Example usage for org.apache.commons.cli Option setRequired

List of usage examples for org.apache.commons.cli Option setRequired

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Introduction

In this page you can find the example usage for org.apache.commons.cli Option setRequired.

Prototype

public void setRequired(boolean required)

Source Link

Document

Sets whether this Option is mandatory.

Usage

From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFMapQueryThrownExceptions.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*w  ww  . j a  v  a 2s.  com*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);
    options.addOption(optFileOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = NeoEMFMapQueryThrownExceptions.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<TypeAccess> list = ASE2015JavaQueries.getThrownExceptions(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFMapQuerySpecificInvisibleMethodDeclarations.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*from w  ww.  j  ava  2  s.co  m*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);
    options.addOption(optFileOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = NeoEMFMapQuerySpecificInvisibleMethodDeclarations.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = ASE2015JavaQueries.getSpecificInvisibleMethodDeclarations(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.genentech.retrival.SDFExport.SDFSDFExporter.java

public static void main(String[] args) throws ParseException, JDOMException, IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option("sqlFile", true, "sql-xml file");
    opt.setRequired(false);
    options.addOption(opt);/*from   w  w  w .  j a va  2  s .  c o m*/

    opt = new Option("sqlName", true, "name of SQL element in xml file, Default sql.xml in 'sdfExport' config");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("selectStatement", true, "select statement to execute");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("paramTypes", true,
            "'|' separated list of parameter types to pass tostatment int,float,string,date");
    opt.setRequired(false);
    options.addOption(opt);

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

    opt = new Option("i", "in", true,
            "input file, oe or .tab each record executes the query once. Use '.tab' to read from stdin");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("queryTags", true, "'|' separetaed list of tags whose values is passt to the sql.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("newLineReplacement", true,
            "If given newlines in fields will be replaced by this string.");
    options.addOption(opt);

    opt = new Option("filterIfNoRecords", false,
            "If no rows are returned by the query that record is filtered out.");
    options.addOption(opt);

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

    String outFile = cmd.getOptionValue("o");
    String inFile = cmd.getOptionValue("i");
    String sqlFile = cmd.getOptionValue("sqlFile");
    String sqlName = cmd.getOptionValue("sqlName");
    String selStr = cmd.getOptionValue("selectStatement");
    String pTypes = cmd.getOptionValue("paramTypes");
    String newLineReplacement = cmd.getOptionValue("newLineReplacement");
    boolean printIfNoRecord = !cmd.hasOption("filterIfNoRecords");
    String[] tagStr = cmd.getOptionValue("queryTags").trim().split("\\|");

    try {
        SDFSDFExporter exporter = null;
        if ((sqlFile != null && sqlFile.length() > 0) || (sqlName != null && sqlName.length() > 0)) {
            if ((selStr != null && selStr.length() > 0) || (pTypes != null && pTypes.length() > 0)) {
                System.err.println("sqlFile and sqlName may not be used with selectStatement and paramTypes");
                exitWithHelp(options);
            }

            exporter = createFromFile(sqlFile, sqlName, inFile, outFile, tagStr, printIfNoRecord,
                    newLineReplacement);

        } else if (selStr == null || selStr.length() == 0 || pTypes == null || pTypes.length() == 0) {
            System.err.println("sqlFile and sqlName or selectStatement and paramTypes must be given");
            exitWithHelp(options);

        } else {
            exporter = createFromStatementStr(selStr, pTypes, inFile, outFile, tagStr, printIfNoRecord,
                    newLineReplacement);
        }

        exporter.export();
        exporter.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println();
        exitWithHelp(options);
    }

}

From source file:ekb.elastic.ingest.TaxiQuery.java

public static void main(String... args) {

    Options options = new Options();
    HelpFormatter help = new HelpFormatter();

    try {//ww  w. j a  v a  2 s.  c  o  m
        Option hostOpt = new Option("h", "host", true, "ElasticSearch URL");
        hostOpt.setArgs(1);
        hostOpt.setRequired(true);
        Option portOpt = new Option("p", "port", true, "ElasticSearch URL");
        portOpt.setArgs(1);
        portOpt.setRequired(true);
        Option clusterOpt = new Option("c", "cluster", true, "Cluster");
        clusterOpt.setArgs(1);
        clusterOpt.setRequired(true);
        Option indexOpt = new Option("i", "index", true, "The index");
        indexOpt.setArgs(1);
        indexOpt.setRequired(true);

        Option pickupTimeOpt = new Option("u", "pickup", true, "The pickup time");
        pickupTimeOpt.setArgs(1);
        pickupTimeOpt.setRequired(true);
        Option dropTimeOpt = new Option("d", "dropoff", true, "The dropoff time");
        dropTimeOpt.setArgs(1);
        dropTimeOpt.setRequired(true);

        options.addOption(hostOpt);
        options.addOption(portOpt);
        options.addOption(clusterOpt);
        options.addOption(indexOpt);
        options.addOption(pickupTimeOpt);
        options.addOption(dropTimeOpt);

        GnuParser parser = new GnuParser();
        CommandLine cmd = parser.parse(options, args);

        Settings settings = ImmutableSettings.settingsBuilder().put("cluster.name", cmd.getOptionValue('c'))
                .build();
        Client client = new TransportClient(settings).addTransportAddress(new InetSocketTransportAddress(
                cmd.getOptionValue('h'), Integer.parseInt(cmd.getOptionValue('p'))));

        TaxiQuery tq = new TaxiQuery();

        TaxiStats stats = tq.getTaxiStats(client, cmd.getOptionValues("i"));

        log.info("Results:\n" + stats.toDateString());

        sdf.parse(cmd.getOptionValue("u"));
        sdf.parse(cmd.getOptionValue("d"));

        // 2013-01-01T10:10:00

        ArrayList<TaxiBucket> list = tq.getInterval(client, cmd.getOptionValues("index"),
                cmd.getOptionValue("u"), cmd.getOptionValue("d"), 60);

        log.info("List size is: " + list.size());

        client.close();

    } catch (ParseException pe) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);

        help.printUsage(pw, 80, TaxiQuery.class.getName(), options);

        log.error(sw.toString());

    } catch (TaxiQueryException e) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);
        e.printStackTrace(pw);
        log.error(sw.toString());
    } catch (java.text.ParseException e) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);
        e.printStackTrace(pw);
        log.error(sw.toString());
    }
}

From source file:com.genentech.chemistry.tool.align.SDFAlign.java

public static void main(String... args) {
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);
    options.addOption(opt);//from  w  w  w .ja  va  2 s .  c om

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

    opt = new Option("method", true, "fss|sss|MCS|clique (default mcs).");
    options.addOption(opt);

    opt = new Option("ref", true,
            "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported");
    options.addOption(opt);

    opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image.");
    options.addOption(opt);

    opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output.");
    options.addOption(opt);

    opt = new Option("atomMatch", true,
            "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n"
                    + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n"
                    + "Queryfeatures are considered only if default is used.");
    options.addOption(opt);

    opt = new Option("bondMatch", true,
            "Sequence of none|default specifing how bonds are matched cf. oe document.");
    options.addOption(opt);

    opt = new Option("keepCoreHydrogens", false,
            "If not specified the hydrigen atoms are removed from the core.");
    options.addOption(opt);

    opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd.");
    options.addOption(opt);

    opt = new Option("doNotOptimize", false,
            "If specified the RMSD is computed without moving optimizing the overlay.");
    options.addOption(opt);

    opt = new Option("quiet", false, "Reduced warining messages");
    options.addOption(opt);

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

    if (cmd.getArgs().length > 0)
        exitWithHelp("To many arguments", options);

    // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms
    int atomExpr = OEExprOpts.DefaultAtoms;
    int bondExpr = OEExprOpts.DefaultBonds;

    String atomMatch = cmd.getOptionValue("atomMatch");
    if (atomMatch == null)
        atomMatch = "";
    atomMatch = '|' + atomMatch.toLowerCase() + '|';

    String bondMatch = cmd.getOptionValue("bondMatch");
    if (bondMatch == null)
        bondMatch = "";
    bondMatch = '|' + bondMatch.toLowerCase() + '|';

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");
    String method = cmd.getOptionValue("method");
    String rmsdTag = cmd.getOptionValue("rmsdTag");
    String oMol = cmd.getOptionValue("outputMol");
    boolean doMirror = cmd.hasOption("mirror");
    boolean doOptimize = !cmd.hasOption("doNotOptimize");
    boolean quiet = cmd.hasOption("quiet");

    OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase());

    if (atomMatch.startsWith("|none"))
        atomExpr = 0;
    if (atomMatch.contains("|hcount|"))
        atomExpr |= OEExprOpts.HCount;
    if (atomMatch.contains("|noAromatic|"))
        atomExpr &= (~OEExprOpts.Aromaticity);

    if (bondMatch.startsWith("|none"))
        bondExpr = 0;

    ArrayList<OEMol> refmols = new ArrayList<OEMol>();
    if (refFile != null) {
        oemolistream reffs = new oemolistream(refFile);
        if (!is3DFormat(reffs.GetFormat()))
            oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");
        reffs.SetFormat(OEFormat.MDL);

        int aromodel = OEIFlavor.Generic.OEAroModelOpenEye;
        int qflavor = reffs.GetFlavor(reffs.GetFormat());
        reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel));

        OEMol rmol = new OEMol();
        while (oechem.OEReadMDLQueryFile(reffs, rmol)) {
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);
            refmols.add(rmol);
            rmol = new OEMol();
        }
        rmol.delete();

        if (refmols.size() == 0)
            throw new Error("reference file had no entries");

        reffs.close();
    }

    oemolistream fitfs = new oemolistream(inFile);
    if (!is3DFormat(fitfs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");

    oemolostream ofs = new oemolostream(outFile);
    if (!is3DFormat(ofs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates");

    AlignInterface aligner = null;
    OEGraphMol fitmol = new OEGraphMol();

    if (oechem.OEReadMolecule(fitfs, fitmol)) {
        if (refmols.size() == 0) {
            OEMol rmol = new OEMol(fitmol);
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);

            refmols.add(rmol);
        }

        if ("sss".equalsIgnoreCase(method)) {
            aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("clique".equalsIgnoreCase(method)) {
            aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("fss".equalsIgnoreCase(method)) {
            if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch"))
                exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options);
            aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror);

        } else {
            aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);
        }

        do {
            aligner.align(fitmol);
            oechem.OEWriteMolecule(ofs, fitmol);
        } while (oechem.OEReadMolecule(fitfs, fitmol));

    }

    fitmol.delete();
    if (aligner != null)
        aligner.close();
    for (OEMolBase mol : refmols)
        mol.delete();
    fitfs.close();
    ofs.close();
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosGraphCreator.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);//w  w w .  j a v a2  s.  c  om
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output directory");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(optFileOpt);

    CommandLineParser parser = new PosixParser();

    try {

        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(OUT)));

        Class<?> inClazz = KyanosGraphCreator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();

        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource sourceResource = resourceSet.createResource(sourceUri);
        Map<String, Object> loadOpts = new HashMap<String, Object>();
        if ("zxmi".equals(sourceUri.fileExtension())) {
            loadOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        }

        Runtime.getRuntime().gc();
        long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory before loading: {0}",
                MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
        LOG.log(Level.INFO, "Loading source resource");
        sourceResource.load(loadOpts);
        LOG.log(Level.INFO, "Source resource loaded");
        Runtime.getRuntime().gc();
        long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory after loading: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
        LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));

        Resource targetResource = resourceSet.createResource(targetUri);

        Map<String, Object> saveOpts = new HashMap<String, Object>();

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                saveOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        storeOptions.add(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        saveOpts.put(BlueprintsResourceOptions.STORE_OPTIONS, storeOptions);
        targetResource.save(saveOpts);

        LOG.log(Level.INFO, "Start moving elements");
        targetResource.getContents().clear();
        targetResource.getContents().addAll(sourceResource.getContents());
        LOG.log(Level.INFO, "End moving elements");
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saved");

        if (targetResource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) targetResource);
        } else {
            targetResource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:illarion.compile.Compiler.java

public static void main(final String[] args) {
    ByteArrayOutputStream stdOutBuffer = new ByteArrayOutputStream();
    PrintStream orgStdOut = System.out;
    System.setOut(new PrintStream(stdOutBuffer));

    SLF4JBridgeHandler.removeHandlersForRootLogger();
    SLF4JBridgeHandler.install();/*www .  j  a v  a  2 s  .com*/

    Options options = new Options();

    final Option npcDir = new Option("n", "npc-dir", true,
            "The place where the compiled NPC files are stored.");
    npcDir.setArgs(1);
    npcDir.setArgName("directory");
    npcDir.setRequired(false);
    options.addOption(npcDir);

    final Option questDir = new Option("q", "quest-dir", true,
            "The place where the compiled Quest files are stored.");
    questDir.setArgs(1);
    questDir.setArgName("directory");
    questDir.setRequired(false);
    options.addOption(questDir);

    final Option type = new Option("t", "type", true,
            "This option is used to set what kind of parser is supposed to be used in case"
                    + " the content of standard input is processed.");
    type.setArgs(1);
    type.setArgName("type");
    type.setRequired(false);
    options.addOption(type);

    CommandLineParser parser = new GnuParser();
    try {
        CommandLine cmd = parser.parse(options, args);

        String[] files = cmd.getArgs();
        if (files.length > 0) {
            System.setOut(orgStdOut);
            stdOutBuffer.writeTo(orgStdOut);

            processFileMode(cmd);
        } else {
            System.setOut(orgStdOut);
            processStdIn(cmd);
        }
    } catch (final ParseException e) {
        final HelpFormatter helpFormatter = new HelpFormatter();
        helpFormatter.printHelp("java -jar compiler.jar [Options] File", options, true);
        System.exit(-1);
    } catch (final IOException e) {
        LOGGER.error(e.getLocalizedMessage());
        System.exit(-1);
    }
}

From source file:com.github.braully.graph.UtilResultCompare.java

public static void main(String... args) throws Exception {
    Options options = new Options();

    Option input = new Option("i", "input", true, "input file path");
    input.setRequired(false);
    options.addOption(input);/*  w w  w. j a v  a 2 s . co m*/

    Option output = new Option("o", "output", true, "output file");
    output.setRequired(false);
    options.addOption(output);

    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("UtilResult", options);

        System.exit(1);
        return;
    }

    String inputFilePath = cmd.getOptionValue("input");
    if (inputFilePath == null) {
        inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-quartic-ht.txt";

        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-mft-parcial-ht.txt";
        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-highlyirregular-ht.txt";
        //            inputFilePath = "/home/strike/Documentos/grafos-processados/mtf/resultado-ht.txt";
        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-hypo-parcial-ht.txt";
        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-eul-ht.txt";
        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-almhypo-ht.txt";
        //            inputFilePath = "/home/strike/Dropbox/documentos/mestrado/resultado-processamento-grafos/resultado-Almost_hypohamiltonian_graphs_cubic-parcial-ht.txt";
    }
    if (inputFilePath != null) {
        if (inputFilePath.toLowerCase().endsWith(".txt")) {
            processFileTxt(inputFilePath);
        } else if (inputFilePath.toLowerCase().endsWith(".json")) {
            processFileJson(inputFilePath);
        }
    }
}

From source file:com.genentech.chemistry.openEye.apps.enumerate.SDFEnumerator.java

public static void main(String... args) throws IOException {
    Options options = new Options();
    Option opt = new Option("out", true, "output file oe-supported");
    opt.setRequired(true);
    options.addOption(opt);/*from w  w  w. ja  v a  2 s  .c  o m*/

    opt = new Option("hydrogenExplicit", false, "Use explicit hydrogens");
    options.addOption(opt);

    opt = new Option("correctValences", false, "Correct valences after the enumeration");
    options.addOption(opt);

    opt = new Option("regenerate2D", false, "Regenerate 2D coordinates for the products");
    options.addOption(opt);

    opt = new Option("reactAllSites", false, "Generate a product for each match in a reagent.");
    options.addOption(opt);

    opt = new Option("randomFraction", true, "Only output a fraction of the products.");
    options.addOption(opt);

    opt = new Option("maxAtoms", true, "Only output products with <= maxAtoms.");
    options.addOption(opt);

    opt = new Option("notReacted", true,
            "Output file for reagents that didn't produce at leaste one output molecule, useful for debugging SMIRKS.");
    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 < 2) {
        exitWithHelp("Transformation and/or reagentFiles missing", options);
    }
    String smirks = args[0];
    if (new File(smirks).canRead())
        smirks = IOUtil.fileToString(smirks).trim();
    if (!smirks.contains(">>"))
        smirks = scaffoldToSmirks(smirks);
    String[] reagentSmiOrFiles = Arrays.copyOfRange(args, 1, args.length);

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

    String outFile = cmd.getOptionValue("out");
    OELibraryGen lg = new OELibraryGen();
    lg.Init(smirks);
    if (!lg.IsValid())
        exitWithHelp("Invalid Transform: " + smirks, options);

    lg.SetExplicitHydrogens(cmd.hasOption("hydrogenExplicit"));
    lg.SetValenceCorrection(cmd.hasOption("correctValences"));
    lg.SetRemoveUnmappedFragments(true);

    boolean regenerate2D = cmd.hasOption("regenerate2D");
    boolean reactAllSites = cmd.hasOption("reactAllSites");
    String unreactedFile = null;
    if (cmd.hasOption("notReacted")) {
        unreactedFile = cmd.getOptionValue("notReacted");
    }

    double randomFract = 2;
    if (cmd.hasOption("randomFraction"))
        randomFract = Double.parseDouble(cmd.getOptionValue("randomFraction"));

    int maxAtoms = 0;
    if (cmd.hasOption("maxAtoms"))
        maxAtoms = Integer.parseInt(cmd.getOptionValue("maxAtoms"));

    SDFEnumerator en = new SDFEnumerator(lg, reactAllSites, reagentSmiOrFiles);
    en.generateLibrary(outFile, maxAtoms, randomFract, regenerate2D, unreactedFile);
    en.delete();
}

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

/**
 * @param args//from  w ww. j a  va2  s .  co m
 */
public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option(OPT_INFILE, true,
            "input file oe-supported Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_REFFILE, true,
            "Reference file of molecules which define pre-existign exclusion spheres.");
    options.addOption(opt);

    opt = new Option(OPT_RADIUS, true, "Radius of exclusion spehre in A2.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_GROUPBY, true,
            "Group by fieldname, run sphere exclusion for consecutive groups of records with same value for this field.");
    options.addOption(opt);

    opt = new Option(OPT_DONotOpt, false,
            "If specified the RMSD is computed without trying to optimize the alignment.");
    options.addOption(opt);

    opt = new Option(OPT_PRINT_All, false, "print all molecule, check includeIdx tag");
    options.addOption(opt);

    opt = new Option(OPT_MIRROR, false, "For non-chiral molecules also try mirror image");
    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 (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    String refFile = cmd.getOptionValue(OPT_REFFILE);
    String groupBy = cmd.getOptionValue(OPT_GROUPBY);
    boolean doOptimize = !cmd.hasOption(OPT_DONotOpt);
    double radius = Double.parseDouble(cmd.getOptionValue(OPT_RADIUS));
    boolean printAll = cmd.hasOption(OPT_PRINT_All);
    boolean doMirror = cmd.hasOption(OPT_MIRROR);

    SdfRMSDSphereExclusion sphereExclusion = new SdfRMSDSphereExclusion(refFile, outFile, radius, printAll,
            doMirror, doOptimize, groupBy);

    sphereExclusion.run(inFile);
    sphereExclusion.close();
}