Uses of Class
com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

Packages that use SpectrumIdentificationAssumption

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.

Uses of SpectrumIdentificationAssumption in com.compomics.util.experiment.identification.modification.scores

Method parameters in com.compomics.util.experiment.identification.modification.scores with type arguments of type SpectrumIdentificationAssumption

Modifier and Type	Method	Description
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.

Uses of SpectrumIdentificationAssumption in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SpectrumIdentificationAssumption

Modifier and Type	Method	Description
static NeutralLossesMap	SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	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.

Uses of SpectrumIdentificationAssumption in com.compomics.util.experiment.identification.spectrum_assumptions

Subclasses of SpectrumIdentificationAssumption in com.compomics.util.experiment.identification.spectrum_assumptions

Modifier and Type	Class	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.