Package | Description |
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com.compomics.util.experiment.biology.genes |
Classes related to genes.
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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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GeneMaps |
GeneFactory.getGeneMaps(GenePreferences genePreferences,
WaitingHandler waitingHandler)
Returns the gene maps for the FASTA file loaded in the factory.
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Modifier and Type | Method and Description |
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GenePreferences |
GenePreferencesDialog.getGenePreferences()
Returns the gene preferences.
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Constructor and Description |
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GenePreferencesDialog(JDialog owner,
GenePreferences genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a dialog as owner.
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GenePreferencesDialog(JFrame parent,
GenePreferences genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a frame as owner.
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Modifier and Type | Method and Description |
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GenePreferences |
IdentificationParameters.getGenePreferences()
Returns the gene preferences.
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Modifier and Type | Method and Description |
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boolean |
GenePreferences.equals(GenePreferences genePreferences)
Compares these preferences to other preferences.
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void |
IdentificationParameters.setGenePreferences(GenePreferences genePreferences)
Sets the gene preferences.
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Constructor and Description |
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GenePreferences(GenePreferences genePreferences)
Creates new gene preferences based on a GenePreferences object.
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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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