Uses of Class
com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Package | Description |
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com.compomics.util.experiment.identification.modification.scores |
PTM scores.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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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, 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. -
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.