Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.biology.ions |
This package contains experiment classes related to ions.
|
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
|
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.identification.scoring | |
com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
|
com.compomics.util.preferences |
Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double massTolerance)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
java.lang.String ptmName)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
|
java.util.ArrayList<Ion> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide.
|
static java.lang.String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
boolean |
Peptide.isSameAs(Peptide anotherPeptide)
A method which compares two peptides.
|
boolean |
Peptide.isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
boolean |
Peptide.sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
Constructor and Description |
---|
PrecursorIon(Peptide peptide)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
SpectrumAnnotator.getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.
|
Peptide |
PeptideAssumption.getPeptide()
Get the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given
peptide.
|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted
for.
|
boolean |
SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses,
Ion theoreticIon,
Peptide peptide)
Returns a boolean indicating whether the neutral losses of the given
fragment ion are fit the requirement of the given neutral losses map.
|
java.util.ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
void |
SpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge)
Sets a new peptide to match.
|
Constructor and Description |
---|
PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score)
Constructor for a peptide assumption.
|
PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score,
java.lang.String identificationFile)
Constructor for a peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideMatch.getTheoreticPeptide()
Getter for the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
static java.lang.String |
ProteinMatch.getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide.
|
void |
PeptideMatch.setTheoreticPeptide(Peptide theoreticPeptide)
Setter for the theoretic peptide.
|
Constructor and Description |
---|
PeptideMatch(Peptide peptide)
Constructor for the peptide match.
|
PeptideMatch(Peptide peptide,
java.lang.String spectrumMatchKey)
Constructor for the peptide match.
|
ProteinMatch(Peptide peptide)
Constructor for the protein match.
|
Modifier and Type | Method and Description |
---|---|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.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> |
PTMLocationScores.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> |
PTMLocationScores.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<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PTMLocationScores.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 |
PTMLocationScores.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 double |
PsmScores.getAScorePeptideScore(Peptide peptide,
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 a PSM score like the peptide score calculated for the A-score.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
java.util.ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags)
Add reference areas annotating the de novo tags.
|
Constructor and Description |
---|
FragmentIonTable(Peptide currentPeptide,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a traditional fragment ion table with the theoretical mz values
and the detected fragment ions highlighted.
|
FragmentIonTable(Peptide currentPeptide,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<MSnSpectrum> allSpectra,
java.util.ArrayList<java.lang.Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the
intensity of each fragment ion type.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationPreferences.setCurrentSettings(Peptide currentPeptide,
int currentPrecursorCharge,
boolean newSpectrum)
Sets the annotation settings for the current peptide and precursor
charge.
|
boolean |
IdFilter.validateModifications(Peptide peptide)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validateProteins(Peptide peptide)
Validates a peptide depending on its protein inference status
|
Copyright © 2013. All Rights Reserved.