Class BiomartMapping
java.lang.Object
com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
public class BiomartMapping extends Object
Mapping of the species to BioMart dataset.
- Author:
- Marc Vaudel
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Field Summary
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Constructor Summary
Constructors Constructor Description BiomartMapping()
Constructor. -
Method Summary
Modifier and Type Method Description String
getDataset(String assembly)
Returns the Ensembl dataset for the given assembly.void
loadMapping(File ensemblFile, File ensemblGenomeFile)
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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BiomartMapping
public BiomartMapping()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:
ensemblFile
- the Ensembl BioMart fileensemblGenomeFile
- the Ensembl genome BioMart file- Throws:
IOException
- exception thrown whenever an error occurred while reading the file.
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getDataset
Returns the Ensembl dataset for the given assembly. Null if not found.- Parameters:
assembly
- the assembly- Returns:
- the Ensembl dataset
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