public abstract class Identification extends ExperimentObject
Modifier and Type | Field and Description |
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protected String |
dbDirectory
The directory where the database stored.
|
protected int |
methodUsed
The method used.
|
protected HashSet<String> |
peptideIdentification
List of the keys of all imported peptides.
|
protected HashSet<String> |
proteinIdentification
List of the keys of all imported proteins.
|
protected HashMap<String,HashSet<String>> |
proteinMap
A map linking protein accessions to all their protein matches keys.
|
protected String |
reference
The reference of the identification.
|
protected HashMap<String,HashSet<String>> |
spectrumIdentificationMap
List of all imported PSMs indexed by mgf file name.
|
Constructor and Description |
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Identification() |
Modifier and Type | Method and Description |
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void |
addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions,
boolean newSpectrum)
Adds the assumptions corresponding to a spectrum.
|
void |
addAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions,
boolean overwriteExisting,
boolean newSpectrum)
Adds the assumptions corresponding to a spectrum to the database.
|
void |
addPeptideMatchParameter(String key,
UrParameter urParameter)
Adds a peptide match parameter to the database.
|
void |
addProteinMatchParameter(String key,
UrParameter urParameter)
Adds a protein match parameter to the database.
|
void |
addRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions)
Adds the raw assumptions corresponding to a spectrum to the database.
|
void |
addSpectrumMatch(SpectrumMatch newMatch)
Adds a spectrum match to the identification.
|
void |
addSpectrumMatches(Iterable<SpectrumMatch> spectrumMatches)
Add a set of spectrumMatches to the model.
|
void |
addSpectrumMatchParameter(String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database.
|
void |
buildPeptidesAndProteins(String spectrumMatchKey,
SequenceMatchingPreferences sequenceMatchingPreferences)
Creates the peptides and protein instances based on the given spectrum
match.
|
void |
buildPeptidesAndProteins(WaitingHandler waitingHandler,
SequenceMatchingPreferences sequenceMatchingPreferences)
Creates the peptides and protein instances based on the spectrum matches.
|
void |
close()
Closes the database connection.
|
void |
establishConnection(String dbFolder,
boolean deleteOldDatabase,
ObjectsCache objectsCache)
Establishes a connection to the database.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
getAssumptions(String spectrumKey)
Returns a the assumptions of a spectrum.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
getAssumptions(String spectrumKey,
boolean useDB)
Returns the assumptions of a spectrum.
|
String |
getDatabaseDirectory()
Returns the database directory.
|
static String |
getDefaultReference(String experimentReference,
String sampleReference,
int replicateNumber)
Returns the default reference for an identification.
|
IdentificationDB |
getIdentificationDB()
Returns the identification database object used to interact with the
back-end database.
|
IdentificationMatch.MatchType |
getMatchType(String matchKey)
Returns the kind of match pointed by the given key in the identification
mappings.
|
int |
getMethodUsed()
Getter for the identification method used.
|
ArrayList<String> |
getOrderedSpectrumFileNames()
Returns the ordered list of spectrum file names.
|
HashSet<String> |
getPeptideIdentification()
Returns a list of the keys of all encountered peptides.
|
PeptideMatch |
getPeptideMatch(String peptideKey)
Returns a peptide match.
|
PeptideMatch |
getPeptideMatch(String peptideKey,
boolean useDB)
Returns a peptide match.
|
PeptideMatchesIterator |
getPeptideMatchesIterator(ArrayList<String> peptideKeys,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator.
|
PeptideMatchesIterator |
getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator iterating all peptides.
|
UrParameter |
getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter.
|
UrParameter |
getPeptideMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter.
|
HashSet<String> |
getProteinIdentification()
Returns a list of the keys of all encountered proteins.
|
HashMap<String,HashSet<String>> |
getProteinMap()
Returns a map of all the protein matches which can be ascribed to a
protein indexed by its accession.
|
ProteinMatch |
getProteinMatch(String proteinKey)
Returns a protein match.
|
ProteinMatch |
getProteinMatch(String proteinKey,
boolean useDB)
Returns a protein match.
|
HashSet<String> |
getProteinMatches(Peptide peptide)
Returns the keys of the protein matches where a peptide can be found.
|
ProteinMatchesIterator |
getProteinMatchesIterator(ArrayList<String> proteinKeys,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator.
|
ProteinMatchesIterator |
getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator iterating all protein matches.
|
UrParameter |
getProteinMatchParameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter.
|
UrParameter |
getProteinMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter.
|
PsmIterator |
getPsmIterator(ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
getPsmIterator(ArrayList<String> spectrumKeys,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
getPsmIterator(boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
PsmIterator |
getPsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
getPsmIterator(String spectrumFile,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
PsmIterator |
getPsmIterator(String spectrumFile,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
getRawAssumptions(String spectrumKey)
Returns a the raw assumptions of a spectrum.
|
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> |
getRawAssumptions(String spectrumKey,
boolean useDB)
Returns the raw assumptions of a spectrum.
|
ArrayList<String> |
getSpectrumFiles()
Returns the names of the mgf files used in the spectrum identification
map as a list.
|
HashSet<String> |
getSpectrumIdentification(String spectrumFile)
Returns the keys of the spectrum identifications for a given spectrum
file name.
|
HashMap<String,HashSet<String>> |
getSpectrumIdentificationMap()
Returns the keys of all identified spectra indexed by the spectrum file.
|
int |
getSpectrumIdentificationSize()
Returns the number of spectrum identifications.
|
SpectrumMatch |
getSpectrumMatch(String spectrumKey)
Returns a spectrum match.
|
SpectrumMatch |
getSpectrumMatch(String spectrumKey,
boolean useDB)
Returns a spectrum match.
|
UrParameter |
getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter.
|
UrParameter |
getSpectrumMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter.
|
boolean |
isConnectionActive()
Indicates whether the connection to the DB is active.
|
boolean |
isUniqueInDatabase(Peptide peptide)
Indicates whether a peptide is found in a single protein match.
|
void |
loadAssumptions(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the assumptions of the spectrum matches indicated by the given keys
in the cache of the database.
|
void |
loadAssumptions(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum matches of the file in the cache of the database.
|
void |
loadPeptideMatches(ArrayList<String> peptideKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired peptide matches of the given type in the cache of the
database.
|
void |
loadPeptideMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide matches in the cache of the database.
|
void |
loadPeptideMatchParameters(ArrayList<String> peptideKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired peptide match parameters of the given type in the cache
of the database.
|
void |
loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
loadProteinMatches(ArrayList<String> proteinKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired protein matches of the given type in the cache of the
database.
|
void |
loadProteinMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein matches in the cache of the database.
|
void |
loadProteinMatchParameters(ArrayList<String> proteinKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired protein match parameters of the given type in the cache
of the database.
|
void |
loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
loadRawAssumptions(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the raw assumptions of the spectrum matches indicated by the given
keys in the cache of the database.
|
void |
loadSpectrumMatches(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the spectrum matches corresponding to the given keys in cache.
|
void |
loadSpectrumMatches(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum matches of the file in cache.
|
void |
loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum match parameters of the given type in the cache of the
database
|
boolean |
matchExists(String matchKey)
Indicates whether a match indexed by the given key exists.
|
boolean |
peptideDetailsInCache(String peptideKey)
Indicates whether the peptide and spectrum matches corresponding to a
peptide match key are loaded in the cache.
|
boolean |
proteinDetailsInCache(String proteinKey)
Indicates whether the protein, peptide and spectrum matches corresponding
to a protein match key are loaded in the cache.
|
void |
removeAssumptions(String matchKey)
Removes the assumptions of a spectrum.
|
void |
removePeptideMatch(String matchKey)
Removes a peptide match from the model.
|
void |
removeProteinMatch(String matchKey)
Removes a protein match from the model.
|
void |
removeRawAssumptions(String matchKey)
Removes the raw assumptions of a spectrum.
|
void |
removeSpectrumMatch(String matchKey)
Removes a spectrum match from the model.
|
void |
restoreConnection(String dbFolder,
boolean deleteOldDatabase,
ObjectsCache objectsCache)
Restores the connection to the database.
|
void |
setOrderedListOfSpectrumFileNames(ArrayList<String> orderedSpectrumFileNames)
Set the ordered list of spectrum file names.
|
void |
updateAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Updates the assumptions of a spectrum.
|
void |
updatePeptideMatch(PeptideMatch peptideMatch)
Updates a peptide match in the database.
|
void |
updatePeptideMatch(String oldKey,
String newKey,
PeptideMatch peptideMatch)
Updates a peptide match where the key was changed.
|
void |
updatePeptideMatchParameter(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(String key,
UrParameter urParameter)
Updates a protein match parameter in the database.
|
void |
updateRawAssumptions(String spectrumKey,
HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions)
Updates the raw assumptions of a spectrum.
|
void |
updateSpectrumMatch(SpectrumMatch spectrumMatch)
Updates a spectrum match in the database.
|
void |
updateSpectrumMatchParameter(String key,
UrParameter urParameter)
Updates a spectrum match parameter in the database.
|
addUrParam, getParameterKey, getUrParam
protected HashSet<String> proteinIdentification
protected HashSet<String> peptideIdentification
protected HashMap<String,HashSet<String>> spectrumIdentificationMap
protected HashMap<String,HashSet<String>> proteinMap
protected int methodUsed
protected String dbDirectory
protected String reference
public ArrayList<String> getOrderedSpectrumFileNames()
public void setOrderedListOfSpectrumFileNames(ArrayList<String> orderedSpectrumFileNames) throws IllegalArgumentException
orderedSpectrumFileNames
- the ordered list of spectrum file namesIllegalArgumentException
- thrown if the length of the ordered file
names as to be the same as the number of spectrum filespublic ArrayList<String> getSpectrumFiles()
public int getSpectrumIdentificationSize()
public void loadAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
fileName
- the file namewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKeys
- the spectrum keyswaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadRawAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
fileName
- the file namewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadSpectrumMatches(String fileName, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
fileName
- the file namewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKeys
- the spectrum keyswaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
fileName
- the file nameurParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKeys
- the key of the spectrum match of the parameters to be
loadedurParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
peptideKeys
- the list of peptide keys to loadwaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadPeptideMatches(WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
waitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
urParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadPeptideMatchParameters(ArrayList<String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
peptideKeys
- the list of peptide keys of the parameters to loadurParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadProteinMatches(WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
waitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
proteinKeys
- the list of protein keys to loadwaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
urParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void loadProteinMatchParameters(ArrayList<String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) throws SQLException, IOException, ClassNotFoundException, InterruptedException
proteinKeys
- the list of protein keys of the parameters to loadurParameter
- the parameter typewaitingHandler
- the waiting handler allowing displaying progress
and cancelling the processdisplayProgress
- boolean indicating whether the progress of this
method should be displayed on the waiting handlerSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getSpectrumMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the PSM keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getSpectrumMatchParameter(String key, UrParameter urParameter, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the PSM keyurParameter
- the match parameteruseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addSpectrumMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, InterruptedException
key
- the PSM keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getPeptideMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the peptide keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getPeptideMatchParameter(String key, UrParameter urParameter, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the peptide keyurParameter
- the match parameteruseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addPeptideMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, InterruptedException
key
- the peptide keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getProteinMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the protein keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic UrParameter getProteinMatchParameter(String key, UrParameter urParameter, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
key
- the protein keyurParameter
- the match parameteruseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addProteinMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException, InterruptedException
key
- the protein keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void updateSpectrumMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the spectrum keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updatePeptideMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the peptide keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updateProteinMatchParameter(String key, UrParameter urParameter) throws SQLException, IOException
key
- the protein keyurParameter
- the match parameterSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updateAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions) throws SQLException, IOException
spectrumKey
- the key of the spectrumassumptions
- the assumptionsSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updateRawAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> assumptions) throws SQLException, IOException
spectrumKey
- the key of the spectrumassumptions
- the assumptionsSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updateSpectrumMatch(SpectrumMatch spectrumMatch) throws SQLException, IOException
spectrumMatch
- the matchSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updatePeptideMatch(PeptideMatch peptideMatch) throws SQLException, IOException
peptideMatch
- the matchSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic void updatePeptideMatch(String oldKey, String newKey, PeptideMatch peptideMatch) throws SQLException, IOException, InterruptedException, ClassNotFoundException
oldKey
- the old peptide keynewKey
- the new peptide keypeptideMatch
- the new peptide matchSQLException
- exception thrown whenever an SQL error occurred
while interacting with the databaseIOException
- exception thrown whenever an IO issue occurred while
interacting with the databaseInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databaseClassNotFoundException
- exception thrown whenever a
casting issue occurred while interacting with the databasepublic void updateProteinMatch(ProteinMatch proteinMatch) throws SQLException, IOException
proteinMatch
- the matchSQLException
- exception thrown whenever an error occurred while
adding the object in the databaseIOException
- exception thrown whenever an error occurred while
writing the objectpublic String getDatabaseDirectory()
public void removeAssumptions(String matchKey) throws SQLException, IOException
matchKey
- the key of the spectrumSQLException
- exception thrown whenever an error occurred while
deleting the matchIOException
- exception thrown whenever an IO issue occurred while
interacting with the databasepublic void removeRawAssumptions(String matchKey) throws SQLException, IOException
matchKey
- the key of the spectrumSQLException
- exception thrown whenever an error occurred while
deleting the matchIOException
- exception thrown whenever an IO issue occurred while
interacting with the databasepublic void removeSpectrumMatch(String matchKey) throws SQLException, IOException
matchKey
- the key of the match to removeSQLException
- exception thrown whenever an error occurred while
deleting the matchIOException
- exception thrown whenever an IO issue occurred while
interacting with the databasepublic void removePeptideMatch(String matchKey) throws SQLException, IOException
matchKey
- the key of the match to removeSQLException
- exception thrown whenever an error occurred while
deleting the matchIOException
- exception thrown whenever an IO issue occurred while
interacting with the databasepublic void removeProteinMatch(String matchKey) throws SQLException, IOException
matchKey
- the key of the match to removeSQLException
- exception thrown whenever an error occurred while
deleting the matchIOException
- exception thrown whenever an IO issue occurred while
interacting with the databasepublic boolean matchExists(String matchKey)
matchKey
- the key of the match looked forpublic HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getAssumptions(String spectrumKey, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumuseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getAssumptions(String spectrumKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getRawAssumptions(String spectrumKey, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumuseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> getRawAssumptions(String spectrumKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic SpectrumMatch getSpectrumMatch(String spectrumKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the matchSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic SpectrumMatch getSpectrumMatch(String spectrumKey, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the matchuseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic PeptideMatch getPeptideMatch(String peptideKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
peptideKey
- the key of the matchSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic PeptideMatch getPeptideMatch(String peptideKey, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
peptideKey
- the key of the matchuseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic ProteinMatch getProteinMatch(String proteinKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
proteinKey
- the key of the matchSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic ProteinMatch getProteinMatch(String proteinKey, boolean useDB) throws SQLException, IOException, ClassNotFoundException, InterruptedException
proteinKey
- the key of the matchuseDB
- if useDB is false, null will be returned if the object is
not in the cacheSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic boolean proteinDetailsInCache(String proteinKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
proteinKey
- the key of the protein matchSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic boolean peptideDetailsInCache(String peptideKey) throws SQLException, IOException, ClassNotFoundException, InterruptedException
peptideKey
- the peptide keySQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic HashSet<String> getProteinIdentification()
public HashSet<String> getPeptideIdentification()
public HashSet<String> getSpectrumIdentification(String spectrumFile)
spectrumFile
- the name of the spectrum filepublic HashMap<String,HashSet<String>> getSpectrumIdentificationMap()
public void addAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions, boolean overwriteExisting, boolean newSpectrum) throws IOException, SQLException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumnewAssumptions
- the assumptions to add to the mappingoverwriteExisting
- if true any existing assumption will be
overwrittennewSpectrum
- if this is the first time this spectrum is seenSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions, boolean newSpectrum) throws IOException, SQLException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumnewAssumptions
- the assumptions to add to the mappingnewSpectrum
- if this is the first time this spectrum is seenSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addRawAssumptions(String spectrumKey, HashMap<Integer,HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>> newAssumptions) throws IOException, SQLException, ClassNotFoundException, InterruptedException
spectrumKey
- the key of the spectrumnewAssumptions
- the assumptions to add to the mappingSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addSpectrumMatch(SpectrumMatch newMatch) throws IOException, SQLException, ClassNotFoundException, InterruptedException
newMatch
- the new matchSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void buildPeptidesAndProteins(WaitingHandler waitingHandler, SequenceMatchingPreferences sequenceMatchingPreferences) throws SQLException, IOException, ClassNotFoundException, InterruptedException
waitingHandler
- the waiting handler displaying the progress. Can be
null. The progress will be displayed as secondary.sequenceMatchingPreferences
- the sequence matching preferencesSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void buildPeptidesAndProteins(String spectrumMatchKey, SequenceMatchingPreferences sequenceMatchingPreferences) throws SQLException, IOException, ClassNotFoundException, InterruptedException
spectrumMatchKey
- The key of the spectrum match to addsequenceMatchingPreferences
- the sequence matching preferencesSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic void addSpectrumMatches(Iterable<SpectrumMatch> spectrumMatches) throws IOException, SQLException, ClassNotFoundException, InterruptedException
spectrumMatches
- the spectrum matchesSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic int getMethodUsed()
public HashMap<String,HashSet<String>> getProteinMap()
public void close() throws SQLException
SQLException
- exception thrown whenever an error occurred while
closing the database connectionpublic IdentificationMatch.MatchType getMatchType(String matchKey)
matchKey
- the match keypublic void establishConnection(String dbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache) throws SQLException, IOException, ClassNotFoundException, InterruptedException
dbFolder
- the absolute path to the folder where the database is
locateddeleteOldDatabase
- if true, tries to delete the old databaseobjectsCache
- the objects cacheSQLException
- exception thrown whenever an error occurred while
establishing the connection, typically when another software already has
a connection openIOException
- exception thrown whenever an error occurs while
reading or writing a fileClassNotFoundException
- exception thrown whenever an error
occurred while deserializing a file from the databaseInterruptedException
- exception thrown if a threading error occurs
while interacting with the databasepublic void restoreConnection(String dbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache) throws SQLException, IOException, ClassNotFoundException, InterruptedException
dbFolder
- the folder where the database is locateddeleteOldDatabase
- if true, tries to delete the old databaseobjectsCache
- the objects cacheSQLException
- exception thrown whenever an error occurred while
establishing the connection, typically when another software already has
a connection openIOException
- exception thrown whenever an error occurs while
reading or writing a fileClassNotFoundException
- exception thrown whenever an error
occurred while deserializing a file from the databaseInterruptedException
- exception thrown if a threading error occurs
while interacting with the databasepublic boolean isConnectionActive()
public static String getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)
experimentReference
- the experiment referencesampleReference
- the sample referencereplicateNumber
- the replicate numberpublic HashSet<String> getProteinMatches(Peptide peptide) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the peptide of interestSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic boolean isUniqueInDatabase(Peptide peptide) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the peptide of interestSQLException
- exception thrown whenever an error occurred while
loading the object from the databaseIOException
- exception thrown whenever an error occurred while
reading the object in the databaseClassNotFoundException
- exception thrown whenever an error
occurred while casting the database input in the desired match classInterruptedException
- thrown whenever a threading issue occurred
while interacting with the databasepublic PsmIterator getPsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler)
spectrumFile
- the file to iteratespectrumKeys
- specific keys to iteratepsmParameters
- the parameters to load along with the matchesloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PsmIterator getPsmIterator(String spectrumFile, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler)
spectrumFile
- the file to iteratepsmParameters
- the parameters to load along with the matchesloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PsmIterator getPsmIterator(String spectrumFile, boolean loadAssumptions, WaitingHandler waitingHandler)
spectrumFile
- the file to iterateloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PsmIterator getPsmIterator(ArrayList<String> spectrumKeys, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler)
spectrumKeys
- specific keys to iteratepsmParameters
- the parameters to load along with the matchesloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PsmIterator getPsmIterator(ArrayList<String> spectrumKeys, boolean loadAssumptions, WaitingHandler waitingHandler)
spectrumKeys
- specific keys to iterateloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PsmIterator getPsmIterator(boolean loadAssumptions, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler)
psmParameters
- the parameters to load along with the matchesloadAssumptions
- if true the assumptions will be loaded as wellwaitingHandler
- the waiting handlerpublic PeptideMatchesIterator getPeptideMatchesIterator(ArrayList<String> peptideKeys, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler)
peptideKeys
- the keys of the peptides to iteratepeptideParameters
- the peptide parameters to load along with the
matchesloadPsms
- if true PSMs of the peptides will be loaded as wellpsmParameters
- the PSM parameters to load along with the PSMswaitingHandler
- the waiting handlerpublic PeptideMatchesIterator getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler)
peptideParameters
- the peptide parameters to load along with the
matchesloadPsms
- if true PSMs of the peptides will be loaded as wellpsmParameters
- the PSM parameters to load along with the PSMswaitingHandler
- the waiting handlerpublic ProteinMatchesIterator getProteinMatchesIterator(ArrayList<String> proteinKeys, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler)
proteinKeys
- the keys of the proteins to iterateproteinParameters
- the protein parameters to load along with the
matchesloadPeptides
- if true the peptides corresponding to these proteins
will be batch loaded along with the proteinspeptideParameters
- the parameters to load along with the peptide
matchesloadPsms
- if true the PSMs of the peptides will be batch loaded
along with the matchespsmParameters
- the parameters to load along with the matcheswaitingHandler
- the waiting handlerpublic ProteinMatchesIterator getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler)
proteinParameters
- the protein parameters to load along with the
matchesloadPeptides
- if true the peptides corresponding to these proteins
will be batch loaded along with the proteinspeptideParameters
- the parameters to load along with the peptide
matchesloadPsms
- if true the PSMs of the peptides will be batch loaded
along with the matchespsmParameters
- the parameters to load along with the matcheswaitingHandler
- the waiting handlerpublic IdentificationDB getIdentificationDB()
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