Class EnsemblGenomesSpecies
java.lang.Object
com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
public class EnsemblGenomesSpecies extends Object
This class provides information about the species mapping in Ensembl Genomes
(Bacteria, Fungi, Metazoa, Plants, Protists).
- Author:
- Marc Vaudel
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
EnsemblGenomesSpecies.EnsemblGenomeDivision
Enum of the different Ensembl genome divisions. -
Field Summary
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Constructor Summary
Constructors Constructor Description EnsemblGenomesSpecies()
Constructor. -
Method Summary
Modifier and Type Method Description String
getAssembly(Integer taxon)
Returns the Ensembl assembly corresponding to the given NCBI taxon.EnsemblGenomesSpecies.EnsemblGenomeDivision
getDivision(Integer taxon)
Returns the division corresponding to the given NCBI taxon.String
getName(Integer taxon)
Returns the name corresponding to the given NCBI taxon.HashSet<Integer>
getTaxons()
Returns the taxons in this map.void
loadMapping(File speciesFile)
Loads the species mapping from a file.
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Field Details
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SEPARATOR
The separator used to separate line contents.- See Also:
- Constant Field Values
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Constructor Details
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EnsemblGenomesSpecies
public EnsemblGenomesSpecies()Constructor.
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Method Details
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loadMapping
Loads the species mapping from a file. Previous mapping will be overwritten.- Parameters:
speciesFile
- the species file- Throws:
IOException
- exception thrown whenever an error occurred while reading the file.
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getName
Returns the name corresponding to the given NCBI taxon.- Parameters:
taxon
- the NCBI taxon- Returns:
- the name
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getDivision
Returns the division corresponding to the given NCBI taxon.- Parameters:
taxon
- the NCBI taxon- Returns:
- the division
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getAssembly
Returns the Ensembl assembly corresponding to the given NCBI taxon.- Parameters:
taxon
- the NCBI taxon- Returns:
- the Ensembl assembly
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getTaxons
Returns the taxons in this map.- Returns:
- the taxons in this map
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