availableProcessors(); } queryFile = new File(args[1]); wordSize = Integer.valueOf(args[0]); SequenceType refSeqType = null; querySeqType = SeqUtils.guessSequenceType(queryFile); queryReader = new SequenceReader(queryFile); if (querySeqType == SequenceType.Protein) { throw new Exception("Expected nucl query sequences"); } refSeqType = SeqUtils .guessSequenceType(new File(args[2].contains("=") ? args[2].split("=")[1] : args[2])); translQuery = refSeqType == SequenceType.Protein; if (translQuery && wordSize % 3 != 0) { throw new Exception("Word size must be a multiple of 3 for nucl ref seqs"); } int trieWordSize; if (translQuery) { trieWordSize = wordSize / 3; } else { trieWordSize = wordSize; } kmerTrie = new KmerTrie(trieWordSize, translQuery); for (int index = 2; index < args.length; index++) { String refName; String refFileName = args[index]; if (refFileName.contains("=")) { String[] lexemes = refFileName.split("="); refName = lexemes[0]; refFileName = lexemes[1]; } else { String tmpName = new File(refFileName).getName(); if (tmpName.contains(".")) { refName = tmpName.substring(0, tmpName.lastIndexOf(".")); } else { refName = tmpName; } } File refFile = new File(refFileName); if (refSeqType != SeqUtils.guessSequenceType(refFile)) { throw new Exception( "Reference file " + refFile + " contains " + SeqUtils.guessFileFormat(refFile) + " sequences but expected " + refSeqType + " sequences"); } SequenceReader seqReader = new SequenceReader(refFile); Sequence seq; while ((seq = seqReader.readNextSequence()) != null) { if (seq.getSeqName().startsWith("#")) { continue; } if (alignedSeqs) { kmerTrie.addModelSequence(seq, refLabels.size()); } else { kmerTrie.addSequence(seq, refLabels.size()); } } seqReader.close(); refLabels.add(refName); } } catch (Exception e) { new HelpFormatter().printHelp("KmerSearch <word_size> <query_file> [name=]<ref_file> ...", options); System.err.println(e.getMessage()); e.printStackTrace(); System.exit(1); throw new RuntimeException("Stupid jvm"); //While this will never get thrown it is required to make sure javac doesn't get confused about uninitialized variables } long startTime = System.currentTimeMillis(); long seqCount = 0; final int maxTasks = 25000; /* * if (args.length == 4) { maxThreads = Integer.valueOf(args[3]); } else { */ //} System.err.println("Starting kmer mapping at " + new Date()); System.err.println("* Number of threads: " + maxThreads); System.err.println("* References: " + refLabels); System.err.println("* Reads file: " + queryFile); System.err.println("* Kmer length: " + kmerTrie.getWordSize()); final AtomicInteger processed = new AtomicInteger(); final AtomicInteger outstandingTasks = new AtomicInteger(); ExecutorService service = Executors.newFixedThreadPool(maxThreads); Sequence querySeq; while ((querySeq = queryReader.readNextSequence()) != null) { seqCount++; String seqString = querySeq.getSeqString(); if (seqString.length() < 3) { System.err.println("Sequence " + querySeq.getSeqName() + "'s length is less than 3"); continue; } final Sequence threadSeq = querySeq; Runnable r = new Runnable() { public void run() { try { processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, false); processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, true); } catch (IOException e) { throw new RuntimeException(e); } processed.incrementAndGet(); outstandingTasks.decrementAndGet(); } }; outstandingTasks.incrementAndGet(); service.submit(r); while (outstandingTasks.get() >= maxTasks) ; if ((processed.get() + 1) % 1000000 == 0) { System.err.println("Processed " + processed + " sequences in " + (System.currentTimeMillis() - startTime) + " ms"); } } service.shutdown(); service.awaitTermination(1, TimeUnit.DAYS); System.err.println("Finished Processed " + processed + " sequences in " + (System.currentTimeMillis() - startTime) + " ms"); out.close(); }
From source file:com.hpe.nv.samples.basic.BasicAnalyzeNVTransactions.java
public static void main(String[] args) { try {/* w w w. j a va 2s . c o m*/ // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicAnalyzeNVTransactions.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates how to run transactions as part of an NV test. ***" + newLine + "*** ***" + newLine + "*** In this sample, the NV test starts with the \"3G Busy\" network scenario, running three transactions (see below). ***" + newLine + "*** After the sample stops and analyzes the NV test, it prints the analysis .zip file path to the console. ***" + newLine + "*** ***" + newLine + "*** This sample runs three NV transactions: ***" + newLine + "*** 1. \"Home Page\" transaction: Navigates to the home page in the HPE Network Virtualization website ***" + newLine + "*** 2. \"Get Started\" transaction: Navigates to the Get Started Now page in the HPE Network Virtualization website ***" + newLine + "*** 3. \"Overview\" transaction: Navigates back to the home page in the HPE Network Virtualization website ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicAnalyzeNVTransactions.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Start the NV test with the "3G Busy" network scenario *****/ printPartDescription("\b------ Part 1 - Start the NV test with the \"3G Busy\" network scenario"); initTestManager(); startTest(); testRunning = true; printPartSeparator(); /***** Part 2 - Run three transactions - "Home Page", "Get Started" and "Overview" *****/ printPartDescription( "------ Part 2 - Run three transactions - \"Home Page\", \"Get Started\" and \"Overview\""); connectToTransactionManager(); startTransaction(1); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(1); transactionInProgress = false; startTransaction(2); transactionInProgress = true; seleniumGetStartedClick(); stopTransaction(2); transactionInProgress = false; startTransaction(3); transactionInProgress = true; seleniumOverviewClick(); stopTransaction(3); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 3 - Stop the NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 3 - Stop the NV test, analyze it and print the results to the console"); stopTestAndAnalyze(); testRunning = false; printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:edu.msu.cme.rdp.abundstats.cli.AbundMain.java
public static void main(String[] args) throws IOException { File inputFile;/*from ww w . ja va 2 s.co m*/ File resultDir = new File("."); RPlotter plotter = null; boolean isClusterFile = true; List<AbundStatsCalculator> statCalcs = new ArrayList(); double clustCutoffFrom = Double.MIN_VALUE, clustCutoffTo = Double.MAX_VALUE; String usage = "Main [options] <cluster file>"; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("result-dir")) { resultDir = new File(line.getOptionValue("result-dir")); if (!resultDir.exists() && !resultDir.mkdirs()) { throw new Exception( "Result directory " + resultDir + " does not exist and could not be created"); } } if (line.hasOption("R-location")) { plotter = new RPlotter(); plotter.setCommandTemplate(rplotterTemplate); plotter.setRPath(line.getOptionValue("R-location")); plotter.setOutFileExt(".png"); if (!new File(plotter.getRPath()).canExecute()) { throw new Exception(plotter.getRPath() + " does not exist or is not exectuable"); } } if (line.hasOption("lower-cutoff")) { clustCutoffFrom = Double.valueOf(line.getOptionValue("lower-cutoff")); } if (line.hasOption("upper-cutoff")) { clustCutoffTo = Double.valueOf(line.getOptionValue("upper-cutoff")); } if (line.hasOption("jaccard")) { statCalcs.add(new Jaccard(true)); } if (line.hasOption("sorensen")) { statCalcs.add(new Sorensen(true)); } if (line.hasOption("otu-table")) { isClusterFile = false; } if (statCalcs.isEmpty()) { throw new Exception("Must specify at least one stat to compute (jaccard, sorensen)"); } args = line.getArgs(); if (args.length != 1) { throw new Exception("Unexpected number of command line arguments"); } inputFile = new File(args[0]); } catch (Exception e) { new HelpFormatter().printHelp(usage, options); System.err.println("Error: " + e.getMessage()); return; } if (isClusterFile) { RDPClustParser parser; parser = new RDPClustParser(inputFile); try { if (parser.getClusterSamples().size() == 1) { throw new IOException("Cluster file must have more than one sample"); } List<Cutoff> cutoffs = parser.getCutoffs(clustCutoffFrom, clustCutoffTo); if (cutoffs.isEmpty()) { throw new IOException( "No cutoffs in cluster file in range [" + clustCutoffFrom + "-" + clustCutoffTo + "]"); } for (Cutoff cutoff : cutoffs) { List<Sample> samples = new ArrayList(); for (ClusterSample clustSample : parser.getClusterSamples()) { Sample s = new Sample(clustSample.getName()); for (Cluster clust : cutoff.getClusters().get(clustSample.getName())) { s.addSpecies(clust.getNumberOfSeqs()); } samples.add(s); } processSamples(samples, statCalcs, resultDir, cutoff.getCutoff() + "_", plotter); } } finally { parser.close(); } } else { List<Sample> samples = new ArrayList(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); String line = reader.readLine(); if (line == null || line.split("\\s+").length < 2) { throw new IOException("Must be 2 or more samples for abundance statistic calculations!"); } int numSamples = line.split("\\s+").length; boolean header = true; try { Integer.valueOf(line.split("\\s+")[0]); header = false; } catch (Exception e) { } if (header) { for (String s : line.split("\\s+")) { samples.add(new Sample(s)); } } else { int sample = 0; for (String s : line.split("\\s+")) { samples.add(new Sample("" + sample)); samples.get(sample).addSpecies(Integer.valueOf(s)); sample++; } } int lineno = 2; while ((line = reader.readLine()) != null) { if (line.trim().equals("")) { continue; } int sample = 0; if (line.split("\\s+").length != numSamples) { System.err.println( "Line number " + lineno + " didn't have the expected number of samples (contained " + line.split("\\s+").length + ", expected " + numSamples + ")"); } for (String s : line.split("\\s+")) { samples.get(sample).addSpecies(Integer.valueOf(s)); sample++; } lineno++; } processSamples(samples, statCalcs, resultDir, inputFile.getName(), plotter); } }