com.compomics.util.experiment.identification

Class IdentificationDB

java.lang.Object

com.compomics.util.experiment.identification.IdentificationDB

All Implemented Interfaces:

Serializable

public class IdentificationDB
extends Object
implements Serializable

This class uses a database to manage identification matches.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
String	dbName The name which will be used for the database.

Constructor Summary

Constructors

Constructor and Description
IdentificationDB(String folder, String name, boolean deleteOldDatabase, ObjectsCache objectCache) Constructor creating the database and the protein and protein parameters tables.

Method Summary

Modifier and Type	Method and Description
void	addAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions) Adds assumptions for a given match to the database.
void	addMatch(IdentificationMatch match) Adds an identification match to the database.
void	addPeptideMatch(PeptideMatch peptideMatch) Adds a peptide match to the database.
void	addPeptideMatchParameter(String key, UrParameter urParameter) Adds a peptide match parameter to the database.
void	addProteinMatch(ProteinMatch proteinMatch) Adds a protein match to the database.
void	addProteinMatchParameter(String key, UrParameter urParameter) Adds a protein match parameter to the database.
void	addRawAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions) Adds raw assumptions for a given match to the database.
void	addSpectrumMatch(SpectrumMatch spectrumMatch) Adds a spectrum match to the database.
void	addSpectrumMatchParameter(String key, UrParameter urParameter) Adds a spectrum match parameter to the database.
void	checkTable(Collection<String> tableList, String tableName) Verifies that a table exists and creates it if not.
void	close() Closes the db connection.
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>>	getAssumptions(String key, boolean useDB) Returns the assumptions of the given spectrum in a map: advocate id → score → list of assumptions.
String	getAssumptionTable(String spectrumKey) Returns the assumptions table name associated with the given spectrum key.
Object	getObject(String table, String objectKey, boolean useDB) Returns an object from the database.
ObjectsDB	getObjectsDB() Returns the database used to store matches.
PeptideMatch	getPeptideMatch(String key, boolean useDB) Returns the desired peptide match.
UrParameter	getPeptideMatchParameter(String key, UrParameter urParameter, boolean useDB) Returns the desired peptide match parameter.
ArrayList<String>	getPeptideParametersTables() Returns the names of the tables containing peptide parameters.
String	getPeptideParameterTable(UrParameter urParameter) Returns the table name associated with the given peptide parameter.
ProteinMatch	getProteinMatch(String key, boolean useDB) Returns the desired protein match.
UrParameter	getProteinMatchParameter(String key, UrParameter urParameter, boolean useDB) Returns the desired protein match parameter.
String	getProteinParameterTable(UrParameter urParameter) Returns the table name associated with the given protein parameter.
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>>	getRawAssumptions(String key, boolean useDB) Returns the raw assumptions of the given spectrum in a map: advocate id → score → list of assumptions.
String	getRawAssumptionTable(String spectrumKey) Returns the raw assumptions table name associated with the given spectrum key.
SpectrumMatch	getSpectrumMatch(String key, boolean useDB) Returns the desired spectrum match.
UrParameter	getSpectrumMatchParameter(String key, UrParameter urParameter, boolean useDB) Returns the desired spectrum match parameter.
String	getSpectrumMatchTable(String spectrumKey) Returns the PSM table name associated with the given spectrum key.
String	getSpectrumParameterTable(String spectrumKey, UrParameter urParameter) Returns the table name associated with the given spectrum parameter.
boolean	isConnectionActive() Indicates whether the connection to the DB is active.
void	loadAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all assumptions of the given spectra in the cache of the database.
void	loadAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all assumptions of the given file in the cache of the database.
void	loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide matches of the given type in the cache of the database.
void	loadPeptideMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide matches in the cache of the database.
void	loadPeptideMatchParameters(ArrayList<String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide match parameters of the given type in the cache of the database.
void	loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide match parameters of the given type in the cache of the database.
void	loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein matches of the given type in the cache of the database.
void	loadProteinMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all protein matches in the cache of the database.
void	loadProteinMatchParameters(ArrayList<String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein match parameters of the given type in the cache of the database.
void	loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all protein match parameters of the given type in the cache of the database.
void	loadRawAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all raw assumptions of the given spectra in the cache of the database.
void	loadRawAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all raw assumptions of the given file in the cache of the database.
void	loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all given spectrum matches in the cache of the database.
void	loadSpectrumMatches(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum matches of the given file in the cache of the database.
void	loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all desired spectrum match parameters in the cache of the database.
void	loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum match parameters of the given type in the cache of the database.
boolean	peptideMatchLoaded(String peptideKey) Indicates whether a peptide match is loaded.
boolean	proteinMatchLoaded(String proteinKey) Indicates whether a protein match is loaded.
void	removeAssumptions(String key) Deletes the assumptions corresponding to a given psm from the database.
void	removePeptideMatch(String key) Deletes a peptide match from the database.
void	removeProteinMatch(String key) Deletes a protein match from the database.
void	removeRawAssumptions(String key) Deletes the raw assumptions corresponding to a given psm from the database.
void	removeSpectrumMatch(String key) Deletes a spectrum match from the database.
void	restoreConnection(String dbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache) Restores the connection to the database.
boolean	spectrumMatchLoaded(String spectrumKey) Indicates whether a spectrum match is loaded.
boolean	spectrumMatchTableCreated(String spectrumMatchKey) Indicates whether the table for the given spectrum match key has been created.
void	updateAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptionsMap) Updates the map of assumptions for a given spectrum.
void	updateMatch(IdentificationMatch match) Updates a match.
void	updatePeptideMatch(PeptideMatch peptideMatch) Updates a peptide match.
void	updatePeptideParameter(String key, UrParameter urParameter) Updates a peptide match parameter.
void	updateProteinMatch(ProteinMatch proteinMatch) Updates a protein match.
void	updateProteinParameter(String key, UrParameter urParameter) Updates a protein match parameter.
void	updateRawAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> rawAssumptionsMap) Updates the map of raw assumptions for a given spectrum.
void	updateSpectrumMatch(SpectrumMatch spectrumMatch) Updates a spectrum match.
void	updateSpectrumParameter(String key, UrParameter urParameter) Updates a spectrum match parameter.

Methods inherited from class java.lang.Object

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

Field Detail

dbName

public String dbName

The name which will be used for the database.

Constructor Detail

IdentificationDB

public IdentificationDB(String folder,
                        String name,
                        boolean deleteOldDatabase,
                        ObjectsCache objectCache)
                 throws SQLException,
                        IOException,
                        ClassNotFoundException,
                        InterruptedException

Constructor creating the database and the protein and protein parameters tables.

Parameters:

folder - the folder where to put the database

name - the database name

deleteOldDatabase - if true, tries to delete the old database

objectCache - the objects cache

Throws:

SQLException - exception thrown whenever an error occurs while interacting with the database

IOException - exception thrown whenever an error occurs while reading or writing a file

ClassNotFoundException - exception thrown whenever an error occurred while deserializing a file from the database

InterruptedException - exception thrown if a threading error occurs while interacting with the database

Method Detail

spectrumMatchLoaded

public boolean spectrumMatchLoaded(String spectrumKey)
                            throws SQLException

Indicates whether a spectrum match is loaded.

Parameters:

spectrumKey - the spectrumMatch key

Returns:

a boolean indicating whether a spectrum match is loaded in the given table

Throws:

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

peptideMatchLoaded

public boolean peptideMatchLoaded(String peptideKey)
                           throws SQLException

Indicates whether a peptide match is loaded.

Parameters:

peptideKey - the peptide key

Returns:

a boolean indicating whether a peptide match is loaded in the given table

Throws:

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

proteinMatchLoaded

public boolean proteinMatchLoaded(String proteinKey)
                           throws SQLException

Indicates whether a protein match is loaded.

Parameters:

proteinKey - the protein key

Returns:

a boolean indicating whether a protein match is loaded in the given table

Throws:

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

updateProteinMatch

public void updateProteinMatch(ProteinMatch proteinMatch)
                        throws SQLException,
                               IOException

Updates a protein match.

Parameters:

proteinMatch - the protein match

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updatePeptideMatch

public void updatePeptideMatch(PeptideMatch peptideMatch)
                        throws SQLException,
                               IOException

Updates a peptide match.

Parameters:

peptideMatch - the peptide match

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updateSpectrumMatch

public void updateSpectrumMatch(SpectrumMatch spectrumMatch)
                         throws SQLException,
                                IOException

Updates a spectrum match.

Parameters:

spectrumMatch - the spectrum match

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updateAssumptions

public void updateAssumptions(String spectrumKey,
                              HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptionsMap)
                       throws SQLException,
                              IOException

Updates the map of assumptions for a given spectrum.

Parameters:

spectrumKey - the key of the spectrum

assumptionsMap - map of assumptions

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updateRawAssumptions

public void updateRawAssumptions(String spectrumKey,
                                 HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> rawAssumptionsMap)
                          throws SQLException,
                                 IOException

Updates the map of raw assumptions for a given spectrum.

Parameters:

spectrumKey - the key of the spectrum

rawAssumptionsMap - map of assumptions

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updateMatch

public void updateMatch(IdentificationMatch match)
                 throws SQLException,
                        IOException

Updates a match.

Parameters:

match - the match to update

Throws:

SQLException - exception thrown whenever an error occurred while updating a match in the table

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

updateProteinParameter

public void updateProteinParameter(String key,
                                   UrParameter urParameter)
                            throws SQLException,
                                   IOException

Updates a protein match parameter.

Parameters:

key - the key of the protein match

urParameter - the parameter

Throws:

SQLException - exception thrown whenever an error occurred while updating the parameter in the table

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

updatePeptideParameter

public void updatePeptideParameter(String key,
                                   UrParameter urParameter)
                            throws SQLException,
                                   IOException

Updates a peptide match parameter.

Parameters:

key - the key of the peptide match

urParameter - the parameter

Throws:

SQLException - exception thrown whenever an error occurred while updating the parameter in the table

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

updateSpectrumParameter

public void updateSpectrumParameter(String key,
                                    UrParameter urParameter)
                             throws SQLException,
                                    IOException

Updates a spectrum match parameter.

Parameters:

key - the key of the spectrum match

urParameter - the parameter

Throws:

SQLException - exception thrown whenever an error occurred while updating the parameter in the table

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

removeProteinMatch

public void removeProteinMatch(String key)
                        throws SQLException,
                               IOException

Deletes a protein match from the database.

Parameters:

key - the key of the match

Throws:

SQLException - exception thrown whenever an error occurred while deleting the match

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

removePeptideMatch

public void removePeptideMatch(String key)
                        throws SQLException,
                               IOException

Deletes a peptide match from the database.

Parameters:

key - the key of the match

Throws:

SQLException - exception thrown whenever an error occurred while deleting the match

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

removeSpectrumMatch

public void removeSpectrumMatch(String key)
                         throws SQLException,
                                IOException

Deletes a spectrum match from the database.

Parameters:

key - the key of the match

Throws:

SQLException - exception thrown whenever an error occurred while deleting the match

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

removeAssumptions

public void removeAssumptions(String key)
                       throws SQLException,
                              IOException

Deletes the assumptions corresponding to a given psm from the database.

Parameters:

key - the key of the psm

Throws:

SQLException - exception thrown whenever an error occurred while deleting the match

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

removeRawAssumptions

public void removeRawAssumptions(String key)
                          throws SQLException,
                                 IOException

Deletes the raw assumptions corresponding to a given psm from the database.

Parameters:

key - the key of the psm

Throws:

SQLException - exception thrown whenever an error occurred while deleting the match

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

getPeptideParametersTables

public ArrayList<String> getPeptideParametersTables()

Returns the names of the tables containing peptide parameters.

Returns:

the names of the tables containing peptide parameters

getAssumptions

public HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getAssumptions(String key,
                                                                                                   boolean useDB)
                                                                                            throws SQLException,
                                                                                                   IOException,
                                                                                                   ClassNotFoundException,
                                                                                                   InterruptedException

Returns the assumptions of the given spectrum in a map: advocate id → score → list of assumptions.

Parameters:

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

key - the key of the spectrum

Returns:

the assumptions

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addAssumptions

public void addAssumptions(String spectrumKey,
                           HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
                    throws SQLException,
                           IOException,
                           InterruptedException

Adds assumptions for a given match to the database.

Parameters:

spectrumKey - the key of the spectrum

assumptions - map of all assumptions

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

getRawAssumptions

public HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getRawAssumptions(String key,
                                                                                                      boolean useDB)
                                                                                               throws SQLException,
                                                                                                      IOException,
                                                                                                      ClassNotFoundException,
                                                                                                      InterruptedException

Returns the raw assumptions of the given spectrum in a map: advocate id → score → list of assumptions.

Parameters:

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

key - the key of the spectrum

Returns:

the assumptions

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addRawAssumptions

public void addRawAssumptions(String spectrumKey,
                              HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
                       throws SQLException,
                              IOException,
                              InterruptedException

Adds raw assumptions for a given match to the database.

Parameters:

spectrumKey - the key of the spectrum

assumptions - map of all assumptions

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

getSpectrumMatch

public SpectrumMatch getSpectrumMatch(String key,
                                      boolean useDB)
                               throws SQLException,
                                      IOException,
                                      ClassNotFoundException,
                                      InterruptedException

Returns the desired spectrum match.

Parameters:

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

key - the PSM key

Returns:

the spectrum match

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addSpectrumMatch

public void addSpectrumMatch(SpectrumMatch spectrumMatch)
                      throws SQLException,
                             IOException,
                             InterruptedException

Adds a spectrum match to the database.

Parameters:

spectrumMatch - the spectrum match to be added

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

spectrumMatchTableCreated

public boolean spectrumMatchTableCreated(String spectrumMatchKey)

Indicates whether the table for the given spectrum match key has been created.

Parameters:

spectrumMatchKey - the key of the spectrum match of interest

Returns:

true if the table for the given spectrum match key has been created

getPeptideMatch

public PeptideMatch getPeptideMatch(String key,
                                    boolean useDB)
                             throws SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    InterruptedException

Returns the desired peptide match.

Parameters:

key - the peptide key

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

Returns:

the peptide match

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addPeptideMatch

public void addPeptideMatch(PeptideMatch peptideMatch)
                     throws SQLException,
                            IOException,
                            InterruptedException

Adds a peptide match to the database.

Parameters:

peptideMatch - the peptide match to be added

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

getProteinMatch

public ProteinMatch getProteinMatch(String key,
                                    boolean useDB)
                             throws SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    InterruptedException

Returns the desired protein match.

Parameters:

key - the protein key

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

Returns:

the protein match

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addProteinMatch

public void addProteinMatch(ProteinMatch proteinMatch)
                     throws SQLException,
                            IOException,
                            InterruptedException

Adds a protein match to the database.

Parameters:

proteinMatch - the protein match to be added

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addMatch

public void addMatch(IdentificationMatch match)
              throws SQLException,
                     IOException,
                     InterruptedException

Adds an identification match to the database.

Parameters:

match - the match to be added

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

loadAssumptions

public void loadAssumptions(String fileName,
                            WaitingHandler waitingHandler,
                            boolean displayProgress)
                     throws SQLException,
                            IOException,
                            ClassNotFoundException,
                            InterruptedException

Loads all assumptions of the given file in the cache of the database.

Parameters:

fileName - the file name

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadAssumptions

public void loadAssumptions(ArrayList<String> spectrumKeys,
                            WaitingHandler waitingHandler,
                            boolean displayProgress)
                     throws SQLException,
                            IOException,
                            ClassNotFoundException,
                            InterruptedException

Loads all assumptions of the given spectra in the cache of the database.

Parameters:

spectrumKeys - the key of the spectra

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadRawAssumptions

public void loadRawAssumptions(String fileName,
                               WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException

Loads all raw assumptions of the given file in the cache of the database.

Parameters:

fileName - the file name

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadRawAssumptions

public void loadRawAssumptions(ArrayList<String> spectrumKeys,
                               WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException

Loads all raw assumptions of the given spectra in the cache of the database.

Parameters:

spectrumKeys - the key of the spectra

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadSpectrumMatches

public void loadSpectrumMatches(String fileName,
                                WaitingHandler waitingHandler,
                                boolean displayProgress)
                         throws SQLException,
                                IOException,
                                ClassNotFoundException,
                                InterruptedException

Loads all spectrum matches of the given file in the cache of the database.

Parameters:

fileName - the file name

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadSpectrumMatches

public void loadSpectrumMatches(ArrayList<String> spectrumKeys,
                                WaitingHandler waitingHandler,
                                boolean displayProgress)
                         throws SQLException,
                                IOException,
                                ClassNotFoundException,
                                InterruptedException

Loads all given spectrum matches in the cache of the database.

Parameters:

spectrumKeys - the key of the spectrum matches to be loaded

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadSpectrumMatchParameters

public void loadSpectrumMatchParameters(String fileName,
                                        UrParameter urParameter,
                                        WaitingHandler waitingHandler,
                                        boolean displayProgress)
                                 throws SQLException,
                                        IOException,
                                        ClassNotFoundException,
                                        InterruptedException

Loads all spectrum match parameters of the given type in the cache of the database.

Parameters:

fileName - the file name

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadSpectrumMatchParameters

public void loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
                                        UrParameter urParameter,
                                        WaitingHandler waitingHandler,
                                        boolean displayProgress)
                                 throws SQLException,
                                        IOException,
                                        ClassNotFoundException,
                                        InterruptedException

Loads all desired spectrum match parameters in the cache of the database.

Parameters:

spectrumKeys - the key of the spectrum match of the parameters to be loaded

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - if an InterruptedException is thrown

loadPeptideMatches

public void loadPeptideMatches(WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException,
                               InterruptedException

Loads all peptide matches in the cache of the database.

Parameters:

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadPeptideMatches

public void loadPeptideMatches(ArrayList<String> peptideKeys,
                               WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException

Loads the desired peptide matches of the given type in the cache of the database.

Parameters:

peptideKeys - the list of peptide keys to load

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadPeptideMatchParameters

public void loadPeptideMatchParameters(UrParameter urParameter,
                                       WaitingHandler waitingHandler,
                                       boolean displayProgress)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException

Loads all peptide match parameters of the given type in the cache of the database.

Parameters:

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadPeptideMatchParameters

public void loadPeptideMatchParameters(ArrayList<String> peptideKeys,
                                       UrParameter urParameter,
                                       WaitingHandler waitingHandler,
                                       boolean displayProgress)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException

Loads the desired peptide match parameters of the given type in the cache of the database.

Parameters:

peptideKeys - the list of peptide keys of the parameters to load

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadProteinMatches

public void loadProteinMatches(WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException

Loads all protein matches in the cache of the database.

Parameters:

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadProteinMatches

public void loadProteinMatches(ArrayList<String> proteinKeys,
                               WaitingHandler waitingHandler,
                               boolean displayProgress)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException,
                               InterruptedException

Loads the desired protein matches of the given type in the cache of the database.

Parameters:

proteinKeys - the list of protein keys to load

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadProteinMatchParameters

public void loadProteinMatchParameters(UrParameter urParameter,
                                       WaitingHandler waitingHandler,
                                       boolean displayProgress)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException

Loads all protein match parameters of the given type in the cache of the database.

Parameters:

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

loadProteinMatchParameters

public void loadProteinMatchParameters(ArrayList<String> proteinKeys,
                                       UrParameter urParameter,
                                       WaitingHandler waitingHandler,
                                       boolean displayProgress)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException

Loads the desired protein match parameters of the given type in the cache of the database.

Parameters:

proteinKeys - the list of protein keys of the parameters to load

urParameter - the parameter type

waitingHandler - the waiting handler allowing displaying progress and cancelling the process

displayProgress - boolean indicating whether the progress of this method should be displayed on 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 - exception thrown whenever a threading issue occurred when interacting with the database

getSpectrumMatchParameter

public UrParameter getSpectrumMatchParameter(String key,
                                             UrParameter urParameter,
                                             boolean useDB)
                                      throws SQLException,
                                             IOException,
                                             ClassNotFoundException,
                                             InterruptedException

Returns the desired spectrum match parameter.

Parameters:

key - the PSM key

urParameter - the match parameter

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

Returns:

the spectrum match parameter

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addSpectrumMatchParameter

public void addSpectrumMatchParameter(String key,
                                      UrParameter urParameter)
                               throws SQLException,
                                      IOException,
                                      InterruptedException

Adds a spectrum match parameter to the database.

Parameters:

key - the PSM key

urParameter - the match parameter

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

getPeptideMatchParameter

public UrParameter getPeptideMatchParameter(String key,
                                            UrParameter urParameter,
                                            boolean useDB)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException

Returns the desired peptide match parameter.

Parameters:

key - the peptide key

urParameter - the match parameter

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

Returns:

the peptide match parameter

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addPeptideMatchParameter

public void addPeptideMatchParameter(String key,
                                     UrParameter urParameter)
                              throws SQLException,
                                     IOException,
                                     InterruptedException

Adds a peptide match parameter to the database.

Parameters:

key - the peptide key

urParameter - the match parameter

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

getProteinMatchParameter

public UrParameter getProteinMatchParameter(String key,
                                            UrParameter urParameter,
                                            boolean useDB)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException

Returns the desired protein match parameter.

Parameters:

key - the protein key

urParameter - the match parameter

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

Returns:

the protein match parameter

Throws:

SQLException - exception thrown whenever an error occurred while loading the object from the database

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

ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

addProteinMatchParameter

public void addProteinMatchParameter(String key,
                                     UrParameter urParameter)
                              throws SQLException,
                                     IOException,
                                     InterruptedException

Adds a protein match parameter to the database.

Parameters:

key - the protein key

urParameter - the match parameter

Throws:

SQLException - exception thrown whenever an error occurred while adding the object in the database

IOException - exception thrown whenever an error occurred while writing the object

InterruptedException - exception thrown whenever a threading issue occurred when interacting with the database

checkTable

public void checkTable(Collection<String> tableList,
                       String tableName)
                throws SQLException,
                       IOException,
                       InterruptedException

Verifies that a table exists and creates it if not.

Parameters:

tableList - the list containing the created tables

tableName - the name of the table

Throws:

SQLException - if an SQLException occurs

IOException - if an IOException occurs

InterruptedException - if an InterruptedException occurs

getObject

public Object getObject(String table,
                        String objectKey,
                        boolean useDB)
                 throws SQLException,
                        IOException,
                        ClassNotFoundException,
                        InterruptedException

Returns an object from the database.

Parameters:

table - the name of the table

objectKey - the key of the object

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

Returns:

an object from the database

Throws:

SQLException - if an SQLException occurs

IOException - if an IOException occurs

InterruptedException - if an InterruptedException occurs

ClassNotFoundException - if an ClassNotFoundException occurs

getAssumptionTable

public String getAssumptionTable(String spectrumKey)

Returns the assumptions table name associated with the given spectrum key.

Parameters:

spectrumKey - the given spectrum key

Returns:

the table name of the given spectrum

getRawAssumptionTable

public String getRawAssumptionTable(String spectrumKey)

Returns the raw assumptions table name associated with the given spectrum key.

Parameters:

spectrumKey - the given spectrum key

Returns:

the table name of the given spectrum

getSpectrumMatchTable

public String getSpectrumMatchTable(String spectrumKey)

Returns the PSM table name associated with the given spectrum key.

Parameters:

spectrumKey - the given spectrum key

Returns:

the table name of the given spectrum

getSpectrumParameterTable

public String getSpectrumParameterTable(String spectrumKey,
                                        UrParameter urParameter)

Returns the table name associated with the given spectrum parameter.

Parameters:

spectrumKey - the given spectrum key

urParameter - the parameter

Returns:

the table name of the given spectrum parameter

getPeptideParameterTable

public String getPeptideParameterTable(UrParameter urParameter)

Returns the table name associated with the given peptide parameter.

Parameters:

urParameter - the parameter

Returns:

the table name of the given peptide parameter

getProteinParameterTable

public String getProteinParameterTable(UrParameter urParameter)

Returns the table name associated with the given protein parameter.

Parameters:

urParameter - the parameter

Returns:

the table name of the given protein parameter

restoreConnection

public void restoreConnection(String dbFolder,
                              boolean deleteOldDatabase,
                              ObjectsCache objectsCache)
                       throws SQLException,
                              IOException,
                              ClassNotFoundException,
                              InterruptedException

Restores the connection to the database.

Parameters:

dbFolder - the folder where the database is located

deleteOldDatabase - if true, tries to delete the old database

objectsCache - the objects cache

Throws:

SQLException - exception thrown whenever an error occurs while interacting with the database

IOException - exception thrown whenever an error occurs while reading or writing a file

ClassNotFoundException - exception thrown whenever an error occurred while deserializing a file from the database

InterruptedException - exception thrown if a threading error occurs while interacting with the database

isConnectionActive

public boolean isConnectionActive()

Indicates whether the connection to the DB is active.

Returns:

true if the connection to the DB is active

getObjectsDB

public ObjectsDB getObjectsDB()

Returns the database used to store matches.

Returns:

the database used to store matches

close

public void close()
           throws SQLException

Closes the db connection.

Throws:

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