Uses of Class
com.compomics.util.parameters.identification.search.ModificationParameters

Packages that use ModificationParameters

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
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.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation	This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
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.gui.parameters.identification.algorithm	Search algorithm settings dialogs.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

Uses of ModificationParameters in com.compomics.util.experiment.biology.aminoacids.sequence

Methods in com.compomics.util.experiment.biology.aminoacids.sequence with parameters of type ModificationParameters

Modifier and Type	Method	Description
String[]	AminoAcidSequence.getFixedModifications(boolean nTerm, boolean cTerm, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the fixed modifications for this sequence based on the given modification parameters.

Uses of ModificationParameters in com.compomics.util.experiment.biology.ions

Methods in com.compomics.util.experiment.biology.ions with parameters of type ModificationParameters

Modifier and Type	Method	Description
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a peptide.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns all the theoretic ions expected from a peptide.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a tag.
static HashSet<String>	IonFactory.getNeutralLosses(ModificationParameters modificationParameters)	Returns a list containing the default neutral losses and the losses found in the given modifications.
static HashSet<Integer>	IonFactory.getReporterIons(ModificationParameters modificationParameters)	Returns the reporter ions to annotate with the given PTM settings.

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

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

Modifier and Type	Method	Description
String	ModificationFactory.convertPridePtm(String pridePtmName, ModificationParameters modProfile, ArrayList<String> unknownPtms, boolean isFixed)	Tries to convert a PRIDE Modification to utilities Modification name, and add it to the modification profile.

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

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

Modifier and Type	Method	Description
void	Peptide.estimateTheoreticMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Estimates the theoretic mass of the peptide.
String[]	Peptide.getFixedModifications(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the fixed modifications for this peptide based on the given modification parameters.
double	Peptide.getMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the mass, estimates it if not done before.
String	Peptide.getTaggedModifiedSequence(ModificationParameters modificationProfile, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.

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

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

Modifier and Type	Method	Description
String	Tag.getCTerminal(boolean includeTerminalGaps, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the C-terminal tag of this tag as a string for sequence display.
String	Tag.getNTerminal(boolean includeTerminalGaps, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the N-terminal tag of this tag as a string for sequence display.
String	Tag.getTaggedModifiedSequence(ModificationParameters modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean includeTerminalGaps, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
static String	Tag.getTaggedModifiedSequence(ModificationParameters modificationParameters, Tag tag, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean includeTerminalGaps, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.

Uses of ModificationParameters in com.compomics.util.experiment.identification.filtering

Methods in com.compomics.util.experiment.identification.filtering with parameters of type ModificationParameters

Modifier and Type	Method	Description
boolean	PeptideAssumptionFilter.validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)	Verifies that the definition of every modification name is available.

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

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

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 ModificationParameters in com.compomics.util.experiment.identification.modification.scores

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

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 ModificationParameters in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation

Methods in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation with parameters of type ModificationParameters

Modifier and Type	Method	Description
int[]	FeaturesGenerator.getComplementaryIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the ms2pip features for the complementary ions of the given peptide at the given charge.
int[]	FeaturesGenerator.getForwardIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the ms2pip features for the forward ions of the given peptide at the given charge.

Uses of ModificationParameters in com.compomics.util.experiment.identification.psm_scoring

Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type ModificationParameters

Modifier and Type	Method	Description
double	PsmScoresEstimator.getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)	Scores the match between the given peptide and spectrum using the given score.
double	PsmScoresEstimator.getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)	Scores the match between the given peptide and spectrum using the given score.
double	PsmScoresEstimator.getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)	Scores the match between the given peptide and spectrum using the given score.

Uses of ModificationParameters in com.compomics.util.experiment.identification.psm_scoring.psm_scores

Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type ModificationParameters

Modifier and Type	Method	Description
double	HyperScore.getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the hyperscore.
double	SnrScore.getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the score.

Uses of ModificationParameters in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type ModificationParameters

Modifier and Type	Method	Description
IonMatch[]	SpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the currently matched ions with the given settings using the intensity filter.
abstract IonMatch[]	SpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the currently matched ions with the given settings.
static NeutralLossesMap	SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
SpecificAnnotationParameters	AnnotationParameters.getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, SpectrumAnnotator spectrumAnnotator)	Returns the annotation preferences specific to a spectrum and an identification assumption.

Uses of ModificationParameters in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type ModificationParameters

Modifier and Type	Method	Description
Map<Integer,ArrayList<IonMatch>>	PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
IonMatch[]	PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
IonMatch[]	TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
static NeutralLossesMap	PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
static NeutralLossesMap	TagSpectrumAnnotator.getDefaultLosses(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given tag.
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the expected ions in a map indexed by the possible charges.
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)	Returns the expected ions in a map indexed by the possible charges.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in an array of IonMatches.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag)	Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a stream of IonMatches.
ArrayList<IonMatch>	PeptideSpectrumAnnotator.matchPeak(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)	This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.
void	PeptideSpectrumAnnotator.setPeptide(Peptide peptide, int precursorCharge, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings)	Sets a new peptide to annotate.
void	PeptideSpectrumAnnotator.setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)	Sets a new peptide to annotate.
void	TagSpectrumAnnotator.setTag(Tag newTag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, int precursorCharge)	Sets a new tag to match.

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

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

Modifier and Type	Method	Description
static void	ModificationUtils.appendTaggedResidue(StringBuilder stringBuilder, char residue, String modificationName, ModificationParameters modificationProfile, int localizationConfidenceLevel, boolean useHtmlColorCoding, boolean useShortName)	Appends the single residue as a tagged string (HTML color or PTM tag).
static void	ModificationUtils.appendTaggedResidue(StringBuilder stringBuilder, char residue, String confidentModification, String representativeAmbiguousModification, String secondaryAmbiguousModification, String fixedModification, ModificationParameters modificationProfile, boolean useHtmlColorCoding, boolean useShortName)	Returns the single residue as a tagged string (HTML color or PTM tag).
static HashSet<String>	ModificationUtils.getAllModifications(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)	Returns a set of the names of all modifications found on a peptide.
static HashSet<String>	ModificationUtils.getAllModifications(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters sequenceMatchingParameters)	Returns a set of the names of all modifications found on a tag.
static HashMap<Integer,HashSet<String>>	ModificationUtils.getExpectedModifications(double modMass, ModificationParameters modificationParameters, Peptide peptide, double massTolerance, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, SearchParameters searchParameters)	Returns the expected modifications for a given modification mass indexed by site.
static String	PeptideUtils.getFixedModificationsAsString(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the peptide modifications as a string.
static String	ModificationUtils.getTaggedModifiedSequence(ModificationParameters modificationProfile, String sequence, String[] confidentModificationSites, String[] representativeAmbiguousModificationSites, String[] secondaryAmbiguousModificationSites, String[] fixedModificationSites, boolean useHtmlColorCoding, boolean useShortName)	Returns the modified sequence as a tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
static String	PeptideUtils.getTaggedModifiedSequence(Peptide peptide, ModificationParameters modificationParameters, String[] allFixedModifications, String[] allVariableModifications, String[] confidentModificationSites, String[] representativeAmbiguousModificationSites, String[] secondaryAmbiguousModificationSites, String[] fixedModificationSites, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)	Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.

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

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

Modifier	Constructor	Description
	ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Constructor.

Uses of ModificationParameters in com.compomics.util.gui.parameters.identification.algorithm

Methods in com.compomics.util.gui.parameters.identification.algorithm that return ModificationParameters

Modifier and Type	Method	Description
ModificationParameters	XTandemParametersDialog.getModificationProfile()	Returns the modification profile corresponding to the input by the user.

Constructors in com.compomics.util.gui.parameters.identification.algorithm with parameters of type ModificationParameters

Modifier	Constructor	Description
	XTandemParametersDialog(Dialog owner, Frame parent, XtandemParameters xtandemParameters, ModificationParameters modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable)	Creates new form XtandemParametersDialog with a dialog as owner.
	XTandemParametersDialog(Frame parent, XtandemParameters xtandemParameters, ModificationParameters modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable)	Creates new form XtandemParametersDialog with a frame as owner.

Uses of ModificationParameters in com.compomics.util.gui.spectrum

Methods in com.compomics.util.gui.spectrum with parameters of type ModificationParameters

Modifier and Type	Method	Description
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.

Constructors in com.compomics.util.gui.spectrum with parameters of type ModificationParameters

Modifier	Constructor	Description
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, ArrayList<Spectrum> allSpectra, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
	SequenceFragmentationPanel(String aSequence, IonMatch[] aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.
	SequenceFragmentationPanel(String taggedModifiedSequence, IonMatch[] aIonMatches, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.

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

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

Modifier and Type	Method	Description
ModificationParameters	SearchParameters.getModificationParameters()	Returns the modification settings.

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

Modifier and Type	Method	Description
boolean	ModificationParameters.equals(ModificationParameters otherProfile)	Returns true of the two profiles are identical.
void	SearchParameters.setModificationParameters(ModificationParameters modificationParameters)	Sets the modification settings.

Constructors in com.compomics.util.parameters.identification.search with parameters of type ModificationParameters

Modifier	Constructor	Description
	ModificationParameters(ModificationParameters modificationParameters)	Constructor creating a new Modification profile based on the given one.

Uses of ModificationParameters in com.compomics.util.parameters.identification.tool_specific

Methods in com.compomics.util.parameters.identification.tool_specific with parameters of type ModificationParameters

Modifier and Type	Method	Description
void	OmssaParameters.setPtmIndexes(ModificationParameters modificationProfile)	Set the PTM indexes of the modifications searched.