Uses of Class
com.compomics.util.experiment.biology.modifications.Modification

Packages that use Modification

Package	Description
com.compomics.cli.modifications	Command line for the handling of modifications.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.

Uses of Modification in com.compomics.cli.modifications

Methods in com.compomics.cli.modifications that return Modification

Modifier and Type	Method	Description
Modification	ModificationsCLIInputBean.getModificationToAdd()	Returns the modification to add.

Uses of Modification in com.compomics.util.experiment.biology.modifications

Methods in com.compomics.util.experiment.biology.modifications that return Modification

Modifier and Type	Method	Description
Modification	ModificationFactory.getModification(String name)
Modification	ModificationProvider.getModification(String name)	Returns the modification with the given name name.
static Modification	ModificationFactory.getSingleAAModification(Modification modification)	Returns a clone of the given Modification targeting a single amino acid instead of a pattern.
Modification	ModificationFactory.getSingleAAModification(String modificationName)	Returns a clone of the given Modification targeting a single amino acid instead of a pattern.

Methods in com.compomics.util.experiment.biology.modifications with parameters of type Modification

Modifier and Type	Method	Description
void	ModificationFactory.addUserModification(Modification modification)	Adds a new user modification.
static Modification	ModificationFactory.getSingleAAModification(Modification modification)	Returns a clone of the given Modification targeting a single amino acid instead of a pattern.
boolean	Modification.isSameAs(Modification anotherModification)	Returns true if the modification is the same as another one.
boolean	Modification.isSameAtomicComposition(Modification anotherModification)	Returns true if the atomic composition of the modification is the same as another one.
boolean	Modification.isSamePattern(Modification anotherModification)	Returns true if the targeted pattern of the modification is the same as another one.

Uses of Modification in com.compomics.util.experiment.biology.proteins

Methods in com.compomics.util.experiment.biology.proteins with parameters of type Modification

Modifier and Type	Method	Description
ArrayList<Integer>	Peptide.getPotentialModificationSitesNoCombination(Modification modification, String proteinSequence, int peptideStart)	Returns the potential modification sites as an ordered list of sites.

Uses of Modification in com.compomics.util.experiment.identification.amino_acid_tags

Methods in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type Modification

Modifier and Type	Method	Description
ArrayList<Integer>	Tag.getPotentialModificationSites(Modification modification, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the potential modification sites as an ordered list of string.

Uses of Modification in com.compomics.util.experiment.identification.modification

Methods in com.compomics.util.experiment.identification.modification with parameters of type Modification

Modifier and Type	Method	Description
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>>	ModificationtableContent.getModificationPlotData(Peptide peptide, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the modification plot series in the JFreechart format for one PSM.
static ModificationtableContent	ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Get the table content.

Uses of Modification in com.compomics.util.experiment.identification.modification.scores

Method parameters in com.compomics.util.experiment.identification.modification.scores with type arguments of type Modification

Modifier and Type	Method	Description
static HashMap<Integer,Double>	PhosphoRS.getSequenceProbabilities(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of Modification in com.compomics.util.experiment.identification.protein_inference.fm_index

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type Modification

Modifier and Type	Method	Description
void	FMIndex.addModificationPattern(Modification modification)	Adds a modification pattern for bitwise pattern search.

Uses of Modification in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type Modification

Modifier and Type	Method	Description
static int[]	ModificationUtils.getPossibleModificationSites(AminoAcidSequence aminoAcidSequence, boolean nTerm, boolean cTerm, Modification modification, SequenceMatchingParameters sequenceMatchingParameters)	Returns an array of the possible modification sites for the given modification on the given peptide.
static int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)	Returns an array of the possible modification sites for the given modification on the given peptide.
static int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, ModificationProvider modificationProvider, boolean avoidOverlap)	Returns an array of the possible modification sites for the given modification on the given peptide.

Uses of Modification in com.compomics.util.gui.modification

Constructors in com.compomics.util.gui.modification with parameters of type Modification

Modifier	Constructor	Description
	ModificationDialog(JDialog parent, Modification currentModification, boolean editable)	Creates a new Modification dialog.
	ModificationDialog(JFrame parent, PtmToPrideMap modificationToPrideMap, Modification currentModification, boolean editable)	Creates a new Modification dialog.
	ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Constructor.

Uses of Modification in com.compomics.util.parameters.identification.search

Methods in com.compomics.util.parameters.identification.search that return Modification

Modifier and Type	Method	Description
Modification	ModificationParameters.getModification(String modName)	Returns the back-ed up modification with the given name.

Methods in com.compomics.util.parameters.identification.search that return types with arguments of type Modification

Modifier and Type	Method	Description
HashMap<String,Modification>	ModificationParameters.getBackedUpModifications()	Returns the modifications backed-up as a map.

Methods in com.compomics.util.parameters.identification.search with parameters of type Modification

Modifier and Type	Method	Description
void	ModificationParameters.addFixedModification(Modification modification)	Adds a fixed modification.
void	ModificationParameters.addRefinementFixedModification(Modification modification)	Adds a fixed refinement modification.
void	ModificationParameters.addRefinementVariableModification(Modification modification)	Adds a variable refinement modification.
void	ModificationParameters.addVariableModification(Modification modification)	Adds a variable modification.