Identification (computational omics utilities 3.28.20 API)

java.lang.Object
- com.compomics.util.experiment.personalization.ExperimentObject
- - com.compomics.util.experiment.identification.Identification

All Implemented Interfaces:

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

Constructor Summary

Constructors
Constructor and Description

Identification()

Constructors
Constructor and Description
`Identification()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addMatchParameter(String key, UrParameter urParameter)` Deprecated. use the database match specific methods instead
`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`	`addSpectrumMatch(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(String key, UrParameter urParameter)` Adds a spectrum match parameter to the database.
`void`	`buildPeptidesAndProteins(String spectrumMatchKey, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Creates the peptides and protein instances based on the given spectrum match.
`void`	`buildPeptidesAndProteins(WaitingHandler waitingHandler, AminoAcidPattern.MatchingType matchingType, Double massTolerance)` Creates the peptides and protein instances based on the spectrum matches.
`void`	`close()` Closes the database connection.
`void`	`convert(WaitingHandler waitingHandler, String newDirectory, String newName, ObjectsCache objectsCache, File directory)` Converts a serialization based structure into a database based one.
`void`	`establishConnection(String dbFolder, boolean deleteOldDatabase, ObjectsCache objectsCache)` Establishes a connection to the database.
`static String`	`getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)` Returns the default reference for an identification.
`String`	`getFileName(String key)` Deprecated. use the database methods instead
`UrParameter`	`getMatchParameter(String matchKey, UrParameter urParameter)` Deprecated. use the database match specific methods instead
`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.
`ArrayList<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.
`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.
`ArrayList<String>`	`getProteinIdentification()` Returns a list of the keys of all encountered proteins.
`HashMap<String,ArrayList<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.
`ArrayList<String>`	`getProteinMatches(Peptide peptide)` Returns the keys of the protein matches where a peptide can be found.
`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.
`String`	`getSerializationDirectory()` Returns the serialization directory.
`ArrayList<String>`	`getSpectrumFiles()` Returns the names of the mgf files used in the spectrum identification map as a list.
`ArrayList<String>`	`getSpectrumIdentification()` Deprecated. use file specific names instead
`ArrayList<String>`	`getSpectrumIdentification(String spectrumFile)` Returns the keys of the spectrum identifications for a given spectrum file name.
`HashMap<String,ArrayList<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`	`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(ArrayList<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(ArrayList<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(ArrayList<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(ArrayList<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(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler)` Loads the given spectrum matches in the cache of the database.
`void`	`loadSpectrumMatches(String fileName, WaitingHandler waitingHandler)` Loads all spectrum matches of the file in the cache of the database.
`void`	`loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler)` Loads all desired spectrum match parameters in the cache of the database.
`void`	`loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler)` 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`	`removeMatch(String matchKey)` Deprecated. it is advised to use the specific psm/peptide/protein method instead
`void`	`removePeptideMatch(String matchKey)` Removes a peptide match from the model.
`void`	`removeProteinMatch(String matchKey)` Removes a protein match from the model.
`void`	`removeSpectrumMatch(String matchKey)` Removes a spectrum match from the model.
`void`	`setDirectory(String serializationDirectory, boolean deleteOldDatabase)` Deprecated. use establishConnection(String dbFolder) instead
`void`	`setIsDB(Boolean isDB)` Sets whether the identification matches should be stored in a database or serialized files.
`void`	`setOrderedListOfSpectrumFileNames(ArrayList<String> orderedSpectrumFileNames)` Set the ordered list of spectrum file names.
`void`	`updatePeptideMatch(PeptideMatch peptideMatch)` Updates a peptide match in the database.
`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`	`updateSpectrumMapping()` Converts the old spectrum keys structure into the mapped version.
`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.

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 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 ArrayList<String> proteinIdentification
```
    List of the keys of all imported proteins.
  - peptideIdentification
```
protected ArrayList<String> peptideIdentification
```
    List of the keys of all imported peptides.
  - spectrumIdentificationMap
```
protected HashMap<String,ArrayList<String>> spectrumIdentificationMap
```
    List of all imported PSMs indexed by mgf file name.
  - spectrumIdentification
```
protected ArrayList<String> spectrumIdentification
```
    Deprecated. use file specific mapping instead
    
    List of the keys of all imported PSMs.
  - proteinMap
```
protected HashMap<String,ArrayList<String>> proteinMap
```
    A map linking protein accessions to all their protein matches keys.
  - methodUsed
```
protected int methodUsed
```
    The method used.
  - serializationDirectory
```
protected String serializationDirectory
```
    The directory where matches will be serialized/the database stored.
  - urParameters
```
protected HashMap<String,HashMap<String,UrParameter>> urParameters
```
    Deprecated. use the database instead
    
    Map of the user's parameters.
  - longKeys
```
protected ArrayList<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 String reference
```
    The reference of the identification.
- Constructor Detail
  - Identification
```
public Identification()
```
- Method Detail
  - getOrderedSpectrumFileNames
```
public ArrayList<String> getOrderedSpectrumFileNames()
```
    Returns the ordered list of spectrum file names.
    
    Returns:
    the ordered list of spectrum file names
  - setOrderedListOfSpectrumFileNames
```
public void setOrderedListOfSpectrumFileNames(ArrayList<String> orderedSpectrumFileNames)
                                       throws 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:
    
    IllegalArgumentException - thrown if the length of the ordered file names as to be the same as the number of spectrum files
  - getSpectrumFiles
```
public ArrayList<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(String key,
                     UrParameter urParameter)
                       throws SQLException,
                              IOException,
                              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:
    
    InterruptedException
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - getMatchParameter
```
public UrParameter getMatchParameter(String matchKey,
                            UrParameter urParameter)
                              throws SQLException,
                                     IOException,
                                     ClassNotFoundException,
                                     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:
    
    InterruptedException
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
  - loadSpectrumMatchParameters
```
public void loadSpectrumMatchParameters(String fileName,
                               UrParameter urParameter,
                               WaitingHandler waitingHandler)
                                 throws SQLException,
                                        IOException,
                                        ClassNotFoundException,
                                        InterruptedException
```
    Loads all spectrum match parameters of the given type in the cache of the database
    
    Parameters:
    fileName - the file name
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadSpectrumMatchParameters
```
public void loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
                               UrParameter urParameter,
                               WaitingHandler waitingHandler)
                                 throws SQLException,
                                        IOException,
                                        ClassNotFoundException,
                                        InterruptedException
```
    Loads all desired spectrum match parameters in the cache of the database.
    
    Parameters:
    spectrumKeys - the key of the spectrum match of the parameters to be loaded
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadPeptideMatchParameters
```
public void loadPeptideMatchParameters(UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException
```
    Loads all peptide match parameters of the given type in the cache of the database.
    
    Parameters:
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadPeptideMatchParameters
```
public void loadPeptideMatchParameters(ArrayList<String> peptideKeys,
                              UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException
```
    Loads the desired peptide match parameters of the given type in the cache of the database.
    
    Parameters:
    peptideKeys - the list of peptide keys of the parameters to load
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadPeptideMatches
```
public void loadPeptideMatches(ArrayList<String> peptideKeys,
                      WaitingHandler waitingHandler)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException
```
    Loads the desired peptide matches of the given type in the cache of the database.
    
    Parameters:
    peptideKeys - the list of peptide keys to load
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadProteinMatchParameters
```
public void loadProteinMatchParameters(UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException
```
    Loads all protein match parameters of the given type in the cache of the database.
    
    Parameters:
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadProteinMatchParameters
```
public void loadProteinMatchParameters(ArrayList<String> proteinKeys,
                              UrParameter urParameter,
                              WaitingHandler waitingHandler)
                                throws SQLException,
                                       IOException,
                                       ClassNotFoundException,
                                       InterruptedException
```
    Loads the desired protein match parameters of the given type in the cache of the database.
    
    Parameters:
    proteinKeys - the list of protein keys of the parameters to load
    urParameter - the parameter type
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadProteinMatches
```
public void loadProteinMatches(WaitingHandler waitingHandler)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException
```
    Loads all protein matches in the cache of the database.
    
    Parameters:
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadProteinMatches
```
public void loadProteinMatches(ArrayList<String> proteinKeys,
                      WaitingHandler waitingHandler)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               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:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadPeptideMatches
```
public void loadPeptideMatches(WaitingHandler waitingHandler)
                        throws SQLException,
                               IOException,
                               ClassNotFoundException,
                               InterruptedException
```
    Loads all peptide matches in the cache of the database.
    
    Parameters:
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadSpectrumMatches
```
public void loadSpectrumMatches(String fileName,
                       WaitingHandler waitingHandler)
                         throws SQLException,
                                IOException,
                                ClassNotFoundException,
                                InterruptedException
```
    Loads all spectrum matches of the file in the cache of the database.
    
    Parameters:
    fileName - the file name
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - loadSpectrumMatches
```
public void loadSpectrumMatches(ArrayList<String> spectrumKeys,
                       WaitingHandler waitingHandler)
                         throws SQLException,
                                IOException,
                                ClassNotFoundException,
                                InterruptedException
```
    Loads the given spectrum matches in the cache of the database.
    
    Parameters:
    spectrumKeys - the spectrum keys
    waitingHandler - the waiting handler
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while interrogating the database
    
    IOException - exception thrown whenever an error occurred while reading the database
    
    ClassNotFoundException - exception thrown whenever the class of the object is not found when deserializing it.
    
    InterruptedException
  - getSpectrumMatchParameter
```
public UrParameter getSpectrumMatchParameter(String key,
                                    UrParameter urParameter)
                                      throws SQLException,
                                             IOException,
                                             ClassNotFoundException,
                                             InterruptedException
```
    Returns the desired spectrum match parameter.
    
    Parameters:
    key - the PSM key
    urParameter - the match parameter
    
    Returns:
    the spectrum match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getSpectrumMatchParameter
```
public UrParameter getSpectrumMatchParameter(String key,
                                    UrParameter urParameter,
                                    boolean useDB)
                                      throws SQLException,
                                             IOException,
                                             ClassNotFoundException,
                                             InterruptedException
```
    Returns the desired spectrum match parameter.
    
    Parameters:
    key - the PSM key
    urParameter - the match parameter
    useDB - if useDB is false, null will be returned if the object is not in the cache
    
    Returns:
    the spectrum match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - addSpectrumMatchParameter
```
public void addSpectrumMatchParameter(String key,
                             UrParameter urParameter)
                               throws SQLException,
                                      IOException,
                                      InterruptedException
```
    Adds a spectrum match parameter to the database.
    
    Parameters:
    key - the PSM key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
    
    InterruptedException
  - getPeptideMatchParameter
```
public UrParameter getPeptideMatchParameter(String key,
                                   UrParameter urParameter)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException
```
    Returns the desired peptide match parameter.
    
    Parameters:
    key - the peptide key
    urParameter - the match parameter
    
    Returns:
    the peptide match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getPeptideMatchParameter
```
public UrParameter getPeptideMatchParameter(String key,
                                   UrParameter urParameter,
                                   boolean useDB)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException
```
    Returns the desired peptide match parameter.
    
    Parameters:
    key - the peptide key
    urParameter - the match parameter
    useDB - if useDB is false, null will be returned if the object is not in the cache
    
    Returns:
    the peptide match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - addPeptideMatchParameter
```
public void addPeptideMatchParameter(String key,
                            UrParameter urParameter)
                              throws SQLException,
                                     IOException,
                                     InterruptedException
```
    Adds a peptide match parameter to the database.
    
    Parameters:
    key - the peptide key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
    
    InterruptedException
  - getProteinMatchParameter
```
public UrParameter getProteinMatchParameter(String key,
                                   UrParameter urParameter)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException
```
    Returns the desired protein match parameter.
    
    Parameters:
    key - the protein key
    urParameter - the match parameter
    
    Returns:
    the protein match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getProteinMatchParameter
```
public UrParameter getProteinMatchParameter(String key,
                                   UrParameter urParameter,
                                   boolean useDB)
                                     throws SQLException,
                                            IOException,
                                            ClassNotFoundException,
                                            InterruptedException
```
    Returns the desired protein match parameter.
    
    Parameters:
    key - the protein key
    urParameter - the match parameter
    useDB - if useDB is false, null will be returned if the object is not in the cache
    
    Returns:
    the protein match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - addProteinMatchParameter
```
public void addProteinMatchParameter(String key,
                            UrParameter urParameter)
                              throws SQLException,
                                     IOException,
                                     InterruptedException
```
    Adds a protein match parameter to the database.
    
    Parameters:
    key - the protein key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
    
    InterruptedException
  - updateProteinMatchParameter
```
public void updateProteinMatchParameter(String key,
                               UrParameter urParameter)
                                 throws SQLException,
                                        IOException
```
    Updates a protein match parameter in the database.
    
    Parameters:
    key - the protein key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - updatePeptideMatchParameter
```
public void updatePeptideMatchParameter(String key,
                               UrParameter urParameter)
                                 throws SQLException,
                                        IOException
```
    Updates a peptide match parameter in the database.
    
    Parameters:
    key - the peptide key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - updateSpectrumMatchParameter
```
public void updateSpectrumMatchParameter(String key,
                                UrParameter urParameter)
                                  throws SQLException,
                                         IOException
```
    Updates a spectrum match parameter in the database.
    
    Parameters:
    key - the spectrum key
    urParameter - the match parameter
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - updateSpectrumMatch
```
public void updateSpectrumMatch(SpectrumMatch spectrumMatch)
                         throws SQLException,
                                IOException
```
    Updates a spectrum match in the database.
    
    Parameters:
    spectrumMatch - the match
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - updatePeptideMatch
```
public void updatePeptideMatch(PeptideMatch peptideMatch)
                        throws SQLException,
                               IOException
```
    Updates a peptide match in the database.
    
    Parameters:
    peptideMatch - the match
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - updateProteinMatch
```
public void updateProteinMatch(ProteinMatch proteinMatch)
                        throws SQLException,
                               IOException
```
    Updates a protein match in the database.
    
    Parameters:
    proteinMatch - the match
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while adding the object in the database
    
    IOException - exception thrown whenever an error occurred while writing the object
  - getSerializationDirectory
```
public String getSerializationDirectory()
```
    Returns the serialization directory.
    
    Returns:
    the serialization directory
  - setDirectory
```
public void setDirectory(String serializationDirectory,
                boolean deleteOldDatabase)
                  throws 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:
    
    SQLException
  - removeMatch
```
public void removeMatch(String matchKey)
                 throws IllegalArgumentException,
                        SQLException,
                        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:
    
    IllegalArgumentException
    
    SQLException - exception thrown whenever an error occurred while deleting the match
    
    IOException
  - removeSpectrumMatch
```
public void removeSpectrumMatch(String matchKey)
                         throws IllegalArgumentException,
                                SQLException,
                                IOException
```
    Removes a spectrum match from the model.
    
    Parameters:
    matchKey - the key of the match to remove
    
    Throws:
    
    IllegalArgumentException
    
    SQLException - exception thrown whenever an error occurred while deleting the match
    
    IOException
  - removePeptideMatch
```
public void removePeptideMatch(String matchKey)
                        throws IllegalArgumentException,
                               SQLException,
                               IOException
```
    Removes a peptide match from the model.
    
    Parameters:
    matchKey - the key of the match to remove
    
    Throws:
    
    IllegalArgumentException
    
    SQLException - exception thrown whenever an error occurred while deleting the match
    
    IOException
  - removeProteinMatch
```
public void removeProteinMatch(String matchKey)
                        throws IllegalArgumentException,
                               SQLException,
                               IOException
```
    Removes a protein match from the model.
    
    Parameters:
    matchKey - the key of the match to remove
    
    Throws:
    
    IllegalArgumentException
    
    SQLException - exception thrown whenever an error occurred while deleting the match
    
    IOException
  - matchExists
```
public boolean matchExists(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(String spectrumKey)
                               throws IllegalArgumentException,
                                      SQLException,
                                      IOException,
                                      ClassNotFoundException,
                                      InterruptedException
```
    Returns a spectrum match.
    
    Parameters:
    spectrumKey - the key of the match
    
    Returns:
    the desired match
    
    Throws:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getSpectrumMatch
```
public SpectrumMatch getSpectrumMatch(String spectrumKey,
                             boolean useDB)
                               throws IllegalArgumentException,
                                      SQLException,
                                      IOException,
                                      ClassNotFoundException,
                                      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:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getPeptideMatch
```
public PeptideMatch getPeptideMatch(String peptideKey)
                             throws IllegalArgumentException,
                                    SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    InterruptedException
```
    Returns a peptide match.
    
    Parameters:
    peptideKey - the key of the match
    
    Returns:
    the desired match
    
    Throws:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getPeptideMatch
```
public PeptideMatch getPeptideMatch(String peptideKey,
                           boolean useDB)
                             throws IllegalArgumentException,
                                    SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    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:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getProteinMatch
```
public ProteinMatch getProteinMatch(String proteinKey)
                             throws IllegalArgumentException,
                                    SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    InterruptedException
```
    Returns a protein match.
    
    Parameters:
    proteinKey - the key of the match
    
    Returns:
    the desired match
    
    Throws:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - getProteinMatch
```
public ProteinMatch getProteinMatch(String proteinKey,
                           boolean useDB)
                             throws IllegalArgumentException,
                                    SQLException,
                                    IOException,
                                    ClassNotFoundException,
                                    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:
    
    IllegalArgumentException - exception thrown whenever an error occurred while retrieving the match
    
    SQLException - exception thrown whenever an error occurred while loading the object from the database
    
    IOException - exception thrown whenever an error occurred while reading the object in the database
    
    ClassNotFoundException - exception thrown whenever an error occurred while casting the database input in the desired match class
    
    InterruptedException
  - proteinDetailsInCache
```
public boolean proteinDetailsInCache(String proteinKey)
                              throws IllegalArgumentException,
                                     SQLException,
                                     IOException,
                                     ClassNotFoundException,
                                     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:
    
    IllegalArgumentException
    
    SQLException
    
    IOException
    
    ClassNotFoundException
    
    InterruptedException
  - peptideDetailsInCache
```
public boolean peptideDetailsInCache(String peptideKey)
                              throws IllegalArgumentException,
                                     SQLException,
                                     IOException,
                                     ClassNotFoundException,
                                     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:
    
    IllegalArgumentException
    
    SQLException
    
    IOException
    
    ClassNotFoundException
    
    InterruptedException
  - getProteinIdentification
```
public ArrayList<String> getProteinIdentification()
```
    Returns a list of the keys of all encountered proteins.
    
    Returns:
    the corresponding identification results
  - getPeptideIdentification
```
public ArrayList<String> getPeptideIdentification()
```
    Returns a list of the keys of all encountered peptides.
    
    Returns:
    the corresponding identification results
  - getSpectrumIdentification
```
public ArrayList<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 ArrayList<String> getSpectrumIdentification(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 HashMap<String,ArrayList<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 FileNotFoundException,
                             IOException,
                             IllegalArgumentException,
                             SQLException,
                             ClassNotFoundException,
                             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:
    
    FileNotFoundException - exception thrown whenever an error occurred while saving the file
    
    IOException - exception thrown whenever an error occurred while saving the file
    
    IllegalArgumentException - exception thrown whenever an error occurred while saving the file
    
    SQLException - exception thrown whenever an error occurred while saving the file
    
    ClassNotFoundException - exception thrown whenever an error occurred while saving the file
    
    InterruptedException
  - buildPeptidesAndProteins
```
public void buildPeptidesAndProteins(WaitingHandler waitingHandler,
                            AminoAcidPattern.MatchingType matchingType,
                            Double massTolerance)
                              throws IllegalArgumentException,
                                     SQLException,
                                     IOException,
                                     ClassNotFoundException,
                                     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:
    
    IllegalArgumentException
    
    SQLException
    
    IOException
    
    ClassNotFoundException
    
    InterruptedException
  - buildPeptidesAndProteins
```
public void buildPeptidesAndProteins(String spectrumMatchKey,
                            AminoAcidPattern.MatchingType matchingType,
                            Double massTolerance)
                              throws IllegalArgumentException,
                                     SQLException,
                                     IOException,
                                     ClassNotFoundException,
                                     InterruptedException
```
    Creates the peptides and protein instances based on the given spectrum match. Note that only the best peptide assumption is used, the method has no effect if it is null. 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:
    
    IllegalArgumentException
    
    SQLException
    
    ClassNotFoundException
    
    IOException
    
    InterruptedException
  - addSpectrumMatch
```
public void addSpectrumMatch(Set<SpectrumMatch> spectrumMatches,
                    boolean ascendingScore)
                      throws FileNotFoundException,
                             IOException,
                             IllegalArgumentException,
                             SQLException,
                             ClassNotFoundException,
                             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:
    
    FileNotFoundException - exception thrown whenever an error occurred while saving the file
    
    IOException - exception thrown whenever an error occurred while saving the file
    
    IllegalArgumentException - exception thrown whenever an error occurred while saving the file
    
    SQLException - exception thrown whenever an error occurred while saving the file
    
    ClassNotFoundException - exception thrown whenever an error occurred while saving the file
    
    InterruptedException
  - getMethodUsed
```
public int getMethodUsed()
```
    Getter for the identification method used.
    
    Returns:
    the identification method used
  - getProteinMap
```
public HashMap<String,ArrayList<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 String getFileName(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 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(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 SQLException
```
    Closes the database connection.
    
    Throws:
    
    SQLException - exception thrown whenever an error occurred while closing the database connection
  - getMatchType
```
public IdentificationMatch.MatchType getMatchType(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(String dbFolder,
                       boolean deleteOldDatabase,
                       ObjectsCache objectsCache)
                         throws 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:
    
    SQLException - exception thrown whenever an error occurred while establishing the connection
  - convert
```
public void convert(WaitingHandler waitingHandler,
           String newDirectory,
           String newName,
           ObjectsCache objectsCache,
           File directory)
             throws FileNotFoundException,
                    IOException,
                    ClassNotFoundException,
                    SQLException,
                    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:
    
    FileNotFoundException - exception thrown whenever a file is not found
    
    IOException - exception thrown whenever an error occurred while reading/writing a file
    
    ClassNotFoundException - exception thrown whenever an error occurred while deserializing a match
    
    SQLException - exception thrown whenever an error occurred while interacting with the database
    
    InterruptedException
  - updateSpectrumMapping
```
public void updateSpectrumMapping()
```
    Converts the old spectrum keys structure into the mapped version.
  - getDefaultReference
```
public static String getDefaultReference(String experimentReference,
                         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 ArrayList<String> getProteinMatches(Peptide peptide)
                                    throws IOException,
                                           SQLException,
                                           ClassNotFoundException,
                                           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:
    
    IOException
    
    SQLException
    
    InterruptedException
    
    ClassNotFoundException
  - isUnique
```
public boolean isUnique(Peptide peptide)
                 throws IOException,
                        SQLException,
                        ClassNotFoundException,
                        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:
    
    IOException
    
    SQLException
    
    ClassNotFoundException
    
    InterruptedException

Class Identification

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

EXTENTION

proteinIdentification

peptideIdentification

spectrumIdentificationMap

spectrumIdentification

proteinMap

methodUsed

serializationDirectory

urParameters

longKeys

reference

Constructor Detail

Identification

Method Detail

getOrderedSpectrumFileNames

setOrderedListOfSpectrumFileNames

getSpectrumFiles

getSpectrumIdentificationSize

addMatchParameter

getMatchParameter

loadSpectrumMatchParameters

loadSpectrumMatchParameters

loadPeptideMatchParameters

loadPeptideMatchParameters

loadPeptideMatches

loadProteinMatchParameters

loadProteinMatchParameters

loadProteinMatches

loadProteinMatches

loadPeptideMatches

loadSpectrumMatches

loadSpectrumMatches

getSpectrumMatchParameter

getSpectrumMatchParameter

addSpectrumMatchParameter

getPeptideMatchParameter

getPeptideMatchParameter

addPeptideMatchParameter

getProteinMatchParameter

getProteinMatchParameter

addProteinMatchParameter

updateProteinMatchParameter

updatePeptideMatchParameter

updateSpectrumMatchParameter

updateSpectrumMatch

updatePeptideMatch

updateProteinMatch

getSerializationDirectory

setDirectory

removeMatch

removeSpectrumMatch

removePeptideMatch

removeProteinMatch

matchExists

getSpectrumMatch

getSpectrumMatch

getPeptideMatch

getPeptideMatch

getProteinMatch

getProteinMatch

proteinDetailsInCache

peptideDetailsInCache

getProteinIdentification

getPeptideIdentification

getSpectrumIdentification

getSpectrumIdentification

getSpectrumIdentificationMap

addSpectrumMatch

buildPeptidesAndProteins

buildPeptidesAndProteins

addSpectrumMatch

getMethodUsed

getProteinMap