Package | Description |
---|---|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
|
com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
|
com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
|
Modifier and Type | Method and Description |
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static Double |
MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingParameters sequenceMatchingPreferences,
Integer rounding)
Returns the MD score for the given peptide in a spectrum match.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpectrumAnnotator spectrumAnnotator)
Returns the possible neutral losses expected by default for a given
peptide.
|
SpecificAnnotationParameters |
AnnotationParameters.getSpecificAnnotationParameters(String spectrumFile,
String spectrumTitle,
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
SpectrumAnnotator spectrumAnnotator)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideAssumption
This object models the assumption made by an advocate.
|
class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
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