Class GeneParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.GeneParameters
- All Implemented Interfaces:
Serializable
public class GeneParameters extends ExperimentObject
Contains methods for downloading gene and GO mappings.
- Author:
- Harald Barsnes, Marc Vaudel
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description GeneParameters()
Create a new GenePreferences object.GeneParameters(GeneParameters genePreferences)
Creates new gene preferences based on a GenePreferences object. -
Method Summary
Modifier and Type Method Description boolean
equals(GeneParameters genePreferences)
Compares these preferences to other preferences.Boolean
getAutoUpdate()
Indicates whether the gene mappings should be automatically updated.Integer
getBackgroundSpecies()
Returns the taxon of the species selected as background species.String
getShortDescription()
Returns a short description of the parameters.Boolean
getUseGeneMapping()
Returns a boolean indicating whether gene mappings should be used.void
setAutoUpdate(Boolean autoUpdate)
Sets whether the gene mappings should be automatically updated.void
setBackgroundSpecies(Integer selectedBackgroundSpecies)
Sets the taxon of the species selected as background species.void
setBackgroundSpeciesFromFastaSummary(FastaSummary fastaSummary)
Set the background species to the most common species in the FASTA file.void
setUseGeneMapping(Boolean useGeneMapping)
Sets whether gene mappings should be used.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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GeneParameters
public GeneParameters()Create a new GenePreferences object. -
GeneParameters
Creates new gene preferences based on a GenePreferences object.- Parameters:
genePreferences
- the gene preferences
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Method Details
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getUseGeneMapping
Returns a boolean indicating whether gene mappings should be used.- Returns:
- a boolean indicating whether gene mappings should be used
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setUseGeneMapping
Sets whether gene mappings should be used.- Parameters:
useGeneMapping
- a boolean indicating whether gene mappings should be used
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getAutoUpdate
Indicates whether the gene mappings should be automatically updated.- Returns:
- a boolean indicating whether the gene mappings should be automatically updated
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setAutoUpdate
Sets whether the gene mappings should be automatically updated.- Parameters:
autoUpdate
- a boolean indicating whether the gene mappings should be automatically updated
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equals
Compares these preferences to other preferences.- Parameters:
genePreferences
- other preferences to compare to.- Returns:
- a boolean indicating whether the other preferences are the same as these ones.
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getBackgroundSpecies
Returns the taxon of the species selected as background species.- Returns:
- the taxon of the species selected as background species
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setBackgroundSpecies
Sets the taxon of the species selected as background species.- Parameters:
selectedBackgroundSpecies
- the taxon of the species selected as background species
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setBackgroundSpeciesFromFastaSummary
Set the background species to the most common species in the FASTA file.- Parameters:
fastaSummary
- the FASTA summary
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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