Example usage for org.apache.commons.cli CommandLine getArgs

List of usage examples for org.apache.commons.cli CommandLine getArgs

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Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLine getArgs.

Prototype

public String[] getArgs()

Source Link

Document

Retrieve any left-over non-recognized options and arguments

Usage

From source file:com.basingwerk.utilisation.Utilisation.java

public static void main(final String[] args) {
    String dataFile = null;//from   w  w w.j av a2 s  .c  om

    Options options = new Options();

    Option helpOption = new Option("h", "help", false, "print this help");
    Option serverURLOption = new Option("l", "logfile", true, "log file");

    options.addOption(helpOption);
    options.addOption(serverURLOption);

    CommandLineParser argsParser = new PosixParser();

    try {
        CommandLine commandLine = argsParser.parse(options, args);

        if (commandLine.hasOption(helpOption.getOpt())) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("Usage grapher", options);
            System.exit(0);
        }

        dataFile = commandLine.getOptionValue(serverURLOption.getOpt());
        String[] otherArgs = commandLine.getArgs();

        if (dataFile == null || otherArgs.length > 1) {
            System.out.println("Please specify a logfile");
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("Usage grapher", options);
            System.exit(0);
        }

    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } finally {
    }

    final UsagePlotter demo = new UsagePlotter("Usage", new File(dataFile));
    demo.pack();
    RefineryUtilities.centerFrameOnScreen(demo);
    demo.setVisible(true);
}

From source file:com.arsdigita.util.parameter.ParameterPrinter.java

public static final void main(final String[] args) throws IOException {

    CommandLine line = null;
    try {/*from   w  w  w . j  a v  a  2s  .c  o m*/
        line = new PosixParser().parse(OPTIONS, args);
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        System.exit(1);
    }

    String[] outFile = line.getArgs();
    if (outFile.length != 1) {
        System.out.println("Usage: ParameterPrinter [--html] [--file config-list-file] output-file");
        System.exit(1);
    }
    if (line.hasOption("usage")) {
        System.out.println("Usage: ParameterPrinter [--html] [--file config-list-file] output-file");
        System.exit(0);
    }

    if (line.hasOption("file")) {
        String file = line.getOptionValue("file");
        try {
            BufferedReader reader = new BufferedReader(new FileReader(file));
            String configClass;
            while ((configClass = reader.readLine()) != null) {
                register(configClass);
            }
        } catch (IOException e) {
            System.err.println(e.getMessage());
            System.exit(1);
        }
    } else {
        register("com.arsdigita.runtime.RuntimeConfig");
        register("com.arsdigita.web.WebConfig");
        register("com.arsdigita.templating.TemplatingConfig");
        register("com.arsdigita.kernel.KernelConfig");
        register("com.arsdigita.kernel.security.SecurityConfig");
        register("com.arsdigita.mail.MailConfig");
        register("com.arsdigita.versioning.VersioningConfig");
        register("com.arsdigita.search.SearchConfig");
        register("com.arsdigita.search.lucene.LuceneConfig");
        register("com.arsdigita.kernel.security.SecurityConfig");
        register("com.arsdigita.bebop.BebopConfig");
        register("com.arsdigita.dispatcher.DispatcherConfig");
        register("com.arsdigita.workflow.simple.WorkflowConfig");
        register("com.arsdigita.cms.ContentSectionConfig");
    }

    if (line.hasOption("html")) {
        final StringWriter sout = new StringWriter();
        final PrintWriter out = new PrintWriter(sout);

        writeXML(out);

        final XSLTemplate template = new XSLTemplate(
                ParameterPrinter.class.getResource("ParameterPrinter_html.xsl"));

        final Source source = new StreamSource(new StringReader(sout.toString()));
        final Result result = new StreamResult(new File(outFile[0]));

        template.transform(source, result);
    } else {
        final PrintWriter out = new PrintWriter(new FileWriter(outFile[0]));

        writeXML(out);
    }
}

From source file:com.genentech.chemistry.openEye.apps.SDFMDLSSSMatcher.java

public static void main(String... args) throws IOException, InterruptedException {
    oechem.OEUseJavaHeap(false);/*w  w  w .j  a  v  a2 s  . c  o m*/

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.sdf,...]");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("out", true, "output file oe-supported");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("ref", true, "refrence file with MDL query molecules");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("anyMatch", false, "if set all matches are reported not just the first.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("printAll", false, "if set even compounds that do not macht are outputted.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("nCpu", true, "number of CPU's used in parallel, dafault 1");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }

    args = cmd.getArgs();
    if (args.length > 0) {
        exitWithHelp("Unknown param: " + args[0], options);
    }

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    int nCpu = 1;
    boolean firstMatch = !cmd.hasOption("anyMatch");
    boolean printAll = cmd.hasOption("printAll");

    String d = cmd.getOptionValue("nCpu");
    if (d != null)
        nCpu = Integer.parseInt(d);

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");

    SDFMDLSSSMatcher matcher = new SDFMDLSSSMatcher(refFile, outFile, firstMatch, printAll, nCpu);
    matcher.run(inFile);
    matcher.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;/*w  w w  .j av a2  s .  com*/
    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.ctriposs.rest4j.tools.data.FilterSchemaGenerator.java

public static void main(String[] args) {
    final CommandLineParser parser = new GnuParser();
    CommandLine cl = null;
    try {//from w  ww.ja va2 s . c  o  m
        cl = parser.parse(_options, args);
    } catch (ParseException e) {
        _log.error("Invalid arguments: " + e.getMessage());
        reportInvalidArguments();
    }

    final String[] directoryArgs = cl.getArgs();
    if (directoryArgs.length != 2) {
        reportInvalidArguments();
    }

    final File sourceDirectory = new File(directoryArgs[0]);
    if (!sourceDirectory.exists()) {
        _log.error(sourceDirectory.getPath() + " does not exist");
        System.exit(1);
    }
    if (!sourceDirectory.isDirectory()) {
        _log.error(sourceDirectory.getPath() + " is not a directory");
        System.exit(1);
    }
    final URI sourceDirectoryURI = sourceDirectory.toURI();

    final File outputDirectory = new File(directoryArgs[1]);
    if (outputDirectory.exists() && !sourceDirectory.isDirectory()) {
        _log.error(outputDirectory.getPath() + " is not a directory");
        System.exit(1);
    }

    final boolean isAvroMode = cl.hasOption('a');
    final String predicateExpression = cl.getOptionValue('e');
    final Predicate predicate = PredicateExpressionParser.parse(predicateExpression);

    final Collection<File> sourceFiles = FileUtil.listFiles(sourceDirectory, null);
    int exitCode = 0;
    for (File sourceFile : sourceFiles) {
        try {
            final ValidationOptions val = new ValidationOptions();
            val.setAvroUnionMode(isAvroMode);

            final SchemaParser schemaParser = new SchemaParser();
            schemaParser.setValidationOptions(val);

            schemaParser.parse(new FileInputStream(sourceFile));
            if (schemaParser.hasError()) {
                _log.error("Error parsing " + sourceFile.getPath() + ": "
                        + schemaParser.errorMessageBuilder().toString());
                exitCode = 1;
                continue;
            }

            final DataSchema originalSchema = schemaParser.topLevelDataSchemas().get(0);
            if (!(originalSchema instanceof NamedDataSchema)) {
                _log.error(sourceFile.getPath() + " does not contain valid NamedDataSchema");
                exitCode = 1;
                continue;
            }

            final SchemaParser filterParser = new SchemaParser();
            filterParser.setValidationOptions(val);

            final NamedDataSchema filteredSchema = Filters.removeByPredicate((NamedDataSchema) originalSchema,
                    predicate, filterParser);
            if (filterParser.hasError()) {
                _log.error("Error applying predicate: " + filterParser.errorMessageBuilder().toString());
                exitCode = 1;
                continue;
            }

            final String relativePath = sourceDirectoryURI.relativize(sourceFile.toURI()).getPath();
            final String outputFilePath = outputDirectory.getPath() + File.separator + relativePath;
            final File outputFile = new File(outputFilePath);
            final File outputFileParent = outputFile.getParentFile();
            outputFileParent.mkdirs();
            if (!outputFileParent.exists()) {
                _log.error("Unable to write filtered schema to " + outputFileParent.getPath());
                exitCode = 1;
                continue;
            }

            FileOutputStream fout = new FileOutputStream(outputFile);
            fout.write(filteredSchema.toString().getBytes(RestConstants.DEFAULT_CHARSET));
            fout.close();
        } catch (IOException e) {
            _log.error(e.getMessage());
            exitCode = 1;
        }
    }

    System.exit(exitCode);
}

From source file:ee.ria.xroad.common.conf.globalconf.ConfigurationClientMain.java

/**
 * Main entry point of configuration client. Based on the arguments,
 * the client will either:/*  w ww  .  j  av  a2 s . c om*/
 * 1) <anchor file> <configuration path> -- download and exit
 * 2) <anchor file> -- download and verify
 * 3) [no args] -- start as daemon
 * @param args the arguments
 * @throws Exception if an error occurs
 */
public static void main(String[] args) throws Exception {
    CommandLine cmd = getCommandLine(args);

    String[] actualArgs = cmd.getArgs();
    if (actualArgs.length == NUM_ARGS_FROM_CONF_PROXY_FULL) {
        // Run configuration client in one-shot mode downloading the specified global configuration version
        System.exit(download(actualArgs[0], actualArgs[1], actualArgs[2]));
    } else if (actualArgs.length == NUM_ARGS_FROM_CONF_PROXY) {
        // Run configuration client in one-shot mode downloading the current global configuration version
        System.exit(download(actualArgs[0], actualArgs[1],
                String.format("%d", SystemProperties.CURRENT_GLOBAL_CONFIGURATION_VERSION)));
    } else if (actualArgs.length == 1) {
        // Run configuration client in validate mode
        System.exit(validate(actualArgs[0], getParamsValidator(cmd)));
    } else {
        // Run configuration client in daemon mode
        startDaemon();
    }
}

From source file:com.google.testing.pogen.PageObjectGenerator.java

@SuppressWarnings("static-access")
public static void main(String[] args) {
    if (args.length == 0) {
        printUsage(System.out);/*w  w w.j a  va2s. c  om*/
        return;
    }

    String commandName = args[0];
    // @formatter:off
    Options options = new Options()
            .addOption(OptionBuilder.withDescription(
                    "Attribute name to be assigned in tagas containing template variables (default is 'id').")
                    .hasArg().withLongOpt("attr").create('a'))
            .addOption(OptionBuilder.withDescription("Print help for this command.").withLongOpt("help")
                    .create('h'))
            .addOption(OptionBuilder.withDescription("Print processed files verbosely.").withLongOpt("verbose")
                    .create('v'));
    // @formatter:on

    String helpMessage = null;
    if (commandName.equals(GENERATE_COMMAND)) {
        // @formatter:off
        options.addOption(OptionBuilder.withDescription("Package name of generating skeleton test code.")
                .hasArg().isRequired().withLongOpt("package").create('p'))
                .addOption(OptionBuilder.withDescription("Output directory of generating skeleton test code.")
                        .hasArg().isRequired().withLongOpt("out").create('o'))
                .addOption(OptionBuilder.withDescription(
                        "Root input directory of html template files for analyzing the suffixes of the package name.")
                        .hasArg().isRequired().withLongOpt("in").create('i'))
                .addOption(OptionBuilder.withDescription("Regex for finding html template files.").hasArg()
                        .withLongOpt("regex").create('e'))
                .addOption(OptionBuilder.withDescription("Option for finding html template files recursively.")
                        .withLongOpt("recursive").create('r'));
        // @formatter:on
        helpMessage = "java PageObjectGenerator generate -o <test_out_dir> -p <package_name> -i <root_directory> "
                + " [OPTIONS] <template_file1> <template_file2> ...\n"
                + "e.g. java PageObjectGenerator generate -a class -o PageObjectGeneratorTest/src/test/java/com/google/testing/pogen/pages"
                + " -i PageObjectGeneratorTest/src/main/resources -p com.google.testing.pogen.pages -e (.*)\\.html -v";
    } else if (commandName.equals(MEASURE_COMMAND)) {
        helpMessage = "java PageObjectGenerator measure [OPTIONS] <template_file1> <template_file2> ...";
    } else if (commandName.equals(LIST_COMMAND)) {
        helpMessage = "java PageObjectGenerator list <template_file1> <template_file2> ...";
    } else {
        System.err.format("'%s' is not a PageObjectGenerator command.", commandName);
        printUsage(System.err);
        System.exit(-1);
    }

    BasicParser cmdParser = new BasicParser();
    HelpFormatter f = new HelpFormatter();
    try {
        CommandLine cl = cmdParser.parse(options, Arrays.copyOfRange(args, 1, args.length));
        if (cl.hasOption('h')) {
            f.printHelp(helpMessage, options);
            return;
        }

        Command command = null;
        String[] templatePaths = cl.getArgs();
        String attributeName = cl.getOptionValue('a');
        attributeName = attributeName != null ? attributeName : "id";
        if (commandName.equals(GENERATE_COMMAND)) {
            String rootDirectoryPath = cl.getOptionValue('i');
            String templateFilePattern = cl.getOptionValue('e');
            boolean isRecusive = cl.hasOption('r');
            command = new GenerateCommand(templatePaths, cl.getOptionValue('o'), cl.getOptionValue('p'),
                    attributeName, cl.hasOption('v'), rootDirectoryPath, templateFilePattern, isRecusive);
        } else if (commandName.equals(MEASURE_COMMAND)) {
            command = new MeasureCommand(templatePaths, attributeName, cl.hasOption('v'));
        } else if (commandName.equals(LIST_COMMAND)) {
            command = new ListCommand(templatePaths, attributeName);
        }
        try {
            command.execute();
            return;
        } catch (FileProcessException e) {
            System.err.println(e.getMessage());
        } catch (IOException e) {
            System.err.println("Errors occur in processing files.");
            System.err.println(e.getMessage());
        }
    } catch (ParseException e) {
        System.err.println("Errors occur in parsing the command arguments.");
        System.err.println(e.getMessage());
        f.printHelp(helpMessage, options);
    }
    System.exit(-1);
}

From source file:com.github.r351574nc3.amex.assignment1.App.java

public static void main(final String... args) {
    if (args.length < 1) {
        printUsage();/*from   w  ww. j  a  v  a  2  s .  co  m*/
        System.exit(0);
    }

    final Options options = new Options();
    options.addOption(OptionBuilder.withArgName("output").hasArg(true).withDescription("Path for CSV output")
            .create("o"));
    options.addOption(
            OptionBuilder.withArgName("input").hasArg(true).withDescription("Path for CSV input").create("i"));

    final CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.out.println(e.getMessage());
        printUsage();
        System.exit(0);
    }

    if ((cmd.hasOption('o') && cmd.hasOption('i')) || !(cmd.hasOption('o') || cmd.hasOption('i'))
            || (cmd.hasOption('o') && cmd.getArgs().length < 1)) {
        printUsage();
        System.exit(0);
    }

    if (cmd.hasOption('o') && cmd.getArgs().length > 0) {
        final String outputName = cmd.getOptionValue("o");
        final int iterations = Integer.parseInt(cmd.getArgs()[cmd.getArgs().length - 1]);
        new App().run(new File(outputName), iterations);
    } else if (cmd.hasOption('i')) {
        final String inputName = cmd.getOptionValue("i");
        new App().run(new File(inputName));
    }

    System.exit(0);
}

From source file:com.basistech.ninja.Train.java

/**
 * Command line interface to train a model.
 *
 * <pre>//from   w  ww . j a  va 2  s.  c  o  m
 *  usage: Train [options]
 *  --batch-size <arg>      batch size (default = 10)
 *  --epochs <arg>          epochs (default = 5)
 *  --examples <arg>        input examples file (required)
 *  --layer-sizes <arg>     layer sizes, including input/output, e.g. 3 4 2 (required)
 *  --learning-rate <arg>   learning-rate (default = 0.7)
 *  --model <arg>           output model file (required)
 * </pre>
 *
 * @param args command line arguments
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    String defaultBatchSize = "10";
    String deafaultEpochs = "5";
    String defaultLearningRate = "0.7";

    Options options = new Options();
    Option option;
    option = new Option(null, "examples", true, "input examples file (required)");
    option.setRequired(true);
    options.addOption(option);
    option = new Option(null, "model", true, "output model file (required)");
    option.setRequired(true);
    options.addOption(option);
    option = new Option(null, "layer-sizes", true,
            "layer sizes, including input/output, e.g. 3 4 2 (required)");
    option.setRequired(true);
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    option = new Option(null, "batch-size", true, String.format("batch size (default = %s)", defaultBatchSize));
    options.addOption(option);
    option = new Option(null, "epochs", true, String.format("epochs (default = %s)", deafaultEpochs));
    options.addOption(option);
    option = new Option(null, "learning-rate", true,
            String.format("learning-rate (default = %s)", defaultLearningRate));
    options.addOption(option);

    CommandLineParser parser = new GnuParser();
    CommandLine cmdline = null;
    try {
        cmdline = parser.parse(options, args);
    } catch (org.apache.commons.cli.ParseException e) {
        System.err.println(e.getMessage());
        usage(options);
        System.exit(1);
    }
    String[] remaining = cmdline.getArgs();
    if (remaining == null) {
        usage(options);
        System.exit(1);
    }

    List<Integer> layerSizes = Lists.newArrayList();
    for (String s : cmdline.getOptionValues("layer-sizes")) {
        layerSizes.add(Integer.parseInt(s));
    }

    File examplesFile = new File(cmdline.getOptionValue("examples"));
    Train that = new Train(layerSizes, examplesFile);
    int batchSize = Integer.parseInt(cmdline.getOptionValue("batch-size", defaultBatchSize));
    int epochs = Integer.parseInt(cmdline.getOptionValue("epochs", deafaultEpochs));
    double learningRate = Double.parseDouble(cmdline.getOptionValue("learning-rate", defaultLearningRate));
    File modelFile = new File(cmdline.getOptionValue("model"));

    that.train(batchSize, epochs, learningRate, modelFile);
}

From source file:com.genentech.struchk.sdfNormalizer.java

public static void main(String[] args) {
    long start = System.currentTimeMillis();
    int nMessages = 0;
    int nErrors = 0;
    int nStruct = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);//from w  w w  .  j ava  2s.com
    options.addOption(opt);

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("mol", true, "molFile used for output: ORIGINAL(def)|NORMALIZED|TAUTOMERIC");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("shortMessage", false,
            "Limit message to first 80 characters to conform with sdf file specs.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        exitWithHelp(options, e.getMessage());
        throw new Error(e); // avoid compiler errors
    }
    args = cmd.getArgs();

    if (args.length != 0) {
        System.err.print("Unknown options: " + args + "\n\n");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("sdfNormalizer", options);
        System.exit(1);
    }

    String molOpt = cmd.getOptionValue("mol");
    OUTMolFormat outMol = OUTMolFormat.ORIGINAL;
    if (molOpt == null || "original".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.ORIGINAL;
    else if ("NORMALIZED".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.NORMALIZED;
    else if ("TAUTOMERIC".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.TAUTOMERIC;
    else {
        System.err.printf("Unkown option for -mol: %s\n", molOpt);
        System.exit(1);
    }

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    boolean limitMessage = cmd.hasOption("shortMessage");

    try {
        oemolistream ifs = new oemolistream(inFile);
        oemolostream ofs = new oemolostream(outFile);

        URL cFile = OEStruchk.getResourceURL(OEStruchk.class, "Struchk.xml");

        // create OEStruchk from config file
        OEStruchk strchk = new OEStruchk(cFile, CHECKConfig.ASSIGNStructFlag, false);

        OEGraphMol mol = new OEGraphMol();
        StringBuilder sb = new StringBuilder(2000);
        while (oechem.OEReadMolecule(ifs, mol)) {
            if (!strchk.applyRules(mol, null))
                nErrors++;

            switch (outMol) {
            case NORMALIZED:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol("parent"));
                break;
            case TAUTOMERIC:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol(null));
                break;
            case ORIGINAL:
                break;
            }

            oechem.OESetSDData(mol, "CTISMILES", strchk.getTransformedIsoSmiles(null));
            oechem.OESetSDData(mol, "CTSMILES", strchk.getTransformedSmiles(null));
            oechem.OESetSDData(mol, "CISMILES", strchk.getTransformedIsoSmiles("parent"));
            oechem.OESetSDData(mol, "Strutct_Flag", strchk.getStructureFlag().getName());

            List<Message> msgs = strchk.getStructureMessages(null);
            nMessages += msgs.size();
            for (Message msg : msgs)
                sb.append(String.format("\t%s:%s", msg.getLevel(), msg.getText()));
            if (limitMessage)
                sb.setLength(Math.min(sb.length(), 80));

            oechem.OESetSDData(mol, "NORM_MESSAGE", sb.toString());

            oechem.OEWriteMolecule(ofs, mol);

            sb.setLength(0);
            nStruct++;
        }
        strchk.delete();
        mol.delete();
        ifs.close();
        ifs.delete();
        ofs.close();
        ofs.delete();

    } catch (Exception e) {
        throw new Error(e);
    } finally {
        System.err.printf("sdfNormalizer: Checked %d structures %d errors, %d messages in %dsec\n", nStruct,
                nErrors, nMessages, (System.currentTimeMillis() - start) / 1000);
    }
}