Package | Description |
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com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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com.compomics.util.preferences |
Utilities preferences classes.
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Modifier and Type | Method and Description |
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PsmScoringPreferences |
PsmScoringSettingsDialog.getPsmScoringPreferences()
Returns the PSM scoring preferences as set by the user.
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Constructor and Description |
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PsmScoringSettingsDialog(Dialog owner,
Frame parentFrame,
PsmScoringPreferences psmScoringPreferences,
boolean editable)
Creates a new PsmScoringSettingsDialog with a dialog as owner.
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PsmScoringSettingsDialog(Frame parentFrame,
PsmScoringPreferences psmScoringPreferences,
boolean editable)
Creates a new PsmScoringSettingsDialog with a frame as owner.
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Modifier and Type | Method and Description |
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PsmScoringPreferences |
IdentificationParameters.getPsmScoringPreferences()
Returns the scoring preferences used when scoring PSMs.
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Modifier and Type | Method and Description |
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boolean |
PsmScoringPreferences.equals(PsmScoringPreferences otherPsmScoringPreferences)
Returns true if the objects have identical settings.
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void |
IdentificationParameters.setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences)
Sets the scoring preferences used when scoring PSMs.
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Constructor and Description |
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationSettings annotationSettings,
SequenceMatchingPreferences sequenceMatchingPreferences,
GenePreferences genePreferences,
PsmScoringPreferences psmScoringPreferences,
PeptideAssumptionFilter peptideAssumptionFilter,
PTMScoringPreferences ptmScoringPreferences,
ProteinInferencePreferences proteinInferencePreferences,
IdMatchValidationPreferences idValidationPreferences,
FractionSettings fractionSettings)
Constructor.
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