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.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.experiment.identification.tags |
Tag classes.
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com.compomics.util.gui.ptm |
PTM GUI dialogs.
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com.compomics.util.preferences |
Utilities preferences classes.
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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(ModificationProfile modificationProfile,
int index)
Get a PTM according to its OMSSA index.
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PTM |
PTMFactory.getPTM(String name)
Returns the PTM indexed by its name.
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PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern.
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PTM |
PTMFactory.getSearchedPTM(String modificationName)
Returns the standard search compatible PTM corresponding to this pattern,
i.e., a pattern targeting a single amino acid and not a complex pattern.
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Modifier and Type | Method and Description |
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void |
PTMFactory.addUserPTM(PTM ptm)
Adds a new user modification.
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ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
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PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern.
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boolean |
Peptide.isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
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boolean |
PTM.isSameAs(PTM anotherPTM)
Compares two PTMs.
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Modifier and Type | Method and Description |
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static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
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Modifier and Type | Method and Description |
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static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the PTM plot series in the JFreechart format for one PSM.
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static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
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Modifier and Type | Method and Description |
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static HashMap<Integer,HashMap<Integer,Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization > score.
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Modifier and Type | Method and Description |
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static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location without accounting for
neutral losses.
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static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer rounding)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location accounting for neutral
losses.
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static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
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static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
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static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer ptmScoreScale)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
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Modifier and Type | Method and Description |
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ArrayList<Integer> |
Tag.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
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Constructor and Description |
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PtmDialog(JDialog parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
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PtmDialog(JFrame parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
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Modifier and Type | Method and Description |
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PTM |
ModificationProfile.getPtm(String modName)
Returns the back-ed up PTM with the given name.
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Modifier and Type | Method and Description |
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HashMap<String,PTM> |
ModificationProfile.getBackedUpPtmsMap()
Returns the PTMs backed-up as a map.
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Modifier and Type | Method and Description |
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void |
ModificationProfile.addFixedModification(PTM modification)
Adds a fixed modification.
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void |
ModificationProfile.addRefinementFixedModification(PTM modification)
Adds a fixed refinement modification.
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void |
ModificationProfile.addRefinementVariableModification(PTM modification)
Adds a variable refinement modification.
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void |
ModificationProfile.addVariableModification(PTM modification)
Adds a variable modification.
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