Package eu.isas.peptideshaker.scoring.maps

Class SpecificTargetDecoyMap

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

ModificationSpecificMap, SimpleSpecificMap

public abstract class SpecificTargetDecoyMap
extends com.compomics.util.experiment.personalization.ExperimentObject
implements Serializable

This stores target decoy maps grouped by file and category.

Author:

Marc Vaudel

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected final HashMap<Integer,HashSet<String>>	fileSpecificGrouping	Map used to group keys together per file.
protected final HashMap<Integer,HashMap<String,TargetDecoyMap>>	fileSpecificMaps	The map of the target decoy maps indexed by file and category.
protected final HashMap<Integer,TargetDecoyMap>	groupedMaps	The map of the target decoy maps indexed by category.
protected final HashMap<Integer,Integer>	grouping	Map used to group keys together in the grouped maps.

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

NO_KEY

Constructor Summary

Constructors

Constructor	Description
SpecificTargetDecoyMap()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addPoint(String fileName, int category, double score, boolean decoy)	Adds a point representing the corresponding spectrum match at a given score.
abstract void	clean(double minimalFDR)	Handles sparse maps.
void	estimateProbabilities(com.compomics.util.waiting.WaitingHandler waitingHandler)	Estimate the posterior error probabilities of the PSMs.
Set<Integer>	getCategoriesFromGroupedFiles()	Returns a list of categories from grouped files.
HashMap<Integer,ArrayList<Integer>>	getChargeGroupingMap()	Returns the map of grouped categories indexed by representative category.
int	getCorrectedCharge(int category)	For grouped files, returns the reference category of the group.
TreeSet<String>	getFilesAtCategory(int category)	Returns the files at the given category, an empty list if not found.
int[]	getGroupedCategories()	Returns a list of grouped categories from grouped files.
int	getMapsSize()	Returns the overall number of points across all maps.
Set<Integer>	getPossibleCategories()	Returns the categories found in the map
double	getProbability(String file, int category, double score)	Returns the probability of the given spectrum match at the given score.
TargetDecoyMap	getTargetDecoyMap(int category, String spectrumFile)	Returns the desired target decoy map.
ArrayList<TargetDecoyMap>	getTargetDecoyMaps()	Returns a list of the target decoy maps used for scoring.
boolean	isFileGrouped(int category, String fileName)	Indicates whether the given file was grouped for the given category.

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

Field Details

fileSpecificMaps

protected final HashMap<Integer,HashMap<String,TargetDecoyMap>> fileSpecificMaps

The map of the target decoy maps indexed by file and category.

fileSpecificGrouping

protected final HashMap<Integer,HashSet<String>> fileSpecificGrouping

Map used to group keys together per file.

groupedMaps

protected final HashMap<Integer,TargetDecoyMap> groupedMaps

The map of the target decoy maps indexed by category.

grouping

protected final HashMap<Integer,Integer> grouping

Map used to group keys together in the grouped maps.

Constructor Details

SpecificTargetDecoyMap

public SpecificTargetDecoyMap()

Constructor.

Method Details

estimateProbabilities

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

Estimate the posterior error probabilities of the PSMs.

Parameters:

waitingHandler - the handler displaying feedback to the user

getProbability

public double getProbability(String file,
 int category,
 double score)

Returns the probability of the given spectrum match at the given score.

Parameters:

file - the file scored

category - the category scored

score - the corresponding score

Returns:

the probability of the given spectrum match at the given score

addPoint

public void addPoint(String fileName,
 int category,
 double score,
 boolean decoy)

Adds a point representing the corresponding spectrum match at a given score.

Parameters:

fileName - the name of the spectrum file

category - the category of the match

score - the score

decoy - whether the match is target or decoy

clean

public abstract void clean(double minimalFDR)

Handles sparse maps.

Parameters:

minimalFDR - the minimal FDR which should be achievable

getTargetDecoyMap

public TargetDecoyMap getTargetDecoyMap(int category,
 String spectrumFile)

Returns the desired target decoy map.

Parameters:

category - the identified category of the PSM

spectrumFile - the name of the spectrum file

Returns:

the corresponding target decoy map

isFileGrouped

public boolean isFileGrouped(int category,
 String fileName)

Indicates whether the given file was grouped for the given category.

Parameters:

category - the category of interest

fileName - the name of the file

Returns:

a boolean indicating whether the given file was grouped for the given category

getCorrectedCharge

public int getCorrectedCharge(int category)

For grouped files, returns the reference category of the group.

Parameters:

category - the category of the match

Returns:

the category of the group for grouped files, the original category if not found

getPossibleCategories

public Set<Integer> getPossibleCategories()

Returns the categories found in the map

Returns:

the categories found in the map

getCategoriesFromGroupedFiles

public Set<Integer> getCategoriesFromGroupedFiles()

Returns a list of categories from grouped files.

Returns:

a list of categories from grouped files

getGroupedCategories

public int[] getGroupedCategories()

Returns a list of grouped categories from grouped files.

Returns:

a list of grouped categories from grouped files

getChargeGroupingMap

public HashMap<Integer,ArrayList<Integer>> getChargeGroupingMap()

Returns the map of grouped categories indexed by representative category.

Returns:

the map of grouped categories indexed by representative category

getFilesAtCategory

public TreeSet<String> getFilesAtCategory(int category)

Returns the files at the given category, an empty list if not found.

Parameters:

category - the category of interest

Returns:

the files at the given category

getMapsSize

public int getMapsSize()

Returns the overall number of points across all maps.

Returns:

the overall number of points across all maps.

getTargetDecoyMaps

public ArrayList<TargetDecoyMap> getTargetDecoyMaps()

Returns a list of the target decoy maps used for scoring.

Returns:

a list of the target decoy maps used for scoring