public class SpeciesUtils extends Object
Constructor and Description |
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SpeciesUtils() |
Modifier and Type | Method and Description |
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static SpeciesConfiguration.Assembly |
getAssembly(SpeciesConfiguration speciesConfiguration,
String assemblyString)
Check given assembly is valid, case insensitve.
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static SpeciesConfiguration.Assembly |
getDefaultAssembly(SpeciesConfiguration speciesConfiguration)
Get the default assembly for species.
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static Species |
getSpecies(CellBaseConfiguration configuration,
String userProvidedSpecies,
String userProvidedAssembly)
Return species object based on species name and assembly.
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static SpeciesConfiguration |
getSpeciesConfiguration(CellBaseConfiguration configuration,
String species)
Get configuration for the specified species.
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static String |
getSpeciesShortname(SpeciesConfiguration speciesConfiguration)
Formats the species name, e.g.
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public static Species getSpecies(CellBaseConfiguration configuration, String userProvidedSpecies, String userProvidedAssembly) throws CellbaseException
configuration
- configuration file listing the valid species and assembliesuserProvidedSpecies
- name of species, e.g. Homo sapiens or hsapiensuserProvidedAssembly
- assembly versionCellbaseException
- if the species or assembly is invalidpublic static SpeciesConfiguration getSpeciesConfiguration(CellBaseConfiguration configuration, String species)
configuration
- configuration for this cellbase instancespecies
- species of interest, e.g. hsapiens or Homo sapienspublic static SpeciesConfiguration.Assembly getAssembly(SpeciesConfiguration speciesConfiguration, String assemblyString)
speciesConfiguration
- configuration entry for this speciesassemblyString
- name of assemblypublic static SpeciesConfiguration.Assembly getDefaultAssembly(SpeciesConfiguration speciesConfiguration) throws CellbaseException
speciesConfiguration
- configuration entry for this speciesCellbaseException
- if the species has no associated assemblypublic static String getSpeciesShortname(SpeciesConfiguration speciesConfiguration)
speciesConfiguration
- configuration entry for this speciesCopyright © 2019. All rights reserved.