Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.biology.ions |
This package contains experiment classes related to ions.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.identification.ptm.ptmscores | |
com.compomics.util.experiment.identification.scoring | |
com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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com.compomics.util.preferences |
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 without protein mapping.
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static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms,
boolean includeParentProteins)
Returns a version of the peptide which does not contain the inspected
PTMs.
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Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
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HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double massTolerance,
ProteinMatch.MatchingType matchingType)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
String ptmName,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
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.
|
ArrayList<Ion> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide.
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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 without protein mapping.
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static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms,
boolean includeParentProteins)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
static String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
HashMap<Integer,ArrayList<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.
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boolean |
Peptide.isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
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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.
|
boolean |
Peptide.sameModificationsAs(Peptide anotherPeptide,
ArrayList<String> ptms)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
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Constructor and Description |
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PrecursorIon(Peptide peptide)
Constructor.
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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 |
---|---|
HashMap<Integer,ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<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.
|
HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
ArrayList<String> |
Identification.getProteinMatches(Peptide peptide)
Returns the keys of the protein matches where a peptide can be found.
|
ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<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 |
Identification.isUnique(Peptide peptide)
Indicates whether a peptide is found in a single protein match.
|
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.
|
ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<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 |
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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,
String identificationFile)
Constructor for a peptide assumption.
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Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideMatch.getTheoreticPeptide()
Getter for the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
static 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 |
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PeptideMatch(Peptide peptide)
Constructor for the peptide match.
|
PeptideMatch(Peptide peptide,
String spectrumMatchKey)
Constructor for the peptide match.
|
ProteinMatch(Peptide peptide)
Constructor for the protein match.
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Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<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.
|
static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<ArrayList<Integer>,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for
neutral losses.
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static HashMap<ArrayList<Integer>,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
static HashMap<ArrayList<Integer>,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location.
|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
Peptide peptideCandidate,
ArrayList<String> ptms)
Returns the MD score for the given peptide in a spectrum match.
|
static HashMap<Integer,HashMap<Integer,Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score.
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static HashMap<ArrayList<Integer>,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
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Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getAScorePeptideScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns a PSM score like the peptide score calculated for the A-score.
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Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags)
Add reference areas annotating the de novo tags, using default percent
height of 0.9 for the forward ions and 1.0 for the reverse ions default
alpha levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight,
float forwardIonAlphaLevel,
float reverseIonAlphaLevel,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags.
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Constructor and Description |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<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,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
ArrayList<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.
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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,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates a peptide depending on its protein inference status.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
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Copyright © 2013. All Rights Reserved.