| Interface | Description |
|---|---|
| MarshallableParameter |
Interface for a parameter which can be marshalled as .par file.
|
| Class | Description |
|---|---|
| DummyParameters |
Dummy parameters used to retrieve the parameters type.
|
| FractionSettings |
Settings for the handling of fractions.
|
| GenePreferences |
Contains methods for downloading gene and GO mappings.
|
| IdentificationParameters |
Generic class grouping the parameters used for protein identification.
|
| IdMatchValidationPreferences |
Generic class grouping the identification matches validation preferences.
|
| LastSelectedFolder |
Convenience class keeping class of the last selected folders.
|
| ProcessingPreferences |
ProcessingPreferences.
|
| ProteinInferencePreferences |
Generic class grouping the protein inference preferences.
|
| PsmScoringPreferences |
Generic class for peptide spectrum match scoring.
|
| PSProcessingPreferences | Deprecated
replaced by utilities processing preferences and fraction preferences
|
| PTMScoringPreferences |
This class contains the PTM localization scoring preferences.
|
| SequenceMatchingPreferences |
The sequence matching options.
|
| 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 |
|---|---|
| MarshallableParameter.Type |
Enum of the type of parameter which can be encountered in a .par file.
|
| ProcessingPreferences.ProcessingType |
Class indicating the type of processing.
|
| SearchGuiOutputOption |
This enum lists the possible output options.
|
| SequenceMatchingPreferences.MatchingType |
The different types of amino acid matching.
|
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