Package com.compomics.util.experiment.identification.modification.peptide_mapping

Class ModificationPeptideMapping

java.lang.Object

com.compomics.util.experiment.identification.modification.peptide_mapping.ModificationPeptideMapping

public class ModificationPeptideMapping
extends Object

Functions for the mapping of modifications on peptides.

Author:

Dafni Skiadopoulou, Marc Vaudel

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SEPARATOR	Separator for the keys of vertices.

Constructor Summary

Constructors

Constructor	Description
ModificationPeptideMapping()

Method Summary

Modifier and Type	Method	Description
static HashMap<Double,TreeSet<Integer>>	mapModifications(HashMap<Double,int[]> modificationToPossibleSiteMap, HashMap<Double,Integer> modificationOccurrenceMap, HashMap<Double,HashMap<Integer,Double>> modificationToSiteToScore)	Returns map of site to modification mapping.
static HashMap<Double,TreeSet<Integer>>	mapModificationsDeprecated(HashMap<Double,int[]> modificationToPossibleSiteMap, HashMap<Double,Integer> modificationOccurrenceMap, HashMap<Double,HashMap<Integer,Double>> modificationToSiteToScore)	Deprecated. does not handle corner cases

Methods inherited from class java.lang.Object

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

Field Details

SEPARATOR

public static final String SEPARATOR

Separator for the keys of vertices.

See Also:

• Constant Field Values

Constructor Details

ModificationPeptideMapping

public ModificationPeptideMapping()

Method Details

mapModificationsDeprecated

public static HashMap<Double,TreeSet<Integer>> mapModificationsDeprecated(HashMap<Double,int[]> modificationToPossibleSiteMap,
 HashMap<Double,Integer> modificationOccurrenceMap,
 HashMap<Double,HashMap<Integer,Double>> modificationToSiteToScore)

Deprecated.

does not handle corner cases

Returns map of site to modification mapping.

Parameters:

modificationToPossibleSiteMap - Map of modification mass to site to modification names.

modificationOccurrenceMap - Map of modification mass to number of modifications.

modificationToSiteToScore - Map of modification mass to modification site to localization score.

Returns:

The list of best sites per modification.

mapModifications

public static HashMap<Double,TreeSet<Integer>> mapModifications(HashMap<Double,int[]> modificationToPossibleSiteMap,
 HashMap<Double,Integer> modificationOccurrenceMap,
 HashMap<Double,HashMap<Integer,Double>> modificationToSiteToScore)

Returns map of site to modification mapping.

Parameters:

modificationToPossibleSiteMap - Map of modification mass to site to modification names.

modificationOccurrenceMap - Map of modification mass to number of modifications.

modificationToSiteToScore - Map of modification mass to modification site to localization score.

Returns:

The list of best sites per modification.