eu.isas.peptideshaker.scoring.maps

Class InputMap

java.lang.Object

eu.isas.peptideshaker.scoring.maps.InputMap

All Implemented Interfaces:

Serializable

public class InputMap
extends Object
implements Serializable

This class contains basic information about the hits as imported from the various search engine result files.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
InputMap() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addAdvocateContribution(int advocateId, String fileName, boolean unique) Adds an advocate contribution.
void	addEntry(int searchEngine, String spectrumFileName, double eValue, boolean isDecoy) Adds an entry to the input map.
void	addPeptideShakerHit(String fileName, boolean unique) Adds a PeptideShaker hit for the given file.
void	estimateProbabilities(com.compomics.util.waiting.WaitingHandler waitingHandler) Estimates the posterior error probability for each search engine.
int	getAdvocateContribution(int advocateId) Returns the contribution of validated hits of the given advocate for the entire dataset.
int	getAdvocateContribution(int advocateId, String fileName) Returns the contribution of validated hits of the given advocate for the given file.
int	getAdvocateUniqueContribution(int advocateId) Returns the contribution of unique validated hits of the given advocate for the entire dataset.
int	getAdvocateUniqueContribution(int advocateId, String fileName) Returns the contribution of unique validated hits of the given advocate for the given file.
Set<Integer>	getInputAlgorithms() Returns a set containing the indexes of the algorithms scored in this input map.
TreeSet<Integer>	getInputAlgorithmsSorted() Returns the indexes of the algorithms scored in this input map.
Set<Integer>	getIntermediateScoreInputAlgorithms(String fileName) Returns the algorithms having an intermediate score for the given spectrum file.
TargetDecoyMap	getIntermediateScoreMap(String fileName, int advocateIndex, int scoreIndex) Returns the target decoy map associated to a given spectrum file, advocate and score type.
TargetDecoyMap	getMap() Returns the first target/decoy map of the input map in case a single algorithm was used.
int	getNalgorithms() Returns the number of algorithms in the input map.
int	getNEntries() Returns the number of entries in the input map.
int	getNEntriesSpecific() Returns the number of entries in the specific input map.
int	getPeptideShakerHits() Returns the number of PeptideShaker validated hits for the entire dataset.
int	getPeptideShakerHits(String fileName) Returns the number of validated hits for the given file.
int	getPeptideShakerUniqueContribution() Returns the contribution of unique validated hits by PeptideShaker for the entire dataset.
int	getPeptideShakerUniqueContribution(String fileName) Returns the contribution of unique validated hits from PeptideShaker for the given file.
double	getProbability(int searchEngine, double eValue) returns the posterior error probability associated to the given e-value for the given search-engine (indexed by its utilities index)
TargetDecoyMap	getTargetDecoyMap(int algorithm) Returns the target decoy map attached to the given algorithm.
TargetDecoyMap	getTargetDecoyMap(int algorithm, String fileName) Returns the target decoy map attached to the given algorithm for a specific spectrum file.
ArrayList<TargetDecoyMap>	getTargetDecoyMaps() Returns a list of all target decoy maps contained in this mapping.
boolean	hasAdvocateContribution() Indicates whether the advocate contributions are present in this map.
boolean	isMultipleAlgorithms() Returns true for multiple search engines investigations.
void	resetAdvocateContributions() Resets the advocate contribution mappings.
void	resetAdvocateContributions(String fileName) Resets the advocate contribution mappings for the given file.
void	setIntermediateScore(String fileName, int advocateIndex, int scoreIndex, double score, boolean decoy, com.compomics.util.parameters.identification.advanced.PsmScoringParameters psmScoringPreferences) Adds an intermediate score for a given match.

Methods inherited from class java.lang.Object

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

Constructor Detail

InputMap

public InputMap()

Constructor.

Method Detail

isMultipleAlgorithms

public boolean isMultipleAlgorithms()

Returns true for multiple search engines investigations.

Returns:

true for multiple search engines investigations

getNalgorithms

public int getNalgorithms()

Returns the number of algorithms in the input map.

Returns:

the number of algorithms in the input map

getInputAlgorithms

public Set<Integer> getInputAlgorithms()

Returns a set containing the indexes of the algorithms scored in this input map.

Returns:

a set containing the indexes of the algorithms scored in this input map

getInputAlgorithmsSorted

public TreeSet<Integer> getInputAlgorithmsSorted()

Returns the indexes of the algorithms scored in this input map.

Returns:

a set containing the indexes of the algorithms scored in this input map

getIntermediateScoreInputAlgorithms

public Set<Integer> getIntermediateScoreInputAlgorithms(String fileName)

Returns the algorithms having an intermediate score for the given spectrum file.

Parameters:

fileName - the name of the spectrum file of interest

Returns:

the algorithm having an intermediate score for this file

getTargetDecoyMap

public TargetDecoyMap getTargetDecoyMap(int algorithm)

Returns the target decoy map attached to the given algorithm.

Parameters:

algorithm - the utilities index of the algorithm of interest

Returns:

the target decoy map of interest

getTargetDecoyMap

public TargetDecoyMap getTargetDecoyMap(int algorithm,
                                        String fileName)

Returns the target decoy map attached to the given algorithm for a specific spectrum file. Null if not found.

Parameters:

algorithm - the utilities index of the algorithm of interest

fileName - the name of the spectrum file of interest

Returns:

the target decoy map of interest

getMap

public TargetDecoyMap getMap()

Returns the first target/decoy map of the input map in case a single algorithm was used.

Returns:

the first target/decoy map of the input map

estimateProbabilities

public void estimateProbabilities(com.compomics.util.waiting.WaitingHandler waitingHandler)

Estimates the posterior error probability for each search engine.

Parameters:

waitingHandler - the handler displaying feedback to the user

getProbability

public double getProbability(int searchEngine,
                             double eValue)

returns the posterior error probability associated to the given e-value for the given search-engine (indexed by its utilities index)

Parameters:

searchEngine - The search engine

eValue - The e-value

Returns:

the posterior error probability corresponding

addEntry

public void addEntry(int searchEngine,
                     String spectrumFileName,
                     double eValue,
                     boolean isDecoy)

Adds an entry to the input map.

Parameters:

searchEngine - The search engine used referenced by its compomics index

spectrumFileName - the name of the inspected spectrum file

eValue - The search engine e-value

isDecoy - boolean indicating whether the hit was decoy

getNEntries

public int getNEntries()

Returns the number of entries in the input map.

Returns:

the number of entries

getNEntriesSpecific

public int getNEntriesSpecific()

Returns the number of entries in the specific input map.

Returns:

the number of entries

resetAdvocateContributions

public void resetAdvocateContributions(String fileName)

Resets the advocate contribution mappings for the given file.

Parameters:

fileName - the file of interest

resetAdvocateContributions

public void resetAdvocateContributions()

Resets the advocate contribution mappings.

addAdvocateContribution

public void addAdvocateContribution(int advocateId,
                                    String fileName,
                                    boolean unique)

Adds an advocate contribution.

Parameters:

advocateId - the index of the advocate

fileName - the name of the spectrum file of interest

unique - boolean indicating whether the advocate was the only advocate for the considered assumption

addPeptideShakerHit

public void addPeptideShakerHit(String fileName,
                                boolean unique)

Adds a PeptideShaker hit for the given file.

Parameters:

fileName - the name of the spectrum file of interest

unique - boolean indicating whether the advocate was the only advocate for the considered assumption

getAdvocateContribution

public int getAdvocateContribution(int advocateId,
                                   String fileName)

Returns the contribution of validated hits of the given advocate for the given file.

Parameters:

advocateId - the advocate index

fileName - the name of the spectrum file

Returns:

the number of validated hits supported by this advocate

getPeptideShakerHits

public int getPeptideShakerHits(String fileName)

Returns the number of validated hits for the given file.

Parameters:

fileName - the name of the spectrum file

Returns:

the number of validated hits supported by this advocate

getAdvocateContribution

public int getAdvocateContribution(int advocateId)

Returns the contribution of validated hits of the given advocate for the entire dataset.

Parameters:

advocateId - the advocate index

Returns:

the number of validated hits supported by this advocate

getPeptideShakerHits

public int getPeptideShakerHits()

Returns the number of PeptideShaker validated hits for the entire dataset.

Returns:

the number of validated hits supported by this advocate

getAdvocateUniqueContribution

public int getAdvocateUniqueContribution(int advocateId,
                                         String fileName)

Returns the contribution of unique validated hits of the given advocate for the given file.

Parameters:

advocateId - the advocate index

fileName - the name of the spectrum file

Returns:

the number of validated hits uniquely supported by this advocate

getPeptideShakerUniqueContribution

public int getPeptideShakerUniqueContribution(String fileName)

Returns the contribution of unique validated hits from PeptideShaker for the given file.

Parameters:

fileName - the name of the spectrum file

Returns:

the number of validated hits uniquely supported by PeptideShaker

getAdvocateUniqueContribution

public int getAdvocateUniqueContribution(int advocateId)

Returns the contribution of unique validated hits of the given advocate for the entire dataset.

Parameters:

advocateId - the advocate index

Returns:

the number of validated hits uniquely supported by this advocate

getPeptideShakerUniqueContribution

public int getPeptideShakerUniqueContribution()

Returns the contribution of unique validated hits by PeptideShaker for the entire dataset.

Returns:

the number of validated hits uniquely supported by this advocate

getTargetDecoyMaps

public ArrayList<TargetDecoyMap> getTargetDecoyMaps()

Returns a list of all target decoy maps contained in this mapping.

Returns:

all target decoy maps contained in this mapping

hasAdvocateContribution

public boolean hasAdvocateContribution()

Indicates whether the advocate contributions are present in this map.

Returns:

a boolean indicating whether the advocate contributions are present in this map

setIntermediateScore

public void setIntermediateScore(String fileName,
                                 int advocateIndex,
                                 int scoreIndex,
                                 double score,
                                 boolean decoy,
                                 com.compomics.util.parameters.identification.advanced.PsmScoringParameters psmScoringPreferences)

Adds an intermediate score for a given match.

Parameters:

fileName - the name of the spectrum file of interest

advocateIndex - the index of the advocate

scoreIndex - the index of the score

score - the score of the match

decoy - indicates whether the match maps to a target or a decoy protein

psmScoringPreferences - the psm scoring preferences

getIntermediateScoreMap

public TargetDecoyMap getIntermediateScoreMap(String fileName,
                                              int advocateIndex,
                                              int scoreIndex)

Returns the target decoy map associated to a given spectrum file, advocate and score type. Null if not found.

Parameters:

fileName - the name of the spectrum file

advocateIndex - the index of the advocate

scoreIndex - the index of the score

Returns:

the target decoy map associated to the given spectrum file, advocate and score type