import org.mapdb.Atomic; //导入依赖的package包/类
public void saveReferenceNetwork(Network network) throws IOException {
    Objects.requireNonNull(network);
    if (!config.getMapDb().isPersistent()) {
        this.referenceNetwork = network;
    } else if (this.referenceNetwork == null || !this.referenceNetwork.getId().equals(network.getId())) {
        DataSource dataSource = new FileDataSource(storeDir, network.getId());
        Properties parameters = new Properties();
        parameters.setProperty("iidm.export.xml.indent", "true");
        Exporters.export("XIIDM", network, parameters, dataSource);
        Atomic.String reference = db.atomicString("referenceNetwotk").createOrOpen();
        String oldNet = reference.get();
        reference.set(network.getId() + ".xiidm");
        this.referenceNetwork = network;
        if (oldNet != null) {
            Files.delete(Paths.get(storeDir.toString(), oldNet));
        }
    }
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
/**
 * Reads all Metadata internal datastructure from file to the instance of this class
 */
public void loadDataFromFile() {

	AptaLogger.log(Level.CONFIG, this.getClass(), "Reading metadata file from '" + this.metadataPath.toFile());
	
	// Open a connection to disk
	DB db = DBMaker
	        .fileDB(this.metadataPath.toFile())
	        .readOnly()
	        .fileMmapEnableIfSupported()
	        .closeOnJvmShutdown()
	        .make();
	
	// Load all class members from db
	Atomic.Var<Object> variable;
	
	variable = db.atomicVar("qualityScoresForward").createOrOpen();
	qualityScoresForward = (HashMap<String, ConcurrentHashMap<Integer, Accumulator>>) variable.get();

	variable = db.atomicVar("qualityScoresReverse").createOrOpen();
	qualityScoresReverse = (HashMap<String, ConcurrentHashMap<Integer, Accumulator>>) variable.get();
	
	variable = db.atomicVar("nucleotideDistributionForward").createOrOpen();
	nucleotideDistributionForward = (HashMap<String, ConcurrentHashMap<Integer, ConcurrentHashMap<Byte, Integer>>>) variable.get();
	
	variable = db.atomicVar("nucleotideDistributionReverse").createOrOpen();
	nucleotideDistributionReverse = (HashMap<String, ConcurrentHashMap<Integer, ConcurrentHashMap<Byte, Integer>>>) variable.get();

	variable = db.atomicVar("nucleotideDistributionAccepted").createOrOpen();
	nucleotideDistributionAccepted = (HashMap<String, ConcurrentHashMap<Integer, ConcurrentHashMap<Integer, ConcurrentHashMap<Byte, Integer>>>>) variable.get();
	
	variable = db.atomicVar("parserStatistics").createOrOpen();
	parserStatistics = (HashMap<String, Integer>) variable.get();
	
	// Close database connection
       db.close();
	
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
/**
 * Takes the current state of all class members of Metadata and dumps them on disk
 */
public void saveDataToFile() {
	
	// Open a connection to disk
	DB db = DBMaker
	        .fileDB(this.metadataPath.toFile())
	        .fileMmapEnableIfSupported()
	        .closeOnJvmShutdown()
	        .make();
	
	// Load all class members from db
	Atomic.Var<Object> variable;
	
	variable = db.atomicVar("qualityScoresForward").createOrOpen();
	variable.set(qualityScoresForward);

	variable = db.atomicVar("qualityScoresReverse").createOrOpen();
	variable.set(qualityScoresReverse);
	
	variable = db.atomicVar("nucleotideDistributionForward").createOrOpen();
	variable.set(nucleotideDistributionForward);
	
	variable = db.atomicVar("nucleotideDistributionReverse").createOrOpen();
	variable.set(nucleotideDistributionReverse);

	variable = db.atomicVar("nucleotideDistributionAccepted").createOrOpen();
	variable.set(nucleotideDistributionAccepted);
	
	variable = db.atomicVar("parserStatistics").createOrOpen();
	variable.set(parserStatistics);
	
	// Close database connection
       db.close();
	
       AptaLogger.log(Level.CONFIG, this.getClass(), "Saved metadata to file '" + this.metadataPath.toFile());
       
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
public static String createPrefixedURI(final String fullURI, final Map<String, String> uriPrefixedURIMap,
		final Map<String, String> tempNamespacePrefixes, final Map<String, String> inMemoryNamespacePrefixes,
		final Tuple<Atomic.Long, DB> prefixCounterTuple, final GraphDatabaseService database,
		final TransactionHandler tx)
		throws DMPGraphException {

	if (fullURI == null) {

		throw new DMPGraphException("full URI shouldn't be null");
	}

	if (uriPrefixedURIMap != null) {

		if (!uriPrefixedURIMap.containsKey(fullURI)) {

			final String prefixedURI = determinePrefixedURI(fullURI, tempNamespacePrefixes, inMemoryNamespacePrefixes, prefixCounterTuple,
					database, tx);

			uriPrefixedURIMap.put(fullURI, prefixedURI);
		}

		return uriPrefixedURIMap.get(fullURI);
	} else {

		return determinePrefixedURI(fullURI, tempNamespacePrefixes, inMemoryNamespacePrefixes, prefixCounterTuple, database, tx);
	}
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
public static String determinePrefixedURI(final String fullURI, final Map<String, String> tempNamespacePrefixes,
		final Map<String, String> inMemoryNamespacePrefixes, final Tuple<Atomic.Long, DB> prefixCounterTuple, final GraphDatabaseService database,
		final TransactionHandler tx)
		throws DMPGraphException {

	final Tuple<String, String> uriParts = URI.determineParts(fullURI);
	final String namespaceURI = uriParts.v1();
	final String localName = uriParts.v2();

	final String prefix = NamespaceUtils
			.getPrefix(namespaceURI, tempNamespacePrefixes, inMemoryNamespacePrefixes, prefixCounterTuple, database, tx);

	return prefix + NamespaceUtils.PREFIX_DELIMITER + localName;
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
public static Atomic.Long createOrGetLongIndex(final DB db, final String indexName, final long initValue) {

		final Atomic.Long longIndex;

		if (db.getCatalog().containsKey(indexName)) {

			final Atomic.Long atomicLong = db.getAtomicLong(indexName);
			atomicLong.getAndSet(initValue);

			longIndex = atomicLong;

			db.commit();
		} else {

			longIndex = db.createAtomicLong(indexName, initValue);
		}

		return longIndex;
	}
 

import org.mapdb.Atomic; //导入依赖的package包/类
private static long getNewPrefixCount(final Tuple<Atomic.Long, DB> prefixCounterTuple) {

		final Atomic.Long prefixCounter = prefixCounterTuple.v1();
		final DB prefixCounterDB = prefixCounterTuple.v2();

		final long prefixCount = prefixCounter.getAndIncrement();

		prefixCounterDB.commit();

		return prefixCount;
	}
 

import org.mapdb.Atomic; //导入依赖的package包/类
public static Tuple<Atomic.Long, DB> createOrGetPersistentLongIndexGlobalTransactional(final String indexFileName, final String indexName,
		final long initValue) {

	final DB db = createGlobalTransactionalPermanentMapDB(indexFileName);

	return Tuple.tuple(createOrGetLongIndex(db, indexName, initValue), db);
}
 

import org.mapdb.Atomic; //导入依赖的package包/类
public static Atomic.Long createLongIndex(final DB db, final String indexName) {

		return db.getAtomicLong(indexName);
	}