com.compomics.util.preferences

Class PsmScoringPreferences

java.lang.Object

com.compomics.util.preferences.PsmScoringPreferences

All Implemented Interfaces:

Serializable

public class PsmScoringPreferences
extends Object
implements Serializable

Generic class for peptide spectrum match scoring.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PsmScoringPreferences()

Method Summary

Modifier and Type	Method and Description
void	addScore(Integer advocateId, Integer scoreId) Adds a score for a given algorithm to the scoring preferences.
boolean	equals(PsmScoringPreferences otherPsmScoringPreferences) Returns true if the objects have identical settings.
HashSet<Integer>	getScoreForAlgorithm(Integer advocateId) Returns the scores set for a given algorithm.
String	getShortDescription() Returns a short description of the parameters.
boolean	isScoringNeeded(ArrayList<Integer> advocates) Indicates whether a score computation is needed for the given advocates.
boolean	isScoringNeeded(int advocate) Indicates whether a score computation is needed for the given advocate.
boolean	isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates) Indicates whether target decoy databases are needed for PSM scoring.

Methods inherited from class java.lang.Object

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

Constructor Detail

PsmScoringPreferences

public PsmScoringPreferences()

Method Detail

addScore

public void addScore(Integer advocateId,
                     Integer scoreId)

Adds a score for a given algorithm to the scoring preferences.

Parameters:

advocateId - the index of the algorithm

scoreId - the index of the score

getScoreForAlgorithm

public HashSet<Integer> getScoreForAlgorithm(Integer advocateId)

Returns the scores set for a given algorithm.

Parameters:

advocateId - the index of the algorithm

Returns:

the index of the score

isScoringNeeded

public boolean isScoringNeeded(int advocate)

Indicates whether a score computation is needed for the given advocate.

Parameters:

advocate - the index of the advocate of interest

Returns:

a boolean indicating whether a score computation is needed

isScoringNeeded

public boolean isScoringNeeded(ArrayList<Integer> advocates)

Indicates whether a score computation is needed for the given advocates.

Parameters:

advocates - the advocates of interest

Returns:

a boolean indicating whether a score computation is needed

isTargetDecoyNeededForPsmScoring

public boolean isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)

Indicates whether target decoy databases are needed for PSM scoring.

Parameters:

advocates - the advocates of interest

Returns:

a boolean indicating whether a score computation is needed

getShortDescription

public String getShortDescription()

Returns a short description of the parameters.

Returns:

a short description of the parameters

equals

public boolean equals(PsmScoringPreferences otherPsmScoringPreferences)

Returns true if the objects have identical settings.

Parameters:

otherPsmScoringPreferences - the PsmScoringPreferences to compare to

Returns:

true if the objects have identical settings