Class EnsemblSpecies
java.lang.Object
com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
public class EnsemblSpecies extends Object
Mapping of the Ensembl species.
- Author:
- Marc Vaudel
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Field Summary
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Constructor Summary
Constructors Constructor Description EnsemblSpecies()
Constructor. -
Method Summary
Modifier and Type Method Description String
getAssembly(Integer id)
Returns the Ensembl assembly corresponding to the given NCBI taxon.String
getCommonName(Integer id)
Returns the common name corresponding to the given NCBI taxon.String
getScientificName(Integer id)
Returns the scientific 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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EnsemblSpecies
public EnsemblSpecies()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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getScientificName
Returns the scientific name corresponding to the given NCBI taxon.- Parameters:
id
- the NCBI taxon- Returns:
- the scientific name
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getCommonName
Returns the common name corresponding to the given NCBI taxon.- Parameters:
id
- the NCBI taxon- Returns:
- the common name
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getAssembly
Returns the Ensembl assembly corresponding to the given NCBI taxon.- Parameters:
id
- 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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