Example usage for java.util Arrays toString

Introduction

In this page you can find the example usage for java.util Arrays toString.

Prototype

public static String toString(Object[] a) 

Source Link

Document

Returns a string representation of the contents of the specified array.

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);//from   w  w w  .  j a v  a2 s .c o  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 = 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.NeoEMFGraphQueryInvisibleMethodDeclarations.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 . jav a2  s.c  om*/
    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(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_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(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        System.out.println(loadOpts);
        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.getInvisibleMethodDeclarations(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.NeoEMFGraphQuerySpecificInvisibleMethodDeclarations.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);// www .  j  av a2s  . 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(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_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(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        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:edu.umd.cloud9.collection.trec.DemoCountTrecDocuments.java

/**
 * Dispatches command-line arguments to the tool via the {@code ToolRunner}.
 */// w w  w .  j a  va  2  s.  c om
public static void main(String[] args) throws Exception {
    LOG.info("Running " + DemoCountTrecDocuments.class.getCanonicalName() + " with args "
            + Arrays.toString(args));
    ToolRunner.run(new Configuration(), new DemoCountTrecDocuments(), args);
}

---

From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFGraphQueryThrownExceptions.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 a  v a2s  .  c om*/
    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(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_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(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        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.NeoEMFMapQueryInvisibleMethodDeclarations.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);//www  . j a  va  2s  .c o  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 = NeoEMFMapQueryInvisibleMethodDeclarations.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.getInvisibleMethodDeclarations(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   ww w  . j av  a 2  s. c o  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:edu.umd.cloud9.collection.trecweb.RepackTrecWebCollection.java

/**
 * Dispatches command-line arguments to the tool via the {@code ToolRunner}.
 *//*from  ww  w  .  ja v a  2  s.c  o m*/
public static void main(String[] args) throws Exception {
    LOG.info("Running " + RepackTrecWebCollection.class.getCanonicalName() + " with args "
            + Arrays.toString(args));
    ToolRunner.run(new Configuration(), new RepackTrecWebCollection(), args);
}

---

From source file:edu.umd.cloud9.collection.medline.CountMedlineCitations.java

/**
 * Dispatches command-line arguments to the tool via the {@code ToolRunner}.
 *//*from  w  w w . j  a va 2s  . c o  m*/
public static void main(String[] args) throws Exception {
    LOG.info("Running " + CountMedlineCitations.class.getCanonicalName() + " with args "
            + Arrays.toString(args));
    ToolRunner.run(new CountMedlineCitations(), args);
}

---

From source file:eqtlmappingpipeline.util.ModuleEqtWestraReplication.java

/**
 * @param args the command line arguments
 *//*  w w w. j  a  v  a2s . co  m*/
public static void main(String[] args) throws IOException, LdCalculatorException {

    System.out.println(HEADER);
    System.out.println();
    System.out.flush(); //flush to make sure header is before errors
    try {
        Thread.sleep(25); //Allows flush to complete
    } catch (InterruptedException ex) {
    }

    CommandLineParser parser = new PosixParser();
    final CommandLine commandLine;
    try {
        commandLine = parser.parse(OPTIONS, args, true);
    } catch (ParseException ex) {
        System.err.println("Invalid command line arguments: " + ex.getMessage());
        System.err.println();
        new HelpFormatter().printHelp(" ", OPTIONS);
        System.exit(1);
        return;
    }

    final String[] genotypesBasePaths = commandLine.getOptionValues("g");
    final RandomAccessGenotypeDataReaderFormats genotypeDataType;
    final String replicationQtlFilePath = commandLine.getOptionValue("e");
    final String interactionQtlFilePath = commandLine.getOptionValue("i");
    final String outputFilePath = commandLine.getOptionValue("o");
    final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld"));
    final int window = Integer.parseInt(commandLine.getOptionValue("w"));

    System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths));
    System.out.println("Interaction file: " + interactionQtlFilePath);
    System.out.println("Replication file: " + replicationQtlFilePath);
    System.out.println("Output: " + outputFilePath);
    System.out.println("LD: " + ldCutoff);
    System.out.println("Window: " + window);

    try {
        if (commandLine.hasOption("G")) {
            genotypeDataType = RandomAccessGenotypeDataReaderFormats
                    .valueOf(commandLine.getOptionValue("G").toUpperCase());
        } else {
            if (genotypesBasePaths[0].endsWith(".vcf")) {
                System.err.println(
                        "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file.");
                System.exit(1);
                return;
            }
            try {
                genotypeDataType = RandomAccessGenotypeDataReaderFormats
                        .matchFormatToPath(genotypesBasePaths[0]);
            } catch (GenotypeDataException e) {
                System.err
                        .println("Unable to determine input 1 type based on specified path. Please specify -G");
                System.exit(1);
                return;
            }
        }
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G")
                + "\" is not a valid input data format");
        System.exit(1);
        return;
    }

    final RandomAccessGenotypeData genotypeData;

    try {
        genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null,
                0.8);
    } catch (TabixFileNotFoundException e) {
        LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n"
                + "Please see README on how to create a tabix file");
        System.exit(1);
        return;
    } catch (IOException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (IncompatibleMultiPartGenotypeDataException e) {
        LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (GenotypeDataException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    }

    ChrPosTreeMap<ArrayList<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>();

    CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t');
    String[] replicationHeader = replicationQtlReader.readNext();
    String[] replicationLine;
    while ((replicationLine = replicationQtlReader.readNext()) != null) {

        try {

            GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL],
                    Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]));
            if (variant == null) {
                continue;
            }

            Alleles variantAlleles = variant.getVariantAlleles();
            String[] replicationAllelesString = StringUtils.split(replicationLine[REPLICATION_ALLELES_COL],
                    '/');

            Alleles replicationAlleles = Alleles.createBasedOnString(replicationAllelesString[0],
                    replicationAllelesString[1]);
            Allele assessedAlleleReplication = Allele.create(replicationLine[REPLICATION_ALLELE_ASSESSED_COL]);

            boolean isAmbigous = replicationAlleles.isAtOrGcSnp();

            if (!variantAlleles.equals(replicationAlleles)) {
                if (variantAlleles.equals(replicationAlleles.getComplement())) {
                    assessedAlleleReplication = assessedAlleleReplication.getComplement();
                } else {
                    continue;
                }
            }

            ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL],
                    Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]),
                    replicationLine[REPLICATION_GENE_COL],
                    Double.parseDouble(replicationLine[REPLICATION_BETA_COL]),
                    assessedAlleleReplication.getAlleleAsString(), replicationLine, isAmbigous);
            ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(),
                    replicationQtl.getPos());
            if (posReplicationQtls == null) {
                posReplicationQtls = new ArrayList<>();
                replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls);
            }
            posReplicationQtls.add(replicationQtl);

        } catch (Exception e) {
            System.out.println(Arrays.toString(replicationLine));
            throw e;
        }
    }

    int interactionSnpNotInGenotypeData = 0;
    int noReplicationQtlsInWindow = 0;
    int noReplicationQtlsInLd = 0;
    int multipleReplicationQtlsInLd = 0;
    int replicationTopSnpNotInGenotypeData = 0;

    final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0');
    final String[] outputLine = new String[15 + EXTRA_COL_FROM_REPLICATION.length];
    int c = 0;
    outputLine[c++] = "Chr";
    outputLine[c++] = "Pos";
    outputLine[c++] = "SNP";
    outputLine[c++] = "Gene";
    outputLine[c++] = "Module";
    outputLine[c++] = "DiscoveryZ";
    outputLine[c++] = "ReplicationZ";
    outputLine[c++] = "DiscoveryZCorrected";
    outputLine[c++] = "ReplicationZCorrected";
    outputLine[c++] = "DiscoveryAlleleAssessed";
    outputLine[c++] = "ReplicationAlleleAssessed";
    outputLine[c++] = "bestLd";
    outputLine[c++] = "bestLd_dist";
    outputLine[c++] = "nextLd";
    outputLine[c++] = "replicationAmbigous";
    for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
        outputLine[c++] = replicationHeader[EXTRA_COL_FROM_REPLICATION[i]];
    }
    outputWriter.writeNext(outputLine);

    HashSet<String> notFound = new HashSet<>();

    CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t');
    interactionQtlReader.readNext();//skip header
    String[] interactionQtlLine;
    while ((interactionQtlLine = interactionQtlReader.readNext()) != null) {

        String snp = interactionQtlLine[1];
        String chr = interactionQtlLine[2];
        int pos = Integer.parseInt(interactionQtlLine[3]);
        String gene = interactionQtlLine[4];
        String alleleAssessed = interactionQtlLine[9];
        String module = interactionQtlLine[12];
        double discoveryZ = Double.parseDouble(interactionQtlLine[10]);

        GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos);

        if (interactionQtlVariant == null) {
            System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos);
            ++interactionSnpNotInGenotypeData;
            continue;
        }

        ReplicationQtl bestMatch = null;
        double bestMatchR2 = Double.NaN;
        Ld bestMatchLd = null;
        double nextBestR2 = Double.NaN;

        ArrayList<ReplicationQtl> sameSnpQtls = replicationQtls.get(chr, pos);

        if (sameSnpQtls != null) {
            for (ReplicationQtl sameSnpQtl : sameSnpQtls) {
                if (sameSnpQtl.getGene().equals(gene)) {
                    bestMatch = sameSnpQtl;
                    bestMatchR2 = 1;
                }
            }
        }

        NavigableMap<Integer, ArrayList<ReplicationQtl>> potentionalReplicationQtls = replicationQtls
                .getChrRange(chr, pos - window, true, pos + window, true);

        for (ArrayList<ReplicationQtl> potentialReplicationQtls : potentionalReplicationQtls.values()) {

            for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) {

                if (!potentialReplicationQtl.getGene().equals(gene)) {
                    continue;
                }

                GeneticVariant potentialReplicationQtlVariant = genotypeData
                        .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos());
                    ++replicationTopSnpNotInGenotypeData;
                    continue;
                }

                Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant);
                double r2 = ld.getR2();

                if (r2 > 1) {
                    r2 = 1;
                }

                if (bestMatch == null) {
                    bestMatch = potentialReplicationQtl;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                } else if (r2 > bestMatchR2) {
                    bestMatch = potentialReplicationQtl;
                    nextBestR2 = bestMatchR2;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                }

            }
        }

        double replicationZ = Double.NaN;
        double replicationZCorrected = Double.NaN;
        double discoveryZCorrected = Double.NaN;

        String replicationAlleleAssessed = null;

        if (bestMatch != null) {
            replicationZ = bestMatch.getBeta();
            replicationAlleleAssessed = bestMatch.getAssessedAllele();

            if (pos != bestMatch.getPos()) {

                String commonHap = null;
                double commonHapFreq = -1;
                for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) {

                    double f = hapFreq.getValue();

                    if (f > commonHapFreq) {
                        commonHapFreq = f;
                        commonHap = hapFreq.getKey();
                    }

                }

                String[] commonHapAlleles = StringUtils.split(commonHap, '/');

                discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1;
                replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            } else {

                discoveryZCorrected = discoveryZ;
                replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;
                //replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) || alleleAssessed.equals(String.valueOf(Utils.getComplementNucleotide(replicationAlleleAssessed.charAt(0)))) ? replicationZ : replicationZ * -1;

            }

        }

        c = 0;
        outputLine[c++] = chr;
        outputLine[c++] = String.valueOf(pos);
        outputLine[c++] = snp;
        outputLine[c++] = gene;
        outputLine[c++] = module;
        outputLine[c++] = String.valueOf(discoveryZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected);
        outputLine[c++] = alleleAssessed;
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAssessedAllele());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos()));
        outputLine[c++] = String.valueOf(nextBestR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.isIsAmbigous());

        if (bestMatch == null) {
            for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
                outputLine[c++] = "NA";
            }
        } else {
            for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
                outputLine[c++] = bestMatch.getLine()[EXTRA_COL_FROM_REPLICATION[i]];
            }
        }

        outputWriter.writeNext(outputLine);

    }

    outputWriter.close();

    for (String e : notFound) {
        System.err.println("Not found: " + e);
    }

    System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData);
    System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow);
    System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd);
    System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd);
    System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData);

}

---

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