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.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationsCLIInputBean.getModificationToAdd()
Returns the modification to add.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationProvider.getModification(String name)
Returns the modification with the given name name.
|
Modification |
ModificationFactory.getModification(String 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Peptide.getPotentialModificationSitesNoCombination(Modification modification,
String proteinSequence,
int peptideStart)
Returns the potential modification sites as an ordered list of sites.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(Modification modification,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
void |
FMIndex.addModificationPattern(Modification modification)
Adds a modification pattern for bitwise pattern search.
|
Modifier and Type | Method and 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.
|
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationParameters.getModification(String modName)
Returns the back-ed up modification with the given name.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,Modification> |
ModificationParameters.getBackedUpModifications()
Returns the modifications backed-up as a map.
|
Modifier and Type | Method and 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.
|
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