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 java.lang.Object

This factory stores and returns protein trees components from databases.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	dbName The name of the db to use.
static java.lang.String	defaultDbFolderPath The folder containing the databases.
static java.lang.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.
java.io.File	getDbFolder() Returns the folder where the db in the sequence factory is stored.
java.lang.String	getDbFolderName() Returns the folder name where to store information about the protein sequence database loaded in the sequence factory.
java.lang.Integer	getInitialSize() Retrieves the initial tag size from the db.
static ProteinTreeComponentsFactory	getInstance() Static method returning the instance of the factory.
Node	getNode(java.lang.String tag) Retrieves the node of the given tag.
java.lang.Integer	getProteinLength(java.lang.String accession) Retrieves the length of a protein.
java.lang.String	getVersion() 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(java.util.ArrayList<java.lang.String> tags) Loads nodes in the cache.
void	loadParameters() Loads all tree parameters.
void	loadProteinLengths() Loads all protein lengths in cache.
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(java.lang.String tag, Node node) Adds a node to the database.
void	saveNodes(java.util.HashMap<java.lang.String,java.lang.Object> nodes) Adds nodes to the database.
void	saveProteinLengths(java.util.HashMap<java.lang.String,java.lang.Object> lengths) Adds a protein length to the database.
void	setCorrupted(boolean corrupted) Sets whether the database is corrupted.
void	setImportComplete(boolean completed) Sets whether the import was completed.
void	setVersion(java.lang.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

defaultDbFolderPath

public static final java.lang.String defaultDbFolderPath

The folder containing the databases.

folderSeparator

public static final java.lang.String folderSeparator

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

See Also:

Constant Field Values

dbName

public static final java.lang.String dbName

The name of the db to use.

See Also:

Constant Field Values

Method Detail

getInstance

public static ProteinTreeComponentsFactory getInstance()
                                                throws java.io.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:

java.io.IOException

initiate

public boolean initiate()
                 throws java.sql.SQLException,
                        java.io.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:

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

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

delete

public boolean delete()
               throws java.io.IOException

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

Returns:

true if deletion was successful

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException,
                  java.sql.SQLException

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

Throws:

java.io.IOException

java.sql.SQLException - exception thrown if closing the db failed

getDbFolderName

public java.lang.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 java.io.File getDbFolder()
                         throws java.io.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:

java.io.IOException

saveNode

public void saveNode(java.lang.String tag,
            Node node)
              throws java.sql.SQLException,
                     java.io.IOException,
                     java.lang.InterruptedException

Adds a node to the database.

Parameters:

tag - the tag referring to the node of interest

node - the node

Throws:

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

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

java.lang.InterruptedException

saveNodes

public void saveNodes(java.util.HashMap<java.lang.String,java.lang.Object> nodes)
               throws java.sql.SQLException,
                      java.io.IOException

Adds nodes to the database.

Parameters:

nodes - map of the nodes

Throws:

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

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

getNode

public Node getNode(java.lang.String tag)
             throws java.sql.SQLException,
                    java.lang.ClassNotFoundException,
                    java.io.IOException,
                    java.lang.InterruptedException

Retrieves the node of the given tag.

Parameters:

tag - the tag of interest

Returns:

the node at this tag

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

java.io.IOException

java.lang.InterruptedException

loadNodes

public void loadNodes(java.util.ArrayList<java.lang.String> tags)
               throws java.sql.SQLException,
                      java.io.IOException,
                      java.lang.ClassNotFoundException,
                      java.lang.InterruptedException

Loads nodes in the cache.

Parameters:

tags - list of tags corresponding to the nodes to load

Throws:

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

saveProteinLengths

public void saveProteinLengths(java.util.HashMap<java.lang.String,java.lang.Object> lengths)
                        throws java.sql.SQLException,
                               java.io.IOException

Adds a protein length to the database.

Parameters:

lengths - the lengths

Throws:

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

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

getProteinLength

public java.lang.Integer getProteinLength(java.lang.String accession)
                                   throws java.sql.SQLException,
                                          java.lang.ClassNotFoundException,
                                          java.io.IOException,
                                          java.lang.InterruptedException

Retrieves the length of a protein.

Parameters:

accession - the accession of the protein of interest

Returns:

the length of this protein

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

java.io.IOException

java.lang.InterruptedException

saveInitialSize

public void saveInitialSize(int size)
                     throws java.sql.SQLException,
                            java.io.IOException,
                            java.lang.InterruptedException

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

Parameters:

size - the initial tag size

Throws:

java.sql.SQLException

java.io.IOException

java.lang.InterruptedException

getInitialSize

public java.lang.Integer getInitialSize()
                                 throws java.sql.SQLException,
                                        java.io.IOException,
                                        java.lang.ClassNotFoundException,
                                        java.lang.InterruptedException

Retrieves the initial tag size from the db.

Returns:

the initial tag size

Throws:

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

loadProteinLengths

public void loadProteinLengths()
                        throws java.sql.SQLException,
                               java.lang.ClassNotFoundException,
                               java.io.IOException,
                               java.lang.InterruptedException

Loads all protein lengths in cache.

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

java.io.IOException

java.lang.InterruptedException

loadParameters

public void loadParameters()
                    throws java.sql.SQLException,
                           java.lang.ClassNotFoundException,
                           java.io.IOException,
                           java.lang.InterruptedException

Loads all tree parameters.

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

java.io.IOException

java.lang.InterruptedException

setImportComplete

public void setImportComplete(boolean completed)
                       throws java.sql.SQLException,
                              java.io.IOException,
                              java.lang.InterruptedException

Sets whether the import was completed.

Parameters:

completed -

Throws:

java.sql.SQLException

java.io.IOException

java.lang.InterruptedException

importComplete

public boolean importComplete()
                       throws java.sql.SQLException,
                              java.io.IOException,
                              java.lang.ClassNotFoundException,
                              java.lang.InterruptedException

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

Returns:

true if the import was complete

Throws:

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

setCorrupted

public void setCorrupted(boolean corrupted)
                  throws java.sql.SQLException,
                         java.io.IOException,
                         java.lang.InterruptedException

Sets whether the database is corrupted.

Parameters:

corrupted -

Throws:

java.sql.SQLException

java.io.IOException

java.lang.InterruptedException

isCorrupted

public boolean isCorrupted()
                    throws java.sql.SQLException,
                           java.io.IOException,
                           java.lang.ClassNotFoundException,
                           java.lang.InterruptedException

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

Returns:

true if the database is corrupted

Throws:

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

setVersion

public void setVersion(java.lang.String version)
                throws java.sql.SQLException,
                       java.io.IOException,
                       java.lang.InterruptedException

Sets the version.

Parameters:

version - the version

Throws:

java.sql.SQLException

java.io.IOException

java.lang.InterruptedException

getVersion

public java.lang.String getVersion()
                            throws java.sql.SQLException,
                                   java.io.IOException,
                                   java.lang.ClassNotFoundException,
                                   java.lang.InterruptedException

Returns the version. Null if not set.

Returns:

the version

Throws:

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

loadTags

public void loadTags()
              throws java.sql.SQLException

Loads the tags implemented in the database.

Throws:

java.sql.SQLException