Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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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.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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com.compomics.util.experiment.identification.ptm |
Additional PSM scoring classes.
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com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
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com.compomics.util.gui.ptm |
PTM GUI dialogs.
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Modifier and Type | Field and Description |
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static PTM |
PTMFactory.unknownPTM
Unknown modification to be returned when the modification is not found.
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Modifier and Type | Method and Description |
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PTM |
PTMFactory.getPTM(String name)
Returns the PTM indexed by its name.
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static PTM |
PTMFactory.getSingleAAPTM(PTM modification)
Returns a clone of the given PTM targeting a single amino acid instead of
a pattern.
|
PTM |
PTMFactory.getSingleAAPTM(String modificationName)
Returns a clone of the given PTM targeting a single amino acid instead of
a pattern.
|
Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.addUserPTM(PTM ptm)
Adds a new user modification.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
static PTM |
PTMFactory.getSingleAAPTM(PTM modification)
Returns a clone of the given PTM targeting a single amino acid instead of
a pattern.
|
boolean |
Peptide.isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
|
boolean |
PTM.isSameAs(PTM anotherPTM)
Returns true if the PTM is the same as another one.
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boolean |
PTM.isSameAtomicComposition(PTM anotherPTM)
Returns true if the atomic composition of the PTM is the same as another
one.
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boolean |
PTM.isSamePattern(PTM anotherPTM)
Returns true if the targeted pattern of the PTM is the same as another
one.
|
Modifier and Type | Method and Description |
---|---|
static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
Modifier and Type | Method and Description |
---|---|
PTM |
PtmSettings.getPtm(String modName)
Returns the back-ed up PTM with the given name.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,PTM> |
PtmSettings.getBackedUpPtmsMap()
Returns the PTMs backed-up as a map.
|
Modifier and Type | Method and Description |
---|---|
void |
PtmSettings.addFixedModification(PTM modification)
Adds a fixed modification.
|
void |
PtmSettings.addRefinementFixedModification(PTM modification)
Adds a fixed refinement modification.
|
void |
PtmSettings.addRefinementVariableModification(PTM modification)
Adds a variable refinement modification.
|
void |
PtmSettings.addVariableModification(PTM modification)
Adds a variable modification.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Returns the PTM plot series in the JFreechart format for one PSM.
|
static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,HashMap<Integer,Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization > score.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
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Constructor and Description |
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PtmDialog(JDialog parent,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
|
PtmDialog(JFrame parent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
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