List of usage examples for java.lang Exception Exception
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From source file:com.ibm.crail.storage.StorageServer.java
public static void main(String[] args) throws Exception { Logger LOG = CrailUtils.getLogger(); CrailConfiguration conf = new CrailConfiguration(); CrailConstants.updateConstants(conf); CrailConstants.printConf();/*from w ww .j a v a 2 s . c om*/ CrailConstants.verify(); int splitIndex = 0; for (String param : args) { if (param.equalsIgnoreCase("--")) { break; } splitIndex++; } //default values StringTokenizer tokenizer = new StringTokenizer(CrailConstants.STORAGE_TYPES, ","); if (!tokenizer.hasMoreTokens()) { throw new Exception("No storage types defined!"); } String storageName = tokenizer.nextToken(); int storageType = 0; HashMap<String, Integer> storageTypes = new HashMap<String, Integer>(); storageTypes.put(storageName, storageType); for (int type = 1; tokenizer.hasMoreElements(); type++) { String name = tokenizer.nextToken(); storageTypes.put(name, type); } int storageClass = -1; //custom values if (args != null) { Option typeOption = Option.builder("t").desc("storage type to start").hasArg().build(); Option classOption = Option.builder("c").desc("storage class the server will attach to").hasArg() .build(); Options options = new Options(); options.addOption(typeOption); options.addOption(classOption); CommandLineParser parser = new DefaultParser(); try { CommandLine line = parser.parse(options, Arrays.copyOfRange(args, 0, splitIndex)); if (line.hasOption(typeOption.getOpt())) { storageName = line.getOptionValue(typeOption.getOpt()); storageType = storageTypes.get(storageName).intValue(); } if (line.hasOption(classOption.getOpt())) { storageClass = Integer.parseInt(line.getOptionValue(classOption.getOpt())); } } catch (ParseException e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Storage tier", options); System.exit(-1); } } if (storageClass < 0) { storageClass = storageType; } StorageTier storageTier = StorageTier.createInstance(storageName); if (storageTier == null) { throw new Exception("Cannot instantiate datanode of type " + storageName); } String extraParams[] = null; splitIndex++; if (args.length > splitIndex) { extraParams = new String[args.length - splitIndex]; for (int i = splitIndex; i < args.length; i++) { extraParams[i - splitIndex] = args[i]; } } storageTier.init(conf, extraParams); storageTier.printConf(LOG); RpcClient rpcClient = RpcClient.createInstance(CrailConstants.NAMENODE_RPC_TYPE); rpcClient.init(conf, args); rpcClient.printConf(LOG); ConcurrentLinkedQueue<InetSocketAddress> namenodeList = CrailUtils.getNameNodeList(); ConcurrentLinkedQueue<RpcConnection> connectionList = new ConcurrentLinkedQueue<RpcConnection>(); while (!namenodeList.isEmpty()) { InetSocketAddress address = namenodeList.poll(); RpcConnection connection = rpcClient.connect(address); connectionList.add(connection); } RpcConnection rpcConnection = connectionList.peek(); if (connectionList.size() > 1) { rpcConnection = new RpcDispatcher(connectionList); } LOG.info("connected to namenode(s) " + rpcConnection.toString()); StorageServer server = storageTier.launchServer(); StorageRpcClient storageRpc = new StorageRpcClient(storageType, CrailStorageClass.get(storageClass), server.getAddress(), rpcConnection); HashMap<Long, Long> blockCount = new HashMap<Long, Long>(); long sumCount = 0; while (server.isAlive()) { StorageResource resource = server.allocateResource(); if (resource == null) { break; } else { storageRpc.setBlock(resource.getAddress(), resource.getLength(), resource.getKey()); DataNodeStatistics stats = storageRpc.getDataNode(); long newCount = stats.getFreeBlockCount(); long serviceId = stats.getServiceId(); long oldCount = 0; if (blockCount.containsKey(serviceId)) { oldCount = blockCount.get(serviceId); } long diffCount = newCount - oldCount; blockCount.put(serviceId, newCount); sumCount += diffCount; LOG.info("datanode statistics, freeBlocks " + sumCount); } } while (server.isAlive()) { DataNodeStatistics stats = storageRpc.getDataNode(); long newCount = stats.getFreeBlockCount(); long serviceId = stats.getServiceId(); long oldCount = 0; if (blockCount.containsKey(serviceId)) { oldCount = blockCount.get(serviceId); } long diffCount = newCount - oldCount; blockCount.put(serviceId, newCount); sumCount += diffCount; LOG.info("datanode statistics, freeBlocks " + sumCount); Thread.sleep(2000); } }
From source file:org.mzd.shap.spring.io.DescriptionEditor.java
/** * Convenience method for testing pattern matching. * @param args/* w ww . ja va2s .c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { if (args.length != 2) { throw new Exception("Usage: [pattern] [description text]"); } System.out.println("Pattern: " + args[0]); System.out.println("Descrip: " + args[1]); System.out.println("Result: " + new DescriptionEditor(args[0]).getMinimalDescription(args[1])); }
From source file:edu.msu.cme.rdp.kmer.KmerSearch.java
public static void main(String[] args) throws IOException { KmerTrie kmerTrie = null;//from w w w . j a v a2 s.c o m SeqReader queryReader = null; SequenceType querySeqType = SequenceType.Unknown; FastaWriter out = null; boolean exhaustive = true; boolean translQuery = false; int wordSize = -1; int translTable = 11; try { 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 FastaWriter(cmdLine.getOptionValue("out")); } else { out = new FastaWriter(System.out); } if (cmdLine.hasOption("correct")) { exhaustive = false; } else { exhaustive = true; } if (cmdLine.hasOption("transl-table")) { translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table")); } File trainingFile = new File(args[0]); wordSize = Integer.valueOf(args[1]); File queryFile = new File(args[2]); querySeqType = SeqUtils.guessSequenceType(queryFile); queryReader = new SequenceReader(new File(args[2])); kmerTrie = KmerTrie.buildTrie(new SequenceReader(trainingFile), wordSize); if (querySeqType == SequenceType.Protein && kmerTrie.getTreeSeqType() == SequenceType.Nucleotide) { throw new Exception("Trie is made of nucleotide sequences but the query sequences are protein"); } if (querySeqType == SequenceType.Nucleotide && kmerTrie.getTreeSeqType() == SequenceType.Protein) { translQuery = true; System.err.println( "Query sequences are nucleotide but trie is in protein space, query sequences will be translated"); } if (querySeqType == SequenceType.Protein && exhaustive) { System.err.println("Cannot do an exaustive search with protein sequences, disabling"); exhaustive = false; } } catch (Exception e) { new HelpFormatter().printHelp("KmerSearch <ref_file> <word_size> <query_file>", options); System.err.println(e.getMessage()); System.exit(1); } long startTime = System.currentTimeMillis(); long seqCount = 0, passedCount = 0; Sequence querySeq; while ((querySeq = queryReader.readNextSequence()) != null) { seqCount++; List<Sequence> testSequences; if (!exhaustive) { if (translQuery) { testSequences = Arrays.asList(new Sequence(querySeq.getSeqName(), "", ProteinUtils.getInstance() .translateToProtein(querySeq.getSeqString(), true, translTable))); } else { testSequences = Arrays.asList(querySeq); } } else { if (translQuery) { testSequences = ProteinUtils.getInstance().allTranslate(querySeq); } else { testSequences = Arrays.asList(querySeq, new Sequence(querySeq.getSeqName(), "", IUBUtilities.reverseComplement(querySeq.getSeqString()))); } } boolean passed = false; for (Sequence seq : testSequences) { for (char[] kmer : KmerGenerator.getKmers(seq.getSeqString(), wordSize)) { if (kmerTrie.contains(kmer) != null) { passed = true; break; } } if (passed) { out.writeSeq(seq); passedCount++; break; } } } System.err.println("Processed: " + seqCount); System.err.println("Passed: " + passedCount); System.err.println("Failed: " + (seqCount - passedCount)); System.err.println("Time: " + (System.currentTimeMillis() - startTime) + " ms"); }
From source file:eu.annocultor.utils.XmlUtils.java
public static 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 pretty-printed").create(OPT_FN)); // now lets parse the input CommandLineParser parser = new BasicParser(); CommandLine cmd;/* ww w . j a v a 2s. c o m*/ try { cmd = parser.parse(options, Utils.getCommandLineFromANNOCULTOR_ARGS(args)); } catch (ParseException pe) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("pretty", options); return; } List<File> files = Utils.expandFileTemplateFrom(new File("."), cmd.getOptionValue(OPT_FN)); for (File file : files) { // XML pretty print System.out.println("Pretty-print for file " + file); if (file.exists()) prettyPrintXmlFileSAX(file.getCanonicalPath()); else throw new Exception("File not found: " + file.getCanonicalPath()); } }
From source file:edu.msu.cme.rdp.readseq.utils.QualityTrimmer.java
public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file"); options.addOption("l", "less-than", false, "Trim at <= instead of strictly ="); options.addOption("i", "illumina", false, "Illumina trimming mode"); FastqWriter fastqOut = null;//w ww. j av a 2 s . c om FastaWriter fastaOut = null; byte qualTrim = -1; boolean writeFasta = true; boolean trimle = false; boolean illumina = false; List<SeqReader> readers = new ArrayList(); List<File> seqFiles = new ArrayList(); try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("fastq-out")) { writeFasta = false; } if (line.hasOption("less-than")) { trimle = true; } if (line.hasOption("illumina")) { illumina = true; } args = line.getArgs(); if (args.length < 2) { throw new Exception("Unexpected number of arguments"); } if (args[0].length() != 1) { throw new Exception("Expected single character quality score"); } qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0)); for (int index = 1; index < args.length; index++) { File seqFile = new File(args[index]); SeqReader reader; if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) { if (index + 1 == args.length) { throw new Exception("Fasta files must be immediately followed by their quality file"); } File qualFile = new File(args[index + 1]); if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) { throw new Exception(seqFile + " was not followed by a fasta quality file"); } reader = new QSeqReader(seqFile, qualFile); index++; } else { if (seqFile.getName().endsWith(".gz")) { reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile))); } else { reader = new SequenceReader(seqFile); } } readers.add(reader); seqFiles.add(seqFile); } } catch (Exception e) { new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] <ascii_score> <seq_file> [qual_file]", options, true); System.err.println("Error: " + e.getMessage()); System.exit(1); } for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) { File seqFile = seqFiles.get(readerIndex); String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf(".")); if (writeFasta) { fastaOut = new FastaWriter(outStem + ".fasta"); } else { fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction); } int[] lengthHisto = new int[200]; SeqReader reader = readers.get(readerIndex); QSequence qseq; long totalLength = 0; int totalSeqs = 0; long trimmedLength = 0; int trimmedSeqs = 0; int zeroLengthAfterTrimming = 0; long startTime = System.currentTimeMillis(); while ((qseq = (QSequence) reader.readNextSequence()) != null) { char[] bases = qseq.getSeqString().toCharArray(); byte[] qual = qseq.getQuality(); if (bases.length != qual.length) { System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq"); continue; } totalSeqs++; totalLength += bases.length; int trimIndex = -1; if (illumina && qual[bases.length - 1] == qualTrim) { trimIndex = bases.length - 1; while (trimIndex >= 0 && qual[trimIndex] == qualTrim) { trimIndex--; } trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base } else if (!illumina) { for (int index = 0; index < bases.length; index++) { if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) { trimIndex = index; break; } } } String outSeq; byte[] outQual; if (trimIndex == -1) { outSeq = qseq.getSeqString(); outQual = qseq.getQuality(); } else { outSeq = new String(bases, 0, trimIndex); outQual = Arrays.copyOfRange(qual, 0, trimIndex); trimmedSeqs++; } int len = outSeq.length(); trimmedLength += len; if (len >= lengthHisto.length) { lengthHisto = Arrays.copyOf(lengthHisto, len + 1); } lengthHisto[len]++; if (outSeq.length() == 0) { //System.err.println(qseq.getSeqName() + ": length 0 after trimming"); zeroLengthAfterTrimming++; continue; } if (writeFasta) { fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq); } else { fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual); } } reader.close(); if (writeFasta) { fastaOut.close(); } else { fastqOut.close(); } System.out.println( "Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s"); System.out.println("Before trimming:"); System.out.println("Total Sequences: " + totalSeqs); System.out.println("Total Sequence Data: " + totalLength); System.out.println("Average sequence length: " + ((float) totalLength / totalSeqs)); System.out.println(); System.out.println("After trimming:"); System.out.println("Total Sequences: " + (totalSeqs - zeroLengthAfterTrimming)); System.out.println("Sequences Trimmed: " + trimmedSeqs); System.out.println("Total Sequence Data: " + trimmedLength); System.out.println("Average sequence length: " + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming))); System.out.println(); System.out.println("Length\tCount"); for (int index = 0; index < lengthHisto.length; index++) { if (lengthHisto[index] == 0) { continue; } System.out.println(index + "\t" + lengthHisto[index]); } System.out.println(); System.out.println(); System.out.println(); } }
From source file:net.anthonypoon.ngram.correlation.Main.java
public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("a", "action", true, "Action"); options.addOption("i", "input", true, "input"); options.addOption("o", "output", true, "output"); //options.addOption("f", "format", true, "Format"); options.addOption("u", "upbound", true, "Year up bound"); options.addOption("l", "lowbound", true, "Year low bound"); options.addOption("t", "target", true, "Correlation Target URI"); // Can only take file from S# or HDFS options.addOption("L", "lag", true, "Lag factor"); options.addOption("T", "threshold", true, "Correlation threshold"); CommandLineParser parser = new GnuParser(); CommandLine cmd = parser.parse(options, args); Configuration conf = new Configuration(); if (cmd.hasOption("lag")) { conf.set("lag", cmd.getOptionValue("lag")); }//from w w w . j a va2 s.c o m if (cmd.hasOption("threshold")) { conf.set("threshold", cmd.getOptionValue("threshold")); } if (cmd.hasOption("upbound")) { conf.set("upbound", cmd.getOptionValue("upbound")); } else { conf.set("upbound", "9999"); } if (cmd.hasOption("lowbound")) { conf.set("lowbound", cmd.getOptionValue("lowbound")); } else { conf.set("lowbound", "0"); } if (cmd.hasOption("target")) { conf.set("target", cmd.getOptionValue("target")); } else { throw new Exception("Missing correlation target file uri"); } Job job = Job.getInstance(conf); /** if (cmd.hasOption("format")) { switch (cmd.getOptionValue("format")) { case "compressed": job.setInputFormatClass(SequenceFileAsTextInputFormat.class); break; case "text": job.setInputFormatClass(KeyValueTextInputFormat.class); break; } }**/ job.setJarByClass(Main.class); switch (cmd.getOptionValue("action")) { case "get-correlation": job.setOutputKeyClass(Text.class); job.setOutputValueClass(Text.class); for (String inputPath : cmd.getOptionValue("input").split(",")) { MultipleInputs.addInputPath(job, new Path(inputPath), KeyValueTextInputFormat.class, CorrelationMapper.class); } job.setReducerClass(CorrelationReducer.class); break; default: throw new IllegalArgumentException("Missing action"); } String timestamp = new SimpleDateFormat("yyyy_MM_dd_HH_mm_ss").format(new Date()); //FileInputFormat.setInputPaths(job, new Path(cmd.getOptionValue("input"))); FileOutputFormat.setOutputPath(job, new Path(cmd.getOptionValue("output") + "/" + timestamp)); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:com.hortonworks.atlas.trash.DemoClass.java
public static void main(String[] args) throws Exception { // TODO Auto-generated method stub if (args.length < 1) { throw new Exception("Please provide the DGI host url"); }/*w w w . j a v a 2 s.c o m*/ System.setProperty("atlas.conf", "/Users/sdutta/Applications/conf"); String baseUrl = getServerUrl(args); DemoClass dc = new DemoClass(baseUrl); dc.createTypes(); // Shows how to create types in Atlas for your meta model dc.createTypes(); // Shows how to create entities (instances) for the added types in Atlas dc.createEntities(); // Shows some search queries using DSL based on types //dc.search(); }
From source file:com.ibm.crail.namenode.NameNode.java
public static void main(String args[]) throws Exception { LOG.info("initalizing namenode "); CrailConfiguration conf = new CrailConfiguration(); CrailConstants.updateConstants(conf); URI uri = CrailUtils.getPrimaryNameNode(); String address = uri.getHost(); int port = uri.getPort(); if (args != null) { Option addressOption = Option.builder("a").desc("ip address namenode is started on").hasArg().build(); Option portOption = Option.builder("p").desc("port namenode is started on").hasArg().build(); Options options = new Options(); options.addOption(portOption);/*w ww .j a v a 2s .c om*/ options.addOption(addressOption); CommandLineParser parser = new DefaultParser(); try { CommandLine line = parser.parse(options, Arrays.copyOfRange(args, 0, args.length)); if (line.hasOption(addressOption.getOpt())) { address = line.getOptionValue(addressOption.getOpt()); } if (line.hasOption(portOption.getOpt())) { port = Integer.parseInt(line.getOptionValue(portOption.getOpt())); } } catch (ParseException e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Namenode", options); System.exit(-1); } } String namenode = "crail://" + address + ":" + port; long serviceId = CrailUtils.getServiceId(namenode); long serviceSize = CrailUtils.getServiceSize(); if (!CrailUtils.verifyNamenode(namenode)) { throw new Exception("Namenode address/port [" + namenode + "] has to be listed in crail.namenode.address " + CrailConstants.NAMENODE_ADDRESS); } CrailConstants.NAMENODE_ADDRESS = namenode + "?id=" + serviceId + "&size=" + serviceSize; CrailConstants.printConf(); CrailConstants.verify(); RpcNameNodeService service = RpcNameNodeService.createInstance(CrailConstants.NAMENODE_RPC_SERVICE); RpcBinding rpcBinding = RpcBinding.createInstance(CrailConstants.NAMENODE_RPC_TYPE); rpcBinding.init(conf, null); rpcBinding.printConf(LOG); rpcBinding.run(service); System.exit(0); ; }
From source file:net.frontlinesms.DesktopLauncher.java
/** * Main class for launching the FrontlineSMS project. * @param args//from w ww . ja v a 2s .com */ public static void main(String[] args) { FrontlineSMS frontline = null; try { AppProperties appProperties = AppProperties.getInstance(); final String VERSION = BuildProperties.getInstance().getVersion(); LOG.info("FrontlineSMS version [" + VERSION + "]"); UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); String lastVersion = appProperties.getLastRunVersion(); InputStream defaultResourceArchive = ResourceUtils.class.getResourceAsStream("/resources.zip"); if (defaultResourceArchive == null) { LOG.fatal("Default resources archive could not be found!"); throw new Exception("Default resources archive could not be found!"); } ResourceUtils.unzip(defaultResourceArchive, new File(ResourceUtils.getConfigDirectoryPath()), !VERSION.equals(lastVersion)); // This should always get the English bundle, as other languages are only included in // resources.zip rather than in the resources/languages directory LanguageBundle englishBundle = InternationalisationUtils.getDefaultLanguageBundle(); Thinlet.DEFAULT_ENGLISH_BUNDLE = englishBundle.getProperties(); // If the user has currently no User ID defined // We generate one if (appProperties.getUserId() == null) { appProperties.setUserId(generateUserId()); } boolean showWizard = appProperties.isShowWizard(); appProperties.setLastRunVersion(VERSION); appProperties.saveToDisk(); frontline = initFrontline(); if (showWizard) { new FirstTimeWizard(frontline); } else { // Auto-detect phones. new UiGeneratorController(frontline, true); } } catch (Throwable t) { if (frontline != null) frontline.destroy(); // Rather than swallowing the error, we now display it to the user // so that they can give us some feedback :) ErrorUtils.showErrorDialog("Fatal error starting FrontlineSMS!", "A problem ocurred during FrontlineSMS startup.", t, true); } }
From source file:org.switchyard.quickstarts.demo.policy.security.wss.signencrypt.WorkServiceMain.java
public static void main(String... args) throws Exception { Set<String> policies = new HashSet<String>(); for (String arg : args) { arg = Strings.trimToNull(arg);//from ww w .ja v a2 s.c o m if (arg != null) { if (arg.equals(CONFIDENTIALITY) || arg.equals(SIGNENCRYPT) || arg.equals(HELP)) { policies.add(arg); } else { LOGGER.error(MAVEN_USAGE); throw new Exception(MAVEN_USAGE); } } } if (policies.contains(HELP)) { LOGGER.info(MAVEN_USAGE); } else { final String scheme; final int port; if (policies.contains(CONFIDENTIALITY)) { scheme = "https"; port = getPort(8443); SSLContext sslcontext = SSLContext.getInstance("TLS"); sslcontext.init(null, null, null); SSLSocketFactory sf = new SSLSocketFactory(sslcontext, SSLSocketFactory.STRICT_HOSTNAME_VERIFIER); Scheme https = new Scheme(scheme, port, sf); SchemeRegistry sr = new SchemeRegistry(); sr.register(https); } else { scheme = "http"; port = getPort(8080); } boolean signencrypt = policies.contains(SIGNENCRYPT); invokeWorkService(scheme, port, getContext(), signencrypt); } }