Java Namespace.getList方法代码示例

import net.sourceforge.argparse4j.inf.Namespace; //导入方法依赖的package包/类
private void run(String... args) throws Exception {
    Namespace namespace;
    try {
        namespace = argumentParser.parseArgs(args);
    } catch (ArgumentParserException e) {
        argumentParser.handleError(e);
        return;
    }

    List<String> urls = namespace.getList(urlKey);

    try {
        Set<HttpUrl> allUrls = argResolver.getAllUrls(urls);
        if (allUrls.isEmpty())
            LOG.info("No playlists found! Check your args: " + Arrays.toString(args));

        for (HttpUrl url : allUrls)
            getHandler(url).join();
    } catch (Throwable t) {
        LOG.info("Error {}: {}", t.getClass().getSimpleName(), t.getMessage());
        LOG.debug("Detailed error output", t);
    } finally {
        theClosener.close();
    }
}
 

import net.sourceforge.argparse4j.inf.Namespace; //导入方法依赖的package包/类
public static void execute(final Namespace parsedArgs) throws IOException, ValidationException {
    final Map<String, Object> inputMap = new HashMap<>();
    for (String input : parsedArgs.<String>getList("input")) {
        String[] keyValue = input.split("=", 2);
        if (keyValue.length == 2) {
            inputMap.put(keyValue[0], keyValue[1]);
        } else {
            LOG.warn("Invalid input string '{}' - expecting KEY=VALUE");
        }
    }
    LOG.trace("Have {} input parameters", inputMap.size());

    final String name = parsedArgs.getString("name"), script = parsedArgs.getString("script");
    final Map<String, ?> outcome = name != null ?
            evaluateNamespace(parsedArgs, name, inputMap) : evaluateStandalone(parsedArgs, script, inputMap);
    if (outcome != null) {
        System.out.println(
                Planout4jTool.getGson(new Namespace(ImmutableMap.<String, Object>of("pretty", Boolean.TRUE)))
                        .toJson(outcome));
    }
}
 

import net.sourceforge.argparse4j.inf.Namespace; //导入方法依赖的package包/类
/**
 * Cluster the C-alpha chains of a set of PDB ids.
 * @param args the input args - currently none taken
 * @throws IOException an error reading from the URL or the seqeunce file
 */
public static void main(String[] args) throws IOException {
	// Read the arguments
	Namespace ns = parseArgs(args);
	// Get the actual arguments
	String alignMethod = ns.getString("align");
	String filePath = ns.getString("hadoop");
	int minLength = ns.getInt("minlength");
	double sample = ns.getDouble("sample");
	boolean useFiles = ns.getBoolean("files");
	
	// Get the list of PDB ids
	List<String> pdbIdList = ns.<String> getList("pdbId");

	// Get the chains that correpspond to that
	JavaPairRDD<String, Atom[]>  chainRDD;
	if(pdbIdList.size()>0){
		if(useFiles==true){
			StructureDataRDD structureDataRDD = new StructureDataRDD(
					BiojavaSparkUtils.getFromList(convertToFiles(pdbIdList))
					.mapToPair(t -> new Tuple2<String, StructureDataInterface>(t._1, BiojavaSparkUtils.convertToStructDataInt(t._2))));
			chainRDD = BiojavaSparkUtils.getChainRDD(structureDataRDD, minLength);

		}
		else{
			chainRDD = BiojavaSparkUtils.getChainRDD(pdbIdList, minLength);
		}
	}
	else if(!filePath.equals(defaultPath)){
		chainRDD = BiojavaSparkUtils.getChainRDD(filePath, minLength, sample);
	}
	else{
		System.out.println("Must specify PDB ids or an hadoop sequence file");
		return;
	}

	System.out.println("Analysisng " + chainRDD.count() + " chains");
	JavaPairRDD<Tuple2<String,Atom[]>,Tuple2<String, Atom[]>> comparisons = SparkUtils.getHalfCartesian(chainRDD, chainRDD.getNumPartitions());
	JavaRDD<Tuple3<String, String,  AFPChain>> similarities = comparisons.map(t -> new Tuple3<String, String, AFPChain>(t._1._1, t._2._1, 
			AlignmentTools.getBiojavaAlignment(t._1._2, t._2._2, alignMethod)));
	JavaRDD<Tuple6<String, String, Double, Double, Double, Double>> allScores = similarities.map(t -> new Tuple6<String, String, Double, Double, Double, Double>(
			t._1(), t._2(), t._3().getTMScore(), t._3().getTotalRmsdOpt(),  (double) t._3().getTotalLenOpt(),  t._3().getAlignScore())).cache();
	if(alignMethod.equals("DUMMY")){
		JavaDoubleRDD doubleDist = allScores.mapToDouble(t -> t._3());
		System.out.println("Average dist: "+doubleDist.mean());
	}
	else{
		writeData(allScores);
	}
}
 

import net.sourceforge.argparse4j.inf.Namespace; //导入方法依赖的package包/类
@Override
protected void run(Environment environment, Namespace namespace, EmoConfiguration configuration)
        throws Exception {
    String id = namespace.getString("id");

    AllTablesReportOptions options = new AllTablesReportOptions();
    options.setReadOnly(namespace.getBoolean("readOnly"));

    List<String> placements = namespace.getList("placements");
    if (placements != null && !placements.isEmpty()) {
        options.setPlacements(ImmutableSet.copyOf(placements));
    }

    Integer shardId = namespace.getInt("shard");
    if (shardId != null) {
        options.setFromShardId(shardId);
    }

    String table = namespace.getString("table");
    if (table != null) {
        options.setFromTableUuid(TableUuidFormat.decode(table));
    }

    Injector injector = Guice.createInjector(new EmoModule(configuration, environment, EmoServiceMode.CLI_TOOL));

    ContainerLifeCycle containerLifeCycle = new ContainerLifeCycle();
    environment.lifecycle().attach(containerLifeCycle);
    containerLifeCycle.start();
    try {
        AllTablesReportGenerator generator = injector.getInstance(AllTablesReportGenerator.class);
        AllTablesReportResult result = generator.runReport(id, options);

        System.out.println(result);
    } finally {
        containerLifeCycle.stop();
    }
}
 

import net.sourceforge.argparse4j.inf.Namespace; //导入方法依赖的package包/类
@Override
protected void run(Bootstrap<EmoConfiguration> bootstrap, Namespace namespace, EmoConfiguration config)
        throws Exception {
    String host = namespace.getString("host");
    int limit = namespace.getInt("limit");
    String subscription = namespace.getString("subscription");
    String apiKey = namespace.getString("api_key");
    Set<String> tables = Sets.newHashSet(namespace.<String>getList("table"));
    List<String> keys = namespace.getList("key");
    Set<String> keySet = keys != null ? Sets.newHashSet(keys) : null;

    System.out.println("Connecting...");

    URI uri = URI.create(host).resolve(DatabusClient.SERVICE_PATH + "/_raw");
    MetricRegistry metricRegistry = bootstrap.getMetricRegistry();
    Client client = createDefaultJerseyClient(config.getHttpClientConfiguration(), metricRegistry, "");

    QueueService databus = QueueServiceAuthenticator.proxied(new QueueClient(uri, new JerseyEmoClient(client)))
            .usingCredentials(apiKey);

    for (;;) {
        List<Message> events = databus.peek(subscription, 5000);

        List<String> ids = Lists.newArrayList();
        for (Message event : events) {
            //noinspection unchecked
            Map<String, String> coord = (Map<String, String>) checkNotNull(event.getPayload());
            String table = checkNotNull(coord.get("table"));
            String key = checkNotNull(coord.get("key"));
            if (tables.contains(table) && (keySet == null || keySet.contains(key))) {
                ids.add(event.getId());
                if (--limit <= 0) {
                    break;
                }
            }
        }
        if (ids.isEmpty()) {
            System.out.println("All matching events of the first " + events.size() + " have been purged.");
            break;
        }

        System.out.println("Purging " + ids.size() + " events...");
        databus.acknowledge(subscription, ids);

        if (limit == 0) {
            System.out.println("Limit reached.");
            break;
        }
    }
}