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