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

Class ModificationNameMapper

java.lang.Object

com.compomics.util.experiment.identification.modification.search_engine_mapping.ModificationNameMapper

public class ModificationNameMapper
extends Object

Functions mapping search engine modifications to utilities by name.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final double	MOD_MASS_TOLERANCE	The mass tolerance to be used to match modifications from search engines and expected modifications.

Constructor Summary

Constructors

Constructor	Description
ModificationNameMapper()

Method Summary

Modifier and Type	Method	Description
static HashMap<Integer,HashSet<String>>	getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modification names from a search engine modification indexed by site.
static HashMap<Integer,HashSet<String>>	getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible Andromeda modification names.
static HashMap<Integer,HashSet<String>>	getPossibleModificationNamesByMass(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications names by mass.
static HashMap<Integer,HashSet<String>>	getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications by name.
static HashMap<Integer,HashSet<String>>	getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible OMSSA modification names.

Methods inherited from class java.lang.Object

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

Field Details

MOD_MASS_TOLERANCE

public static final double MOD_MASS_TOLERANCE

The mass tolerance to be used to match modifications from search engines and expected modifications. 0.01 by default, the mass resolution in X!Tandem result files.

See Also:

• Constant Field Values

Constructor Details

ModificationNameMapper

public ModificationNameMapper()

Method Details

getPossibleModificationNames

public static HashMap<Integer,HashSet<String>> getPossibleModificationNames(Peptide peptide,
 ModificationMatch modificationMatch,
 IdfileReader idfileReader,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider)

Returns the possible modification names from a search engine modification indexed by site.

Parameters:

peptide - the peptide

modificationMatch - the modification match

idfileReader - the ID file reader

searchParameters - the search parameters

sequenceMatchingParameters - the sequence matching parameters

sequenceProvider - the sequence provider

modificationProvider - the modification provider

Returns:

the possible modification names

getPossibleModificationNamesByMass

public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesByMass(Peptide peptide,
 ModificationMatch modificationMatch,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider)

Returns the possible modifications names by mass.

Parameters:

peptide - the peptide

modificationMatch - the modification match

searchParameters - the search parameters

sequenceMatchingParameters - the sequence matching parameters

sequenceProvider - the sequence provider

modificationProvider - the modification provider

Returns:

the possible modifications names by mass

getPossibleModificationNamesByName

public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesByName(Peptide peptide,
 ModificationMatch modificationMatch,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider)

Returns the possible modifications by name.

Parameters:

peptide - the peptide

modificationMatch - the modification match

searchParameters - the search parameters

sequenceMatchingParameters - the sequence matching parameters

sequenceProvider - the sequence provider

modificationProvider - the modification provider

Returns:

the possible modifications by name

getPossibleModificationNamesOmssa

public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesOmssa(Peptide peptide,
 ModificationMatch modificationMatch,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider)

Returns the possible OMSSA modification names.

Parameters:

peptide - the peptide

modificationMatch - the modification match

searchParameters - the search parameters

sequenceMatchingParameters - the sequence matching parameters

sequenceProvider - the sequence provider

modificationProvider - the modification provider

Returns:

the possible OMSSA modification names

getPossibleModificationNamesAndromeda

public static HashMap<Integer,HashSet<String>> getPossibleModificationNamesAndromeda(Peptide peptide,
 ModificationMatch modificationMatch,
 SearchParameters searchParameters,
 SequenceMatchingParameters sequenceMatchingParameters,
 SequenceProvider sequenceProvider,
 ModificationProvider modificationProvider)

Returns the possible Andromeda modification names.

Parameters:

peptide - the peptide

modificationMatch - the modification match

searchParameters - the search parameters

sequenceMatchingParameters - the sequence matching parameters

sequenceProvider - the sequence provider

modificationProvider - the modification provider

Returns:

the possible Andromeda modification names