Package eu.isas.peptideshaker.scoring

Class PSMaps

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

eu.isas.peptideshaker.scoring.PSMaps

All Implemented Interfaces:

com.compomics.util.experiment.personalization.UrParameter, Serializable

public class PSMaps
extends com.compomics.util.experiment.personalization.ExperimentObject
implements com.compomics.util.experiment.personalization.UrParameter

This class contains all scoring maps from PeptideShaker and will be used to store the information.

Author:

Marc Vaudel

See Also:

• Serialized Form

Field Summary

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

NO_KEY

Constructor Summary

Constructors

Constructor	Description
PSMaps()	Constructor.
PSMaps(InputMap inputMap, TargetDecoyMap psmMap, TargetDecoyMap peptideMap, TargetDecoyMap proteinMap)	Constructor for the PSMaps.

Method Summary

Modifier and Type	Method	Description
InputMap	getInputMap()	Returns the target decoy map of all search engine scores.
long	getParameterKey()
TargetDecoyMap	getPeptideMap()	Returns the target decoy map at the peptide level.
TargetDecoyMap	getProteinMap()	Returns the target decoy map at the protein level.
TargetDecoyMap	getPsmMap()	Returns the target decoy map at the psm level.

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

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Constructor Details

PSMaps

public PSMaps()

Constructor.

PSMaps

public PSMaps(InputMap inputMap,
 TargetDecoyMap psmMap,
 TargetDecoyMap peptideMap,
 TargetDecoyMap proteinMap)

Constructor for the PSMaps.

Parameters:

inputMap - the input map

psmMap - the PSM level map

peptideMap - the peptide level map

proteinMap - the protein level map

Method Details

getInputMap

public InputMap getInputMap()

Returns the target decoy map of all search engine scores.

Returns:

the target decoy map of all search engine scores

getPsmMap

public TargetDecoyMap getPsmMap()

Returns the target decoy map at the psm level.

Returns:

the target decoy map at the psm level

getPeptideMap

public TargetDecoyMap getPeptideMap()

Returns the target decoy map at the peptide level.

Returns:

the target decoy map at the peptide level

getProteinMap

public TargetDecoyMap getProteinMap()

Returns the target decoy map at the protein level.

Returns:

the target decoy map at the protein level

getParameterKey

public long getParameterKey()

Specified by:

getParameterKey in interface com.compomics.util.experiment.personalization.UrParameter