Uses of Class
com.compomics.util.parameters.identification.search.ModificationParameters
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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)
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, SpectrumAnnotator spectrumAnnotator)
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 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 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 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 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.