org.opencb.cellbase.lib

Class SpeciesUtils

java.lang.Object

org.opencb.cellbase.lib.SpeciesUtils

public class SpeciesUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
SpeciesUtils()

Method Summary

Modifier and Type	Method and Description
static SpeciesConfiguration.Assembly	getAssembly(SpeciesConfiguration speciesConfiguration, String assemblyString) Check given assembly is valid, case insensitve.
static SpeciesConfiguration.Assembly	getDefaultAssembly(SpeciesConfiguration speciesConfiguration) Get the default assembly for species.
static Species	getSpecies(CellBaseConfiguration configuration, String userProvidedSpecies, String userProvidedAssembly) Return species object based on species name and assembly.
static SpeciesConfiguration	getSpeciesConfiguration(CellBaseConfiguration configuration, String species) Get configuration for the specified species.
static String	getSpeciesShortname(SpeciesConfiguration speciesConfiguration) Formats the species name, e.g.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SpeciesUtils

public SpeciesUtils()

Method Detail

getSpecies

public static Species getSpecies(CellBaseConfiguration configuration,
                                 String userProvidedSpecies,
                                 String userProvidedAssembly)
                          throws CellbaseException

Return species object based on species name and assembly. If assembly is not provided, default assembly is used (the first one listed in the config file)

Parameters:

configuration - configuration file listing the valid species and assemblies

userProvidedSpecies - name of species, e.g. Homo sapiens or hsapiens

userProvidedAssembly - assembly version

Returns:

species object

Throws:

CellbaseException - if the species or assembly is invalid

getSpeciesConfiguration

public static SpeciesConfiguration getSpeciesConfiguration(CellBaseConfiguration configuration,
                                                           String species)

Get configuration for the specified species.

Parameters:

configuration - configuration for this cellbase instance

species - species of interest, e.g. hsapiens or Homo sapiens

Returns:

configuration for given species

getAssembly

public static SpeciesConfiguration.Assembly getAssembly(SpeciesConfiguration speciesConfiguration,
                                                        String assemblyString)

Check given assembly is valid, case insensitve. NULL if invalid assembly.

Parameters:

speciesConfiguration - configuration entry for this species

assemblyString - name of assembly

Returns:

the assembly name OR NULL of no assembly found.

getDefaultAssembly

public static SpeciesConfiguration.Assembly getDefaultAssembly(SpeciesConfiguration speciesConfiguration)
                                                        throws CellbaseException

Get the default assembly for species. Is naive and just gets the first one. Order not guaranteed, don't rely on this at all.

Parameters:

speciesConfiguration - configuration entry for this species

Returns:

the default assembly

Throws:

CellbaseException - if the species has no associated assembly

getSpeciesShortname

public static String getSpeciesShortname(SpeciesConfiguration speciesConfiguration)

Formats the species name, e.g. Homo sapiens to hsapiens. Used in the download for the species directory.

Parameters:

speciesConfiguration - configuration entry for this species

Returns:

formatted species name