Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.identification.ptm.ptmscores | |
com.compomics.util.gui.ptm | |
com.compomics.util.preferences |
Modifier and Type | Field and Description |
---|---|
static PTM |
PTMFactory.unknownPTM
Unknown modification to be returned when the modification is not found.
|
Modifier and Type | Method and Description |
---|---|
PTM |
PTMFactory.getPTM(double mass,
java.lang.String location,
java.lang.String sequence)
Deprecated.
This method can generate inconsistent results in case a
measurement matches to various PTMs.
|
PTM |
PTMFactory.getPTM(ModificationProfile modificationProfile,
int index)
Get a PTM according to its OMSSA index.
|
PTM |
PTMFactory.getPTM(java.lang.String name)
Returns the PTM indexed by its name.
|
PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern.
|
PTM |
PTMFactory.getSearchedPTM(java.lang.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.
|
Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.addUserPTM(PTM ptm)
Adds a new user modification.
|
java.util.ArrayList<java.lang.Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns the potential modification sites as an ordered list of string.
|
static java.util.ArrayList<java.lang.Integer> |
Peptide.getPotentialModificationSites(java.lang.String sequence,
PTM ptm)
Returns the potential modification sites as an ordered list of string.
|
PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern.
|
boolean |
Peptide.isModifiable(PTM ptm,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Indicates whether the given modification can be found on the peptide.
|
boolean |
PTM.isSameAs(PTM anotherPTM)
Compares two PTMs.
|
Modifier and Type | Method and Description |
---|---|
static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
java.util.ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs without protein mapping.
|
static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
java.util.ArrayList<PTM> ptms,
boolean includeParentProteins)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
Modifier and Type | Method and Description |
---|---|
static java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the PTM plot series in the JFreechart format for one PSM.
|
static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
java.util.ArrayList<java.lang.Integer> possibleSites,
MSnSpectrum spectrum,
java.util.HashMap<java.lang.Integer,MSnSpectrum> spectrumMap,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score.
|
Modifier and Type | Method and Description |
---|---|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for
neutral losses.
|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location.
|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Constructor and Description |
---|
PtmDialog(javax.swing.JDialog parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
|
PtmDialog(javax.swing.JFrame parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog.
|
Modifier and Type | Method and Description |
---|---|
PTM |
ModificationProfile.getPtm(java.lang.String modName)
Returns the back-ed up PTM with the given name.
|
Modifier and Type | Method and Description |
---|---|
void |
ModificationProfile.addFixedModification(PTM modification)
Adds a fixed modification.
|
void |
ModificationProfile.addRefinementModification(PTM modification)
Adds a refinement modification.
|
void |
ModificationProfile.addVariableModification(PTM modification)
Adds a variable modification.
|
Copyright © 2013. All Rights Reserved.