Package com.compomics.util.experiment.identification.peptide_inference

Class PeptideInference

java.lang.Object

com.compomics.util.experiment.identification.peptide_inference.PeptideInference

public class PeptideInference
extends Object

Functions related to peptide inference.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field	Description
final int	CONFIDENT_OTHER_OFFSET	Localization score offset for modification that are confidently localized on another PSM with the same sequence.
final int	CONFIDENT_OWN_OFFSET	Localization score offset for modification that are confidently localized on the PSM investigated.
final int	CONFIDENT_RELATED_OFFSET	Localization score offset for modification that are confidently localized on another PSM with an overlapping sequence.

Constructor Summary

Constructors

Constructor	Description
PeptideInference()

Method Summary

Modifier and Type	Method	Description
void	peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)	Infers the PTM localization and its confidence for the best match of every spectrum.

Methods inherited from class java.lang.Object

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

Field Details

CONFIDENT_OWN_OFFSET

public final int CONFIDENT_OWN_OFFSET

Localization score offset for modification that are confidently localized on the PSM investigated.

See Also:

• Constant Field Values

CONFIDENT_OTHER_OFFSET

public final int CONFIDENT_OTHER_OFFSET

Localization score offset for modification that are confidently localized on another PSM with the same sequence.

See Also:

• Constant Field Values

CONFIDENT_RELATED_OFFSET

public final int CONFIDENT_RELATED_OFFSET

Localization score offset for modification that are confidently localized on another PSM with an overlapping sequence.

See Also:

• Constant Field Values

Constructor Details

PeptideInference

public PeptideInference()

Method Details

peptideInference

public void peptideInference(Identification identification,
 IdentificationParameters identificationParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider,
 WaitingHandler waitingHandler)

Infers the PTM localization and its confidence for the best match of every spectrum.

Parameters:

identification - The identification object containing the matches.

identificationParameters - The identification parameters of the project.

sequenceProvider - The protein sequence provider to use.

modificationProvider - The modification provider to use.

waitingHandler - The waiting handler displaying progress to the user.