public class GeneMapping extends Object
Modifier and Type | Field and Description |
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static String |
SEPARATOR
The separator used to separate line contents.
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Constructor and Description |
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GeneMapping()
Constructor.
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Modifier and Type | Method and Description |
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String |
getChromosome(String geneName)
Returns the chromosome for a given gene.
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String |
getEnsemblAccession(String geneName)
Returns the Ensembl accession for a given gene.
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HashMap<String,String> |
getGeneNameToAccession()
Returns the gene name to protein accession map.
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HashMap<String,String> |
getGeneNameToChromosome()
Returns the gene name to chromosome map.
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void |
importFromFile(File file,
WaitingHandler waitingHandler)
Reads go mappings from a BioMart file.
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public static final String SEPARATOR
public void importFromFile(File file, WaitingHandler waitingHandler) throws IOException
file
- the file containing the mappingwaitingHandler
- a waiting handler allowing display of the progress
and canceling of the process.IOException
- if an exception occurs while reading the filepublic String getChromosome(String geneName)
geneName
- the gene namepublic String getEnsemblAccession(String geneName)
geneName
- the gene namepublic HashMap<String,String> getGeneNameToChromosome()
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