com.compomics.util.experiment.identification.protein_inference.proteintree

Class ProteinTreeComponentsFactory

java.lang.Object

com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory

public class ProteinTreeComponentsFactory
extends Object

This factory stores and returns protein trees components from databases.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String	dbName The name of the db to use.
static String	folderSeparator The splitter in the key between database name and database version.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes the factory, closes all connection and deletes the file.
boolean	delete() Sets the currently loaded database as corrupted and tries to delete it.
static void	deletOutdatedTrees() Deletes the outdated trees.
File	getDbFolder() Returns the folder where the db in the sequence factory is stored.
String	getDbFolderName() Returns the folder name where to store information about the protein sequence database loaded in the sequence factory.
static String	getDefaultDbFolderPath() Returns the default folder to use when storing the trees.
String	getFastaFilePath() Returns the FASTA file path.
static String	getFastaFilePath(ObjectsDB objectsDB) Returns the FASTA file path.
Integer	getInitialSize() Retrieves the initial tag size from the db.
static ProteinTreeComponentsFactory	getInstance() Static method returning the instance of the factory.
Node	getNode(String tag) Retrieves the node of the given tag.
String	getVersion() Returns the version.
static String	getVersion(ObjectsDB objectsDB) Returns the version.
boolean	importComplete() Returns a boolean indicating whether the import was complete.
boolean	initiate() Initiates the connection to the database and indicates whether the corresponding folder is already created.
boolean	isCorrupted() Returns a boolean indicating whether the database is corrupted.
void	loadNodes(ArrayList<String> tags) Loads nodes in the cache.
void	loadParameters() Loads all tree parameters.
void	loadTags() Loads the tags implemented in the database.
void	saveInitialSize(int size) Saves the initial tag size in the parameters table of the DB.
void	saveNode(String tag, Node node) Adds a node to the database.
void	saveNodes(HashMap<String,Object> nodes, WaitingHandler waitingHandler) Adds nodes to the database.
void	setCorrupted(boolean corrupted) Sets whether the database is corrupted.
static void	setDefaultDbFolderPath(String defaultDbFolderPath) Sets the default folder to use when storing the trees.
void	setFastaFilePath(String fastaFilePath) Sets the FASTA file path.
void	setImportComplete(boolean completed) Sets whether the import was completed.
void	setVersion(String version) Sets the version.

Methods inherited from class java.lang.Object

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

Field Detail

folderSeparator

public static final String folderSeparator

The splitter in the key between database name and database version.

See Also:

Constant Field Values

dbName

public static final String dbName

The name of the db to use.

See Also:

Constant Field Values

Method Detail

getInstance

public static ProteinTreeComponentsFactory getInstance()
                                                throws IOException

Static method returning the instance of the factory. Note: the serialization folder should have been already set.

Returns:

the instance of the factory

Throws:

IOException

initiate

public boolean initiate()
                 throws SQLException,
                        IOException

Initiates the connection to the database and indicates whether the corresponding folder is already created.

Returns:

a boolean indicating whether the database folder is already created

Throws:

SQLException - exception thrown whenever an error occurred while attempting to connect to the database

IOException - exception thrown whenever an error occurred while attempting to connect to the database

delete

public boolean delete()
               throws IOException

Sets the currently loaded database as corrupted and tries to delete it.

Returns:

true if deletion was successful

Throws:

IOException

close

public void close()
           throws IOException,
                  SQLException

Closes the factory, closes all connection and deletes the file.

Throws:

IOException

SQLException - exception thrown if closing the db failed

getDbFolderName

public String getDbFolderName()

Returns the folder name where to store information about the protein sequence database loaded in the sequence factory.

Returns:

the folder name where to store information about the protein sequence database loaded in the sequence factory

getDbFolder

public File getDbFolder()
                 throws IOException

Returns the folder where the db in the sequence factory is stored.

Returns:

the folder where the db in the sequence factory is stored

Throws:

IOException

saveNode

public void saveNode(String tag,
            Node node)
              throws SQLException,
                     IOException,
                     InterruptedException

Adds a node to the database.

Parameters:

tag - the tag referring to the node of interest

node - the node

Throws:

SQLException - exception thrown whenever an error occurred while loading data in the database

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

InterruptedException

saveNodes

public void saveNodes(HashMap<String,Object> nodes,
             WaitingHandler waitingHandler)
               throws SQLException,
                      IOException

Adds nodes to the database.

Parameters:

nodes - map of the nodes

waitingHandler - the waiting handler

Throws:

SQLException - exception thrown whenever an error occurred while loading data in the database

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

getNode

public Node getNode(String tag)
             throws SQLException,
                    ClassNotFoundException,
                    IOException,
                    InterruptedException

Retrieves the node of the given tag.

Parameters:

tag - the tag of interest

Returns:

the node at this tag

Throws:

SQLException

ClassNotFoundException

IOException

InterruptedException

loadNodes

public void loadNodes(ArrayList<String> tags)
               throws SQLException,
                      IOException,
                      ClassNotFoundException,
                      InterruptedException

Loads nodes in the cache.

Parameters:

tags - list of tags corresponding to the nodes to load

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

saveInitialSize

public void saveInitialSize(int size)
                     throws SQLException,
                            IOException,
                            InterruptedException

Saves the initial tag size in the parameters table of the DB.

Parameters:

size - the initial tag size

Throws:

SQLException

IOException

InterruptedException

getInitialSize

public Integer getInitialSize()
                       throws SQLException,
                              IOException,
                              ClassNotFoundException,
                              InterruptedException

Retrieves the initial tag size from the db.

Returns:

the initial tag size

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

loadParameters

public void loadParameters()
                    throws SQLException,
                           ClassNotFoundException,
                           IOException,
                           InterruptedException

Loads all tree parameters.

Throws:

SQLException

ClassNotFoundException

IOException

InterruptedException

setImportComplete

public void setImportComplete(boolean completed)
                       throws SQLException,
                              IOException,
                              InterruptedException

Sets whether the import was completed.

Parameters:

completed -

Throws:

SQLException

IOException

InterruptedException

importComplete

public boolean importComplete()
                       throws SQLException,
                              IOException,
                              ClassNotFoundException,
                              InterruptedException

Returns a boolean indicating whether the import was complete. False if not set.

Returns:

true if the import was complete

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

setCorrupted

public void setCorrupted(boolean corrupted)
                  throws SQLException,
                         IOException,
                         InterruptedException

Sets whether the database is corrupted.

Parameters:

corrupted -

Throws:

SQLException

IOException

InterruptedException

isCorrupted

public boolean isCorrupted()
                    throws SQLException,
                           IOException,
                           ClassNotFoundException,
                           InterruptedException

Returns a boolean indicating whether the database is corrupted. False if not set.

Returns:

true if the database is corrupted

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

setVersion

public void setVersion(String version)
                throws SQLException,
                       IOException,
                       InterruptedException

Sets the version.

Parameters:

version - the version

Throws:

SQLException

IOException

InterruptedException

getVersion

public static String getVersion(ObjectsDB objectsDB)
                         throws SQLException,
                                IOException,
                                ClassNotFoundException,
                                InterruptedException

Returns the version. Null if not set.

Parameters:

objectsDB - the objects db to look into

Returns:

the version

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

getVersion

public String getVersion()
                  throws SQLException,
                         IOException,
                         ClassNotFoundException,
                         InterruptedException

Returns the version. Null if not set.

Returns:

the version

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

setFastaFilePath

public void setFastaFilePath(String fastaFilePath)
                      throws SQLException,
                             IOException,
                             InterruptedException

Sets the FASTA file path.

Parameters:

fastaFilePath - the FASTA file path

Throws:

SQLException

IOException

InterruptedException

getFastaFilePath

public String getFastaFilePath()
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException

Returns the FASTA file path.

Returns:

the FASTA file path

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

getFastaFilePath

public static String getFastaFilePath(ObjectsDB objectsDB)
                               throws SQLException,
                                      IOException,
                                      ClassNotFoundException,
                                      InterruptedException

Returns the FASTA file path.

Parameters:

objectsDB - the objects DB to look into

Returns:

the FASTA file path

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

loadTags

public void loadTags()
              throws SQLException

Loads the tags implemented in the database.

Throws:

SQLException

getDefaultDbFolderPath

public static String getDefaultDbFolderPath()

Returns the default folder to use when storing the trees.

Returns:

the default folder to use when storing the trees

setDefaultDbFolderPath

public static void setDefaultDbFolderPath(String defaultDbFolderPath)

Sets the default folder to use when storing the trees.

Parameters:

defaultDbFolderPath - the default folder to use when storing the trees

deletOutdatedTrees

public static void deletOutdatedTrees()
                               throws IOException

Deletes the outdated trees.

Throws:

IOException