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.advanced |
Dialogs for advanced identification parameters.
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com.compomics.util.parameters.identification |
Identification parameters.
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com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
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Modifier and Type | Method and Description |
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GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
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Modifier and Type | Method and Description |
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GeneParameters |
GeneParametersDialog.getGeneParameters()
Returns the gene preferences.
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GeneParameters |
BackgroundSpeciesDialog.getGeneParameters()
Returns the gene preferences.
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Constructor and Description |
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BackgroundSpeciesDialog(JDialog owner,
Frame parentFrame,
GeneParameters genePreferences,
FastaSummary fastaSummary)
Creates a new GenePreferencesDialog with a dialog as owner.
|
BackgroundSpeciesDialog(JFrame parentFrame,
GeneParameters genePreferences,
FastaSummary fastaSummary)
Creates a new GenePreferencesDialog with a frame as owner.
|
GeneParametersDialog(JDialog owner,
Frame parentFrame,
GeneParameters genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a dialog as owner.
|
GeneParametersDialog(JFrame parentFrame,
GeneParameters 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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GeneParameters |
IdentificationParameters.getGeneParameters()
Returns the gene parameters.
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Modifier and Type | Method and Description |
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void |
IdentificationParameters.setGeneParameters(GeneParameters geneParameters)
Sets the gene parameters.
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Constructor and Description |
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters,
FastaParameters fastaParameters)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
GeneParameters.equals(GeneParameters genePreferences)
Compares these preferences to other preferences.
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Constructor and Description |
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GeneParameters(GeneParameters genePreferences)
Creates new gene preferences based on a GenePreferences object.
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