Class | Description |
---|---|
AnnotationPreferences |
This class contains the spectrum annotation preferences.
|
GenePreferences |
Contains methods for downloading gene and GO mappings.
|
IdentificationParameters |
Generic class grouping the parameters used for protein identification.
|
IdFilter |
This class achieves a pre-filtering of the identifications for PeptideShaker.
|
IdMatchValidationPreferences |
Generic class grouping the identification matches validation preferences.
|
LastSelectedFolder |
Convenience class keeping class of the last selected folders.
|
ModificationProfile |
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
ProcessingPreferences |
This class groups the user preferences for the initial PeptideShaker
processing.
|
ProteinInferencePreferences |
Generic class grouping the protein inference preferences.
|
PsmScoringPreferences |
Generic class for peptide spectrum match scoring.
|
PTMScoringPreferences |
This class contains the PTM localization scoring preferences.
|
SequenceMatchingPreferences |
The sequence matching options.
|
SpecificAnnotationPreferences |
The spectrum annotation preferences specific to a spectrum and an
identification assumption.
|
UtilitiesUserPreferences |
Utilities user preferences will be serialized in the user folder and provide
useful information to all compomics software, well as soon as they use it of
course.
|
ValidationQCPreferences |
This class lists the criteria used for quality control of the validated
matches.
|
Enum | Description |
---|---|
SequenceMatchingPreferences.MatchingType |
The different types of amino acid matching.
|
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