com.compomics.util.experiment.identification

Class Identification

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.Identification

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

Ms2Identification

public abstract class Identification
extends ExperimentObject

This class contains identification results.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EXTENTION Deprecated. use the database methods instead
protected java.util.ArrayList<java.lang.String>	longKeys Deprecated. use the database instead
protected int	methodUsed The method used.
protected java.util.ArrayList<java.lang.String>	peptideIdentification List of the keys of all imported peptides.
protected java.util.ArrayList<java.lang.String>	proteinIdentification List of the keys of all imported proteins.
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>>	proteinMap A map linking protein accessions to all their protein matches keys.
protected java.lang.String	reference The reference of the identification.
protected java.lang.String	serializationDirectory The directory where matches will be serialized/the database stored.
protected java.util.ArrayList<java.lang.String>	spectrumIdentification Deprecated. use file specific mapping instead
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>>	spectrumIdentificationMap List of all imported PSMs indexed by mgf file name.
protected java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,UrParameter>>	urParameters Deprecated. use the database instead

Constructor Summary

Constructors

Constructor and Description
Identification()

Method Summary

Methods

Modifier and Type	Method and Description
void	addMatchParameter(java.lang.String key, UrParameter urParameter) Deprecated. use the database match specific methods instead
void	addPeptideMatchParameter(java.lang.String key, UrParameter urParameter) Adds a peptide match parameter to the database.
void	addProteinMatchParameter(java.lang.String key, UrParameter urParameter) Adds a protein match parameter to the database.
void	addSpectrumMatch(java.util.Set<SpectrumMatch> spectrumMatches, boolean ascendingScore) Add a set of spectrumMatches to the model.
void	addSpectrumMatch(SpectrumMatch newMatch, boolean ascendingScore) Adds a spectrum match to the identification.
void	addSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) Adds a spectrum match parameter to the database.
void	buildPeptidesAndProteins(java.lang.String spectrumMatchKey, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Creates the peptides and protein instances based on the given spectrum match.
void	buildPeptidesAndProteins(WaitingHandler waitingHandler, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Creates the peptides and protein instances based on the spectrum matches.
void	close() Closes the database connection.
void	convert(WaitingHandler waitingHandler, java.lang.String newDirectory, java.lang.String newName, ObjectsCache objectsCache, java.io.File directory) Converts a serialization based structure into a database based one.
void	establishConnection(java.lang.String dbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache) Establishes a connection to the database.
static java.lang.String	getDefaultReference(java.lang.String experimentReference, java.lang.String sampleReference, int replicateNumber) Returns the default reference for an identification.
java.lang.String	getFileName(java.lang.String key) Deprecated. use the database methods instead
UrParameter	getMatchParameter(java.lang.String matchKey, UrParameter urParameter) Deprecated. use the database match specific methods instead
IdentificationMatch.MatchType	getMatchType(java.lang.String matchKey) Returns the kind of match pointed by the given key in the identification mappings.
int	getMethodUsed() Getter for the identification method used.
java.util.ArrayList<java.lang.String>	getOrderedSpectrumFileNames() Returns the ordered list of spectrum file names.
java.util.ArrayList<java.lang.String>	getPeptideIdentification() Returns a list of the keys of all encountered peptides.
PeptideMatch	getPeptideMatch(java.lang.String peptideKey) Returns a peptide match.
PeptideMatch	getPeptideMatch(java.lang.String peptideKey, boolean useDB) Returns a peptide match.
UrParameter	getPeptideMatchParameter(java.lang.String key, UrParameter urParameter) Returns the desired peptide match parameter.
UrParameter	getPeptideMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired peptide match parameter.
java.util.ArrayList<java.lang.String>	getProteinIdentification() Returns a list of the keys of all encountered proteins.
java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>>	getProteinMap() Returns a map of all the protein matches which can be ascribed to a protein indexed by its accession.
ProteinMatch	getProteinMatch(java.lang.String proteinKey) Returns a protein match.
ProteinMatch	getProteinMatch(java.lang.String proteinKey, boolean useDB) Returns a protein match.
java.util.ArrayList<java.lang.String>	getProteinMatches(Peptide peptide) Returns the keys of the protein matches where a peptide can be found.
UrParameter	getProteinMatchParameter(java.lang.String key, UrParameter urParameter) Returns the desired protein match parameter.
UrParameter	getProteinMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired protein match parameter.
java.lang.String	getSerializationDirectory() Returns the serialization directory.
java.util.ArrayList<java.lang.String>	getSpectrumFiles() Returns the names of the mgf files used in the spectrum identification map as a list.
java.util.ArrayList<java.lang.String>	getSpectrumIdentification() Deprecated. use file specific names instead
java.util.ArrayList<java.lang.String>	getSpectrumIdentification(java.lang.String spectrumFile) Returns the keys of the spectrum identifications for a given spectrum file name.
java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>>	getSpectrumIdentificationMap() Returns the keys of all identified spectra indexed by the spectrum file.
int	getSpectrumIdentificationSize() Returns the number of spectrum identifications.
SpectrumMatch	getSpectrumMatch(java.lang.String spectrumKey) Returns a spectrum match.
SpectrumMatch	getSpectrumMatch(java.lang.String spectrumKey, boolean useDB) Returns a spectrum match.
UrParameter	getSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) Returns the desired spectrum match parameter.
UrParameter	getSpectrumMatchParameter(java.lang.String key, UrParameter urParameter, boolean useDB) Returns the desired spectrum match parameter.
java.lang.Boolean	isDB() Indicates whether the identification matches should be stored in a database (true, default value) or serialized files (false, deprecated default).
boolean	isUnique(Peptide peptide) Indicates whether a peptide is found in a single protein match.
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 the given spectrum matches in the cache of the database.
void	loadSpectrumMatches(java.lang.String fileName, WaitingHandler waitingHandler) Loads all spectrum matches of the 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	matchExists(java.lang.String matchKey) Indicates whether a match indexed by the given key exists.
boolean	peptideDetailsInCache(java.lang.String peptideKey) Indicates whether the peptide and spectrum matches corresponding to a peptide match key are loaded in the cache.
boolean	proteinDetailsInCache(java.lang.String proteinKey) Indicates whether the protein, peptide and spectrum matches corresponding to a protein match key are loaded in the cache.
void	removeMatch(java.lang.String matchKey) Deprecated. it is advised to use the specific psm/peptide/protein method instead
void	removePeptideMatch(java.lang.String matchKey) Removes a peptide match from the model.
void	removeProteinMatch(java.lang.String matchKey) Removes a protein match from the model.
void	removeSpectrumMatch(java.lang.String matchKey) Removes a spectrum match from the model.
void	setDirectory(java.lang.String serializationDirectory, boolean deleteOldDatabase) Deprecated. use establishConnection(String dbFolder) instead
void	setIsDB(java.lang.Boolean isDB) Sets whether the identification matches should be stored in a database or serialized files.
void	setOrderedListOfSpectrumFileNames(java.util.ArrayList<java.lang.String> orderedSpectrumFileNames) Set the ordered list of spectrum file names.
void	updatePeptideMatch(PeptideMatch peptideMatch) Updates a peptide match in the database.
void	updatePeptideMatchParameter(java.lang.String key, UrParameter urParameter) Updates a peptide match parameter in the database.
void	updateProteinMatch(ProteinMatch proteinMatch) Updates a protein match in the database.
void	updateProteinMatchParameter(java.lang.String key, UrParameter urParameter) Updates a protein match parameter in the database.
void	updateSpectrumMapping() Converts the old spectrum keys structure into the mapped version.
void	updateSpectrumMatch(SpectrumMatch spectrumMatch) Updates a spectrum match in the database.
void	updateSpectrumMatchParameter(java.lang.String key, UrParameter urParameter) Updates a spectrum match parameter in the database.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Field Detail

EXTENTION

public static final java.lang.String EXTENTION

Deprecated. use the database methods instead

Extention for a serialized hit. cuh for Compomics Utilities Hit.

See Also:

Constant Field Values

proteinIdentification

protected java.util.ArrayList<java.lang.String> proteinIdentification

List of the keys of all imported proteins.

peptideIdentification

protected java.util.ArrayList<java.lang.String> peptideIdentification

List of the keys of all imported peptides.

spectrumIdentificationMap

protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> spectrumIdentificationMap

List of all imported PSMs indexed by mgf file name.

spectrumIdentification

protected java.util.ArrayList<java.lang.String> spectrumIdentification

Deprecated. use file specific mapping instead

List of the keys of all imported PSMs.

proteinMap

protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> proteinMap

A map linking protein accessions to all their protein matches keys.

methodUsed

protected int methodUsed

The method used.

serializationDirectory

protected java.lang.String serializationDirectory

The directory where matches will be serialized/the database stored.

urParameters

protected java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,UrParameter>> urParameters

Deprecated. use the database instead

Map of the user's parameters.

longKeys

protected java.util.ArrayList<java.lang.String> longKeys

Deprecated. use the database instead

Map of long keys (>100 characters) which will be referenced by their index for file creation/database storage.

reference

protected java.lang.String reference

The reference of the identification.

Constructor Detail

Identification

public Identification()

Method Detail

getOrderedSpectrumFileNames

public java.util.ArrayList<java.lang.String> getOrderedSpectrumFileNames()

Returns the ordered list of spectrum file names.

Returns:

the ordered list of spectrum file names

setOrderedListOfSpectrumFileNames

public void setOrderedListOfSpectrumFileNames(java.util.ArrayList<java.lang.String> orderedSpectrumFileNames)
                                       throws java.lang.IllegalArgumentException

Set the ordered list of spectrum file names. Note that the list provided has to be the same size as the number of spectrum files used.

Parameters:

orderedSpectrumFileNames - the ordered list of spectrum file names

Throws:

java.lang.IllegalArgumentException - thrown if the length of the ordered file names as to be the same as the number of spectrum files

getSpectrumFiles

public java.util.ArrayList<java.lang.String> getSpectrumFiles()

Returns the names of the mgf files used in the spectrum identification map as a list. To get the complete file path use projectDetails.getSpectrumFile(...).

Returns:

the mgf files used in the spectrum identification map

getSpectrumIdentificationSize

public int getSpectrumIdentificationSize()

Returns the number of spectrum identifications.

Returns:

the number of spectrum identifications

addMatchParameter

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

Deprecated. use the database match specific methods instead

Adds a parameter with a corresponding match key which will be loaded in the memory. Use this method only for frequently used parameters, otherwise attach the parameters to the matches.

Parameters:

key - the key of the parameter

urParameter - the additional 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

getMatchParameter

public UrParameter getMatchParameter(java.lang.String matchKey,
                            UrParameter urParameter)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Deprecated. use the database match specific methods instead

Returns the personalization parameter of the given match.

Parameters:

matchKey - the match key

urParameter - example of parameter to retrieve

Returns:

the personalization parameter

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

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

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

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

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 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 the given spectrum matches in the cache of the database.

Parameters:

spectrumKeys - the spectrum keys

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)
                                      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

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

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)
                                     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

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

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)
                                     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

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

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

updateProteinMatchParameter

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

Updates a protein match parameter in 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

updatePeptideMatchParameter

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

Updates a peptide match parameter in 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

updateSpectrumMatchParameter

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

Updates a spectrum match parameter in the database.

Parameters:

key - the spectrum 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

updateSpectrumMatch

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

Updates a spectrum match in the database.

Parameters:

spectrumMatch - the match

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

updatePeptideMatch

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

Updates a peptide match in the database.

Parameters:

peptideMatch - the match

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

updateProteinMatch

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

Updates a protein match in the database.

Parameters:

proteinMatch - the match

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

getSerializationDirectory

public java.lang.String getSerializationDirectory()

Returns the serialization directory.

Returns:

the serialization directory

setDirectory

public void setDirectory(java.lang.String serializationDirectory,
                boolean deleteOldDatabase)
                  throws java.sql.SQLException

Deprecated. use establishConnection(String dbFolder) instead

Sets the directory where matches will be stored in order to save memory. Matches can be stored in a database (default) or serialized files. If the database option is chosen (see setIsDB(Boolean isDB)) and no database created, the database will be created in the folder.

Parameters:

serializationDirectory - the path of the directory

deleteOldDatabase - if true, tries to delete the old database

Throws:

java.sql.SQLException

removeMatch

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

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

Removes a match from the model.

Parameters:

matchKey - the key of the match to remove

Throws:

java.lang.IllegalArgumentException

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

java.io.IOException

removeSpectrumMatch

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

Removes a spectrum match from the model.

Parameters:

matchKey - the key of the match to remove

Throws:

java.lang.IllegalArgumentException

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

java.io.IOException

removePeptideMatch

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

Removes a peptide match from the model.

Parameters:

matchKey - the key of the match to remove

Throws:

java.lang.IllegalArgumentException

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

java.io.IOException

removeProteinMatch

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

Removes a protein match from the model.

Parameters:

matchKey - the key of the match to remove

Throws:

java.lang.IllegalArgumentException

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

java.io.IOException

matchExists

public boolean matchExists(java.lang.String matchKey)

Indicates whether a match indexed by the given key exists.

Parameters:

matchKey - the key of the match looked for

Returns:

a boolean indicating whether a match indexed by the given key exists

getSpectrumMatch

public SpectrumMatch getSpectrumMatch(java.lang.String spectrumKey)
                               throws java.lang.IllegalArgumentException,
                                      java.sql.SQLException,
                                      java.io.IOException,
                                      java.lang.ClassNotFoundException,
                                      java.lang.InterruptedException

Returns a spectrum match.

Parameters:

spectrumKey - the key of the match

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

getSpectrumMatch

public SpectrumMatch getSpectrumMatch(java.lang.String spectrumKey,
                             boolean useDB)
                               throws java.lang.IllegalArgumentException,
                                      java.sql.SQLException,
                                      java.io.IOException,
                                      java.lang.ClassNotFoundException,
                                      java.lang.InterruptedException

Returns a spectrum match.

Parameters:

spectrumKey - the key of the match

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

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

getPeptideMatch

public PeptideMatch getPeptideMatch(java.lang.String peptideKey)
                             throws java.lang.IllegalArgumentException,
                                    java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.InterruptedException

Returns a peptide match.

Parameters:

peptideKey - the key of the match

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

getPeptideMatch

public PeptideMatch getPeptideMatch(java.lang.String peptideKey,
                           boolean useDB)
                             throws java.lang.IllegalArgumentException,
                                    java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.InterruptedException

Returns a peptide match.

Parameters:

peptideKey - the key of the match

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

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

getProteinMatch

public ProteinMatch getProteinMatch(java.lang.String proteinKey)
                             throws java.lang.IllegalArgumentException,
                                    java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.InterruptedException

Returns a protein match.

Parameters:

proteinKey - the key of the match

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

getProteinMatch

public ProteinMatch getProteinMatch(java.lang.String proteinKey,
                           boolean useDB)
                             throws java.lang.IllegalArgumentException,
                                    java.sql.SQLException,
                                    java.io.IOException,
                                    java.lang.ClassNotFoundException,
                                    java.lang.InterruptedException

Returns a protein match.

Parameters:

proteinKey - the key of the match

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

Returns:

the desired match

Throws:

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match

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

proteinDetailsInCache

public boolean proteinDetailsInCache(java.lang.String proteinKey)
                              throws java.lang.IllegalArgumentException,
                                     java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Indicates whether the protein, peptide and spectrum matches corresponding to a protein match key are loaded in the cache. Note, only one peptide and one spectrum match is tested.

Parameters:

proteinKey - the key of the protein match

Returns:

true if everything is loaded in memory

Throws:

java.lang.IllegalArgumentException

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

peptideDetailsInCache

public boolean peptideDetailsInCache(java.lang.String peptideKey)
                              throws java.lang.IllegalArgumentException,
                                     java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Indicates whether the peptide and spectrum matches corresponding to a peptide match key are loaded in the cache. Note, only one one spectrum match is tested.

Parameters:

peptideKey - the peptide key

Returns:

true if everything is loaded in the cache

Throws:

java.lang.IllegalArgumentException

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

getProteinIdentification

public java.util.ArrayList<java.lang.String> getProteinIdentification()

Returns a list of the keys of all encountered proteins.

Returns:

the corresponding identification results

getPeptideIdentification

public java.util.ArrayList<java.lang.String> getPeptideIdentification()

Returns a list of the keys of all encountered peptides.

Returns:

the corresponding identification results

getSpectrumIdentification

public java.util.ArrayList<java.lang.String> getSpectrumIdentification()

Deprecated. use file specific names instead

Returns a list of the keys of all encountered psms.

Returns:

the corresponding identification results

getSpectrumIdentification

public java.util.ArrayList<java.lang.String> getSpectrumIdentification(java.lang.String spectrumFile)

Returns the keys of the spectrum identifications for a given spectrum file name.

Parameters:

spectrumFile - the name of the spectrum file

Returns:

the corresponding list of spectrum matches keys. See Spectrum.getKey() for more details.

getSpectrumIdentificationMap

public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getSpectrumIdentificationMap()

Returns the keys of all identified spectra indexed by the spectrum file.

Returns:

the keys of all identified spectra indexed by the spectrum file

addSpectrumMatch

public void addSpectrumMatch(SpectrumMatch newMatch,
                    boolean ascendingScore)
                      throws java.io.FileNotFoundException,
                             java.io.IOException,
                             java.lang.IllegalArgumentException,
                             java.sql.SQLException,
                             java.lang.ClassNotFoundException,
                             java.lang.InterruptedException

Adds a spectrum match to the identification.

Parameters:

newMatch - the new match

ascendingScore - indicates whether the score is ascending when hits get better

Throws:

java.io.FileNotFoundException - exception thrown whenever an error occurred while saving the file

java.io.IOException - exception thrown whenever an error occurred while saving the file

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while saving the file

java.sql.SQLException - exception thrown whenever an error occurred while saving the file

java.lang.ClassNotFoundException - exception thrown whenever an error occurred while saving the file

java.lang.InterruptedException

buildPeptidesAndProteins

public void buildPeptidesAndProteins(WaitingHandler waitingHandler,
                            AminoAcidPattern.MatchingType matchingType,
                            java.lang.Double massTolerance)
                              throws java.lang.IllegalArgumentException,
                                     java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Creates the peptides and protein instances based on the spectrum matches. Note that the attribute bestAssumption should be set for every spectrum match at this point. This operation will be very slow if the cache is already full.

Parameters:

waitingHandler - the waiting handler displaying the progress. Can be null. The progress will be displayed as secondary.

matchingType - the amino acid matching type to use to create peptide matches

massTolerance - the mass tolerance

Throws:

java.lang.IllegalArgumentException

java.sql.SQLException

java.io.IOException

java.lang.ClassNotFoundException

java.lang.InterruptedException

buildPeptidesAndProteins

public void buildPeptidesAndProteins(java.lang.String spectrumMatchKey,
                            AminoAcidPattern.MatchingType matchingType,
                            java.lang.Double massTolerance)
                              throws java.lang.IllegalArgumentException,
                                     java.sql.SQLException,
                                     java.io.IOException,
                                     java.lang.ClassNotFoundException,
                                     java.lang.InterruptedException

Creates the peptides and protein instances based on the given spectrum match. Note that the attribute bestAssumption should be set for every spectrum match at this point and peptides should be mapped to proteins. This operation will be very slow if the cache is already full. Note: if proteins are not set for a peptide they will be assigned using the default protein tree and the given matching parameters.

Parameters:

spectrumMatchKey - The key of the spectrum match to add

matchingType - the amino acid matching type to use to create peptide matches

massTolerance - the mass tolerance

Throws:

java.lang.IllegalArgumentException

java.sql.SQLException

java.lang.ClassNotFoundException

java.io.IOException

java.lang.InterruptedException

addSpectrumMatch

public void addSpectrumMatch(java.util.Set<SpectrumMatch> spectrumMatches,
                    boolean ascendingScore)
                      throws java.io.FileNotFoundException,
                             java.io.IOException,
                             java.lang.IllegalArgumentException,
                             java.sql.SQLException,
                             java.lang.ClassNotFoundException,
                             java.lang.InterruptedException

Add a set of spectrumMatches to the model.

Parameters:

spectrumMatches - The spectrum matches

ascendingScore - indicates whether the score is ascending when hits get better

Throws:

java.io.FileNotFoundException - exception thrown whenever an error occurred while saving the file

java.io.IOException - exception thrown whenever an error occurred while saving the file

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while saving the file

java.sql.SQLException - exception thrown whenever an error occurred while saving the file

java.lang.ClassNotFoundException - exception thrown whenever an error occurred while saving the file

java.lang.InterruptedException

getMethodUsed

public int getMethodUsed()

Getter for the identification method used.

Returns:

the identification method used

getProteinMap

public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getProteinMap()

Returns a map of all the protein matches which can be ascribed to a protein indexed by its accession.

Returns:

a map of all the protein matches which can be ascribed to a protein indexed by its accession.

getFileName

public java.lang.String getFileName(java.lang.String key)

Deprecated. use the database methods instead

Returns the name of the file to use for serialization/deserialization.

Parameters:

key - the key of the match

Returns:

the name of the corresponding file

isDB

public java.lang.Boolean isDB()

Indicates whether the identification matches should be stored in a database (true, default value) or serialized files (false, deprecated default).

Returns:

a boolean indicating whether the identification matches should be stored in a database or serialized files

setIsDB

public void setIsDB(java.lang.Boolean isDB)

Sets whether the identification matches should be stored in a database or serialized files.

Parameters:

isDB - a boolean indicating whether the identification matches should be stored in a database or serialized files

close

public void close()
           throws java.sql.SQLException

Closes the database connection.

Throws:

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

getMatchType

public IdentificationMatch.MatchType getMatchType(java.lang.String matchKey)

Returns the kind of match pointed by the given key in the identification mappings. Null if missing from the mapping.

Parameters:

matchKey - the match key

Returns:

the kind of match

establishConnection

public void establishConnection(java.lang.String dbFolder,
                       boolean deleteOldDatabase,
                       ObjectsCache objectsCache)
                         throws java.sql.SQLException

Establishes a connection to the database.

Parameters:

dbFolder - the absolute path to the folder where the database is located

deleteOldDatabase - if true, tries to delete the old database

objectsCache -

Throws:

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

convert

public void convert(WaitingHandler waitingHandler,
           java.lang.String newDirectory,
           java.lang.String newName,
           ObjectsCache objectsCache,
           java.io.File directory)
             throws java.io.FileNotFoundException,
                    java.io.IOException,
                    java.lang.ClassNotFoundException,
                    java.sql.SQLException,
                    java.lang.InterruptedException

Converts a serialization based structure into a database based one. Replaces the space separation by the standard separator.

Parameters:

waitingHandler - the waiting handler

newDirectory - the new directory where to store the data

newName -

objectsCache -

directory - the directory where the data is currently stored

Throws:

java.io.FileNotFoundException - exception thrown whenever a file is not found

java.io.IOException - exception thrown whenever an error occurred while reading/writing a file

java.lang.ClassNotFoundException - exception thrown whenever an error occurred while deserializing a match

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

java.lang.InterruptedException

updateSpectrumMapping

public void updateSpectrumMapping()

Converts the old spectrum keys structure into the mapped version.

getDefaultReference

public static java.lang.String getDefaultReference(java.lang.String experimentReference,
                                   java.lang.String sampleReference,
                                   int replicateNumber)

Returns the default reference for an identification.

Parameters:

experimentReference - the experiment reference

sampleReference - the sample reference

replicateNumber - the replicate number

Returns:

the default reference

getProteinMatches

public java.util.ArrayList<java.lang.String> getProteinMatches(Peptide peptide)
                                                        throws java.io.IOException,
                                                               java.sql.SQLException,
                                                               java.lang.ClassNotFoundException,
                                                               java.lang.InterruptedException

Returns the keys of the protein matches where a peptide can be found. Note: proteins have to be set for the peptide.

Parameters:

peptide - the peptide of interest

Returns:

the keys of the protein matches

Throws:

java.io.IOException

java.sql.SQLException

java.lang.InterruptedException

java.lang.ClassNotFoundException

isUnique

public boolean isUnique(Peptide peptide)
                 throws java.io.IOException,
                        java.sql.SQLException,
                        java.lang.ClassNotFoundException,
                        java.lang.InterruptedException

Indicates whether a peptide is found in a single protein match.

Parameters:

peptide - the peptide of interest

Returns:

true if peptide is found in a single protein match

Throws:

java.io.IOException

java.sql.SQLException

java.lang.ClassNotFoundException

java.lang.InterruptedException