com.compomics.util.experiment.identification

Class IdentificationDB

java.lang.Object

com.compomics.util.experiment.identification.IdentificationDB

All Implemented Interfaces:

java.io.Serializable

public class IdentificationDB
extends java.lang.Object
implements java.io.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
java.lang.String	dbName The name which will be used for the database.

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	addMatch(IdentificationMatch match) Adds an identification match to the database.
void	addMatchParameter(java.lang.String key, UrParameter urParameter) Deprecated. use match specific mapping instead
void	addPeptideMatch(PeptideMatch peptideMatch) Adds a peptide match to the database
void	addPeptideMatchParameter(java.lang.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(java.lang.String key, UrParameter urParameter) Adds a protein match parameter to the database.
void	addSpectrumMatch(SpectrumMatch spectrumMatch) Adds a spectrum match to the database.
void	addSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) Adds a spectrum match parameter to the database.
void	close() Closes the db connection.
UrParameter	getMatchPArameter(java.lang.String key, UrParameter urParameter, boolean useDB) Deprecated. use match specific mapping instead
java.lang.String	getParameterTable(UrParameter urParameter) Deprecated. use match specific mapping instead
PeptideMatch	getPeptideMatch(java.lang.String key, boolean useDB) Returns the desired peptide match.
UrParameter	getPeptideMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired peptide match parameter.
java.lang.String	getPeptideParameterTable(UrParameter urParameter) Returns the table name associated with the given peptide parameter.
ProteinMatch	getProteinMatch(java.lang.String key, boolean useDB) Returns the desired protein match.
UrParameter	getProteinMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired protein match parameter.
java.lang.String	getProteinParameterTable(UrParameter urParameter) Returns the table name associated with the given protein parameter.
SpectrumMatch	getSpectrumMatch(java.lang.String key, boolean useDB) Returns the desired spectrum match.
UrParameter	getSpectrumMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired spectrum match parameter.
java.lang.String	getSpectrumMatchTable(java.lang.String spectrumKey) Returns the table name associated with the given spectrum key.
java.lang.String	getSpectrumParameterTable(java.lang.String spectrumKey, UrParameter urParameter) Returns the table name associated with the given spectrum parameter.
void	loadPeptideMatches(java.util.ArrayList<java.lang.String> peptideKeys, WaitingHandler waitingHandler) Loads the desired peptide matches of the given type in the cache of the database.
void	loadPeptideMatches(WaitingHandler waitingHandler) Loads all peptide matches in the cache of the database.
void	loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler) Loads the desired peptide match parameters of the given type in the cache of the database.
void	loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler) Loads all peptide match parameters of the given type in the cache of the database.
void	loadProteinMatches(java.util.ArrayList<java.lang.String> proteinKeys, WaitingHandler waitingHandler) Loads the desired protein matches of the given type in the cache of the database.
void	loadProteinMatches(WaitingHandler waitingHandler) Loads all protein matches in the cache of the database.
void	loadProteinMatchParameters(java.util.ArrayList<java.lang.String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler) Loads the desired protein match parameters of the given type in the cache of the database.
void	loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler) Loads all protein match parameters of the given type in the cache of the database.
void	loadSpectrumMatches(java.util.ArrayList<java.lang.String> spectrumKeys, WaitingHandler waitingHandler) Loads all given spectrum matches in the cache of the database.
void	loadSpectrumMatches(java.lang.String fileName, WaitingHandler waitingHandler) Loads all spectrum matches of the given file in the cache of the database.
void	loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler) Loads all desired spectrum match parameters in the cache of the database.
void	loadSpectrumMatchParameters(java.lang.String fileName, UrParameter urParameter, WaitingHandler waitingHandler) Loads all spectrum match parameters of the given type in the cache of the database.
boolean	peptideMatchLoaded(java.lang.String peptideKey) Indicates whether a peptide match is loaded.
boolean	proteinMatchLoaded(java.lang.String proteinKey) Indicates whether a protein match is loaded.
void	removeMatch(java.lang.String key) Deprecated. it is advised to use the specific psm/peptide/protein method instead
void	removePeptideMatch(java.lang.String key) Deletes a peptide match from the database.
void	removeProteinMatch(java.lang.String key) Deletes a protein match from the database.
void	removeSpectrumMatch(java.lang.String key) Deletes a spectrum match from the database.
boolean	spectrumMatchLoaded(java.lang.String spectrumKey) Indicates whether a spectrum match is loaded.
void	updateMatch(IdentificationMatch match) Updates a match.
void	updatePeptideMatch(PeptideMatch peptideMatch) Updates a peptide match.
void	updatePeptideParameter(java.lang.String key, UrParameter urParameter) Updates a peptide match parameter.
void	updateProteinMatch(ProteinMatch proteinMatch) Updates a protein match.
void	updateProteinParameter(java.lang.String key, UrParameter urParameter) Updates a protein match parameter.
void	updateSpectrumMatch(SpectrumMatch spectrumMatch) Updates a spectrum match.
void	updateSpectrumParameter(java.lang.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 java.lang.String dbName

The name which will be used for the database.

Constructor Detail

IdentificationDB

public IdentificationDB(java.lang.String folder,
                java.lang.String name,
                boolean deleteOldDatabase,
                ObjectsCache objectCache)
                 throws java.sql.SQLException

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

Parameters:

folder - the folder where to put the database

name -

deleteOldDatabase - if true, tries to delete the old database

objectCache -

Throws:

java.sql.SQLException - an exception thrown whenever an error occurred while creating the database

Method Detail

spectrumMatchLoaded

public boolean spectrumMatchLoaded(java.lang.String spectrumKey)
                            throws java.sql.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:

java.sql.SQLException - exception thrown whenever an exception occurred while interrogating the database

peptideMatchLoaded

public boolean peptideMatchLoaded(java.lang.String peptideKey)
                           throws java.sql.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:

java.sql.SQLException - exception thrown whenever an exception occurred while interrogating the database

proteinMatchLoaded

public boolean proteinMatchLoaded(java.lang.String proteinKey)
                           throws java.sql.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:

java.sql.SQLException - exception thrown whenever an exception occurred while interrogating the database

updateProteinMatch

public void updateProteinMatch(ProteinMatch proteinMatch)
                        throws java.sql.SQLException,
                               java.io.IOException

Updates a protein match.

Parameters:

proteinMatch - the protein match

Throws:

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

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

updatePeptideMatch

public void updatePeptideMatch(PeptideMatch peptideMatch)
                        throws java.sql.SQLException,
                               java.io.IOException

Updates a peptide match.

Parameters:

peptideMatch - the peptide match

Throws:

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

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

updateSpectrumMatch

public void updateSpectrumMatch(SpectrumMatch spectrumMatch)
                         throws java.sql.SQLException,
                                java.io.IOException

Updates a spectrum match.

Parameters:

spectrumMatch - the spectrum match

Throws:

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

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

updateMatch

public void updateMatch(IdentificationMatch match)
                 throws java.sql.SQLException,
                        java.io.IOException

Updates a match.

Parameters:

match - the match to update

Throws:

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

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

updateProteinParameter

public void updateProteinParameter(java.lang.String key,
                          UrParameter urParameter)
                            throws java.sql.SQLException,
                                   java.io.IOException

Updates a protein match parameter.

Parameters:

key - the key of the protein match

urParameter - the parameter

Throws:

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

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

updatePeptideParameter

public void updatePeptideParameter(java.lang.String key,
                          UrParameter urParameter)
                            throws java.sql.SQLException,
                                   java.io.IOException

Updates a peptide match parameter.

Parameters:

key - the key of the peptide match

urParameter - the parameter

Throws:

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

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

updateSpectrumParameter

public void updateSpectrumParameter(java.lang.String key,
                           UrParameter urParameter)
                             throws java.sql.SQLException,
                                    java.io.IOException

Updates a spectrum match parameter.

Parameters:

key - the key of the spectrum match

urParameter - the parameter

Throws:

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

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

removeProteinMatch

public void removeProteinMatch(java.lang.String key)
                        throws java.sql.SQLException,
                               java.io.IOException

Deletes a protein match from the database.

Parameters:

key - the key of the match

Throws:

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

java.io.IOException

removePeptideMatch

public void removePeptideMatch(java.lang.String key)
                        throws java.sql.SQLException,
                               java.io.IOException

Deletes a peptide match from the database.

Parameters:

key - the key of the match

Throws:

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

java.io.IOException

removeSpectrumMatch

public void removeSpectrumMatch(java.lang.String key)
                         throws java.sql.SQLException,
                                java.io.IOException

Deletes a spectrum match from the database.

Parameters:

key - the key of the match

Throws:

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

java.io.IOException

removeMatch

public void removeMatch(java.lang.String key)
                 throws java.sql.SQLException,
                        java.io.IOException

Deprecated. it is advised to use the specific psm/peptide/protein method instead

Deletes a match from the database.

Parameters:

key - the key of the match

Throws:

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

java.io.IOException

getSpectrumMatch

public SpectrumMatch getSpectrumMatch(java.lang.String key,
                             boolean useDB)
                               throws java.sql.SQLException,
                                      java.io.IOException,
                                      java.lang.ClassNotFoundException,
                                      java.lang.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:

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

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

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

java.lang.InterruptedException

addSpectrumMatch

public void addSpectrumMatch(SpectrumMatch spectrumMatch)
                      throws java.sql.SQLException,
                             java.io.IOException,
                             java.lang.InterruptedException

Adds a spectrum match to the database.

Parameters:

spectrumMatch - the spectrum match to be added

Throws:

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

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

java.lang.InterruptedException

getPeptideMatch

public PeptideMatch getPeptideMatch(java.lang.String key,
                           boolean useDB)
                             throws java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.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:

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

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

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

java.lang.InterruptedException

addPeptideMatch

public void addPeptideMatch(PeptideMatch peptideMatch)
                     throws java.sql.SQLException,
                            java.io.IOException,
                            java.lang.InterruptedException

Adds a peptide match to the database

Parameters:

peptideMatch - the peptide match to be added

Throws:

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

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

java.lang.InterruptedException

getProteinMatch

public ProteinMatch getProteinMatch(java.lang.String key,
                           boolean useDB)
                             throws java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.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:

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

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

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

java.lang.InterruptedException

addProteinMatch

public void addProteinMatch(ProteinMatch proteinMatch)
                     throws java.sql.SQLException,
                            java.io.IOException,
                            java.lang.InterruptedException

Adds a protein match to the database.

Parameters:

proteinMatch - the protein match to be added

Throws:

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

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

java.lang.InterruptedException

addMatch

public void addMatch(IdentificationMatch match)
              throws java.sql.SQLException,
                     java.io.IOException,
                     java.lang.InterruptedException

Adds an identification match to the database.

Parameters:

match - the match to be added

Throws:

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

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

java.lang.InterruptedException

loadPeptideMatchParameters

public void loadPeptideMatchParameters(UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws java.sql.SQLException,
                                       java.io.IOException,
                                       java.lang.ClassNotFoundException,
                                       java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadPeptideMatchParameters

public void loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys,
                              UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws java.sql.SQLException,
                                       java.io.IOException,
                                       java.lang.ClassNotFoundException,
                                       java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadPeptideMatches

public void loadPeptideMatches(java.util.ArrayList<java.lang.String> peptideKeys,
                      WaitingHandler waitingHandler)
                        throws java.sql.SQLException,
                               java.io.IOException,
                               java.lang.ClassNotFoundException,
                               java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadProteinMatchParameters

public void loadProteinMatchParameters(UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws java.sql.SQLException,
                                       java.io.IOException,
                                       java.lang.ClassNotFoundException,
                                       java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadProteinMatchParameters

public void loadProteinMatchParameters(java.util.ArrayList<java.lang.String> proteinKeys,
                              UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws java.sql.SQLException,
                                       java.io.IOException,
                                       java.lang.ClassNotFoundException,
                                       java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadProteinMatches

public void loadProteinMatches(WaitingHandler waitingHandler)
                        throws java.sql.SQLException,
                               java.io.IOException,
                               java.lang.ClassNotFoundException,
                               java.lang.InterruptedException

Loads all protein matches in the cache of the database.

Parameters:

waitingHandler - the waiting handler

Throws:

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

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

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

java.lang.InterruptedException

loadProteinMatches

public void loadProteinMatches(java.util.ArrayList<java.lang.String> proteinKeys,
                      WaitingHandler waitingHandler)
                        throws java.sql.SQLException,
                               java.io.IOException,
                               java.lang.ClassNotFoundException,
                               java.lang.InterruptedException,
                               java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadPeptideMatches

public void loadPeptideMatches(WaitingHandler waitingHandler)
                        throws java.sql.SQLException,
                               java.io.IOException,
                               java.lang.ClassNotFoundException,
                               java.lang.InterruptedException,
                               java.lang.InterruptedException

Loads all peptide matches in the cache of the database.

Parameters:

waitingHandler - the waiting handler

Throws:

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

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

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

java.lang.InterruptedException

loadSpectrumMatches

public void loadSpectrumMatches(java.lang.String fileName,
                       WaitingHandler waitingHandler)
                         throws java.sql.SQLException,
                                java.io.IOException,
                                java.lang.ClassNotFoundException,
                                java.lang.InterruptedException

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

Parameters:

fileName - the file name

waitingHandler - the waiting handler

Throws:

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

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

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

java.lang.InterruptedException

loadSpectrumMatches

public void loadSpectrumMatches(java.util.ArrayList<java.lang.String> spectrumKeys,
                       WaitingHandler waitingHandler)
                         throws java.sql.SQLException,
                                java.io.IOException,
                                java.lang.ClassNotFoundException,
                                java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadSpectrumMatchParameters

public void loadSpectrumMatchParameters(java.lang.String fileName,
                               UrParameter urParameter,
                               WaitingHandler waitingHandler)
                                 throws java.sql.SQLException,
                                        java.io.IOException,
                                        java.lang.ClassNotFoundException,
                                        java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

loadSpectrumMatchParameters

public void loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
                               UrParameter urParameter,
                               WaitingHandler waitingHandler)
                                 throws java.sql.SQLException,
                                        java.io.IOException,
                                        java.lang.ClassNotFoundException,
                                        java.lang.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

Throws:

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

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

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

java.lang.InterruptedException

getSpectrumMatchParameter

public UrParameter getSpectrumMatchParameter(java.lang.String key,
                                    UrParameter urParameter,
                                    boolean useDB)
                                      throws java.sql.SQLException,
                                             java.io.IOException,
                                             java.lang.ClassNotFoundException,
                                             java.lang.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:

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

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

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

java.lang.InterruptedException

addSpectrumMatchParameter

public void addSpectrumMatchParameter(java.lang.String key,
                             UrParameter urParameter)
                               throws java.sql.SQLException,
                                      java.io.IOException,
                                      java.lang.InterruptedException

Adds a spectrum match parameter to the database.

Parameters:

key - the PSM key

urParameter - the match parameter

Throws:

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

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

java.lang.InterruptedException

getPeptideMatchParameter

public UrParameter getPeptideMatchParameter(java.lang.String key,
                                   UrParameter urParameter,
                                   boolean useDB)
                                     throws java.sql.SQLException,
                                            java.io.IOException,
                                            java.lang.ClassNotFoundException,
                                            java.lang.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:

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

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

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

java.lang.InterruptedException

addPeptideMatchParameter

public void addPeptideMatchParameter(java.lang.String key,
                            UrParameter urParameter)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.InterruptedException

Adds a peptide match parameter to the database.

Parameters:

key - the peptide key

urParameter - the match parameter

Throws:

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

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

java.lang.InterruptedException

getProteinMatchParameter

public UrParameter getProteinMatchParameter(java.lang.String key,
                                   UrParameter urParameter,
                                   boolean useDB)
                                     throws java.sql.SQLException,
                                            java.io.IOException,
                                            java.lang.ClassNotFoundException,
                                            java.lang.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:

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

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

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

java.lang.InterruptedException

addProteinMatchParameter

public void addProteinMatchParameter(java.lang.String key,
                            UrParameter urParameter)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.InterruptedException

Adds a protein match parameter to the database.

Parameters:

key - the protein key

urParameter - the match parameter

Throws:

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

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

java.lang.InterruptedException

getMatchPArameter

public UrParameter getMatchPArameter(java.lang.String key,
                            UrParameter urParameter,
                            boolean useDB)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Deprecated. use match specific mapping instead

Returns the desired match parameter.

Parameters:

key - the match key

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

urParameter - the match parameter

Returns:

the match match

Throws:

java.lang.InterruptedException

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

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

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

addMatchParameter

public void addMatchParameter(java.lang.String key,
                     UrParameter urParameter)
                       throws java.sql.SQLException,
                              java.io.IOException,
                              java.lang.InterruptedException

Deprecated. use match specific mapping instead

Adds a protein match parameter to the database.

Parameters:

key - the protein key

urParameter - the match parameter

Throws:

java.lang.InterruptedException

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

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

getSpectrumMatchTable

public java.lang.String getSpectrumMatchTable(java.lang.String spectrumKey)

Returns the table name associated with the given spectrum key.

Parameters:

spectrumKey - the given spectrum key

Returns:

the table name of the given spectrum

getSpectrumParameterTable

public java.lang.String getSpectrumParameterTable(java.lang.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 java.lang.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 java.lang.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

getParameterTable

public java.lang.String getParameterTable(UrParameter urParameter)

Deprecated. use match specific mapping instead

Returns the table name associated with the given parameter.

Parameters:

urParameter - the parameter

Returns:

the table name of the given protein parameter

close

public void close()
           throws java.sql.SQLException

Closes the db connection.

Throws:

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