com.compomics.util.db

Class ObjectsDB

java.lang.Object

com.compomics.util.db.ObjectsDB

All Implemented Interfaces:

Serializable

public class ObjectsDB
extends Object
implements Serializable

A database which can easily be used to store objects.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	LONG_KEY_PREFIX Suffix used for long keys.
static String	LONG_KEY_TABLE The table where to save the long keys.
static String	LONG_TABLE_NAMES Name for the long table names.
static int	MAX_KEY_LENGTH The maximum key length before using the key correction for long keys.
static int	TABLE_NAME_MAX_LENGTH The maximal length of a table name.
static int	VARCHAR_MAX_LENGTH The maximal length of a varchar.

Constructor Summary

Constructors

Constructor and Description
ObjectsDB(String folder, String dbName, boolean deleteOldDatabase, ObjectsCache objectsCache) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addTable(String tableName) Adds the desired table in the database.
void	close() Closes the db connection.
String	correctKey(String tableName, String key) Indexes the long keys by a number.
String	correctTableName(String tableName) Surrounds the table name with quotation marks such that spaces etc are allowed.
void	deleteObject(String tableName, String objectKey) Deletes an object from the desired table.
void	establishConnection(String aDbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache) Establishes connection to the database.
String	getName() Returns the database name.
ObjectsCache	getObjectsCache() Returns the cache used by this database.
String	getOriginalKey(String tableName, String correctedKey) Returns the original key of the corrected long key.
boolean	hasTable(String tableName) Indicates whether the database contains the given table.
boolean	inDB(String tableName, String objectKey, boolean cache) Indicates whether an object is loaded in the given table.
void	insertObject(String tableName, String objectKey, Object object, boolean inCache) Stores an object in the desired table.
void	insertObjects(String tableName, HashMap<String,Object> objects, WaitingHandler waitingHandler) Inserts a set of objects in the given table.
void	insertObjects(String tableName, HashMap<String,Object> objects, WaitingHandler waitingHandler, boolean allNewObjects) Inserts a set of objects in the given table.
void	loadObjects(String tableName, ArrayList<String> keys, WaitingHandler waitingHandler) Loads some objects from a table in the cache.
void	loadObjects(String tableName, WaitingHandler waitingHandler) Loads all objects from a table in the cache.
Object	retrieveObject(String tableName, String objectKey, boolean useDB) Retrieves an object from the desired table.
Object	retrieveObject(String tableName, String objectKey, boolean useDB, boolean useCache) Retrieves an object from the desired table.
void	setObjectCache(ObjectsCache objectCache) Sets the object cache to be used by this database.
ArrayList<String>	tableContent(String tableName) Returns an arraylist with the content in the given table.
HashSet<String>	tableContentAsSet(String tableName) Returns a hashset with the content in the given table.
void	updateObject(String tableName, String objectKey, Object object) Updates an object in the cache or in the tables if not in cache.
void	updateObject(String tableName, String objectKey, Object object, boolean cache) Updates an object in the cache or in the tables if not in cache or if cache is wrong.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TABLE_NAME_MAX_LENGTH

public static final int TABLE_NAME_MAX_LENGTH

The maximal length of a table name.

See Also:

Constant Field Values

VARCHAR_MAX_LENGTH

public static final int VARCHAR_MAX_LENGTH

The maximal length of a varchar. Note: 32672 is the max length for a varchar.

See Also:

Constant Field Values

MAX_KEY_LENGTH

public static final int MAX_KEY_LENGTH

The maximum key length before using the key correction for long keys.

See Also:

Constant Field Values

LONG_KEY_PREFIX

public static final String LONG_KEY_PREFIX

Suffix used for long keys.

See Also:

Constant Field Values

LONG_TABLE_NAMES

public static final String LONG_TABLE_NAMES

Name for the long table names.

See Also:

Constant Field Values

LONG_KEY_TABLE

public static final String LONG_KEY_TABLE

The table where to save the long keys.

See Also:

Constant Field Values

Constructor Detail

ObjectsDB

public ObjectsDB(String folder,
         String dbName,
         boolean deleteOldDatabase,
         ObjectsCache objectsCache)
          throws SQLException

Constructor.

Parameters:

folder - absolute path of the folder where to establish the database

dbName - name of the database

deleteOldDatabase - if true, tries to delete the old database

objectsCache -

Throws:

SQLException

Method Detail

getName

public String getName()

Returns the database name.

Returns:

the database name

getObjectsCache

public ObjectsCache getObjectsCache()

Returns the cache used by this database.

Returns:

the cache used by this database

setObjectCache

public void setObjectCache(ObjectsCache objectCache)

Sets the object cache to be used by this database.

Parameters:

objectCache - the object cache to be used by this database

addTable

public void addTable(String tableName)
              throws SQLException

Adds the desired table in the database.

Parameters:

tableName - the name of the table

Throws:

SQLException - exception thrown whenever a problem occurred while working with the database

hasTable

public boolean hasTable(String tableName)
                 throws SQLException

Indicates whether the database contains the given table.

Parameters:

tableName - the name of the table of interest

Returns:

a boolean indicating whether the database contains the given table

Throws:

SQLException - exception thrown whenever a problem occurred while working with the database

insertObject

public void insertObject(String tableName,
                String objectKey,
                Object object,
                boolean inCache)
                  throws SQLException,
                         IOException,
                         InterruptedException

Stores an object in the desired table. When multiple objects are to be inserted, use insertObjects instead.

Parameters:

tableName - the name of the table

objectKey - the key of the object

object - the object to store

inCache - boolean indicating whether the method shall try to put the object in cache or not

Throws:

SQLException - exception thrown whenever an error occurred while storing the object

IOException - exception thrown whenever an error occurred while writing in the database

InterruptedException

insertObjects

public void insertObjects(String tableName,
                 HashMap<String,Object> objects,
                 WaitingHandler waitingHandler)
                   throws SQLException,
                          IOException

Inserts a set of objects in the given table.

Parameters:

tableName - the name of the table

objects - map of the objects (object key -> object)

waitingHandler - a waiting handler displaying the progress (can be null). The progress will be displayed on the secondary progress bar.

Throws:

SQLException

IOException

insertObjects

public void insertObjects(String tableName,
                 HashMap<String,Object> objects,
                 WaitingHandler waitingHandler,
                 boolean allNewObjects)
                   throws SQLException,
                          IOException

Inserts a set of objects in the given table.

Parameters:

tableName - the name of the table

objects - map of the objects (object key -> object)

waitingHandler - a waiting handler displaying the progress (can be null). The progress will be displayed on the secondary progress bar.

allNewObjects - boolean indicating whether all objects are new

Throws:

SQLException

IOException

loadObjects

public void loadObjects(String tableName,
               WaitingHandler waitingHandler)
                 throws SQLException,
                        IOException,
                        ClassNotFoundException,
                        InterruptedException

Loads all objects from a table in the cache.

Parameters:

tableName - the table name

waitingHandler - the waiting handler

Throws:

SQLException - exception thrown whenever an error occurred while interrogating the database

IOException - exception thrown whenever an error occurred while reading the database

ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.

InterruptedException

loadObjects

public void loadObjects(String tableName,
               ArrayList<String> keys,
               WaitingHandler waitingHandler)
                 throws SQLException,
                        IOException,
                        ClassNotFoundException,
                        InterruptedException

Loads some objects from a table in the cache.

Parameters:

tableName - the table name

keys - the keys of the objects to load

waitingHandler - the waiting handler, will only be increased

Throws:

SQLException - exception thrown whenever an error occurred while interrogating the database

IOException - exception thrown whenever an error occurred while reading the database

ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.

InterruptedException

retrieveObject

public Object retrieveObject(String tableName,
                    String objectKey,
                    boolean useDB)
                      throws SQLException,
                             IOException,
                             ClassNotFoundException,
                             InterruptedException

Retrieves an object from the desired table. The key should be unique otherwise the first object will be returned. Returns null if the key is not found. The retrieved object is saved in cache.

Parameters:

tableName - the name of the table

objectKey - the object key

useDB - if useDB is false, null will be returned if the object is not in the cache

Returns:

the object stored in the table.

Throws:

SQLException - exception thrown whenever an error occurred while interrogating the database

IOException - exception thrown whenever an error occurred while reading the database

ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.

InterruptedException

retrieveObject

public Object retrieveObject(String tableName,
                    String objectKey,
                    boolean useDB,
                    boolean useCache)
                      throws SQLException,
                             IOException,
                             ClassNotFoundException,
                             InterruptedException

Retrieves an object from the desired table. The key should be unique otherwise the first object will be returned. Returns null if the key is not found.

Parameters:

tableName - the name of the table

objectKey - the object key

useDB - if useDB is false, null will be returned if the object is not in the cache

useCache - if true the retrieved object will be saved in cache

Returns:

the object stored in the table.

Throws:

SQLException - exception thrown whenever an error occurred while interrogating the database

IOException - exception thrown whenever an error occurred while reading the database

ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.

InterruptedException

inDB

public boolean inDB(String tableName,
           String objectKey,
           boolean cache)
             throws SQLException

Indicates whether an object is loaded in the given table.

Parameters:

tableName - the table name

objectKey - the object key

cache - a boolean indicating whether the cache should be searched as well

Returns:

a boolean indicating whether an object is loaded in the given table

Throws:

SQLException - exception thrown whenever an exception occurred while interrogating the database

tableContent

public ArrayList<String> tableContent(String tableName)
                               throws SQLException

Returns an arraylist with the content in the given table.

Parameters:

tableName - the table to get the content for

Returns:

an arraylist with the content in the given table

Throws:

SQLException

tableContentAsSet

public HashSet<String> tableContentAsSet(String tableName)
                                  throws SQLException

Returns a hashset with the content in the given table.

Parameters:

tableName - the table to get the content for

Returns:

a hashset with the content in the given table

Throws:

SQLException

deleteObject

public void deleteObject(String tableName,
                String objectKey)
                  throws SQLException,
                         IOException

Deletes an object from the desired table.

Parameters:

tableName - the name of the table

objectKey - the object key

Throws:

SQLException - exception thrown whenever an error occurred while interrogating the database

IOException - exception thrown whenever an error occurred while interrogating the database

updateObject

public void updateObject(String tableName,
                String objectKey,
                Object object)
                  throws SQLException,
                         IOException

Updates an object in the cache or in the tables if not in cache.

Parameters:

tableName - the name of the table

objectKey - the key of the object

object - the object to store

Throws:

SQLException - exception thrown whenever an error occurred while storing the object

IOException - exception thrown whenever an error occurred while writing in the database

updateObject

public void updateObject(String tableName,
                String objectKey,
                Object object,
                boolean cache)
                  throws SQLException,
                         IOException

Updates an object in the cache or in the tables if not in cache or if cache is wrong.

Parameters:

tableName - the name of the table

objectKey - the key of the object

object - the object to store

cache - a boolean indicating whether the method should look in the cache

Throws:

SQLException - exception thrown whenever an error occurred while storing the object

IOException - exception thrown whenever an error occurred while writing in the database

close

public void close()
           throws SQLException

Closes the db connection.

Throws:

SQLException - exception thrown whenever an error occurred while closing the database connection

establishConnection

public void establishConnection(String aDbFolder,
                       boolean deleteOldDatabase,
                       ObjectsCache objectsCache)
                         throws SQLException

Establishes connection to the database.

Parameters:

aDbFolder - the folder where the database is located

deleteOldDatabase - if true, tries to delete the old database

objectsCache -

Throws:

SQLException - exception thrown whenever an error occurred while establishing the connection

correctTableName

public String correctTableName(String tableName)

Surrounds the table name with quotation marks such that spaces etc are allowed.

Parameters:

tableName - the table name

Returns:

the corrected table name

correctKey

public String correctKey(String tableName,
                String key)

Indexes the long keys by a number.

Parameters:

tableName - the table name

key - the key of the object to be stored

Returns:

the corrected table name

getOriginalKey

public String getOriginalKey(String tableName,
                    String correctedKey)

Returns the original key of the corrected long key.

Parameters:

tableName - the table

correctedKey - the corrected key, should be prefix + number

Returns:

the original long key