Package org.biojavax.bio.taxa.io
Class SimpleNCBITaxonomyLoader
java.lang.Object
org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
- All Implemented Interfaces:
NCBITaxonomyLoader
Loads NCBI taxon information from names.dmp and nodes.dmp, which are
two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .
This simple implementation makes no attempt to process deletions
or merges - it merely creates instances as it goes along, reusing
any that may already exist.
- Since:
- 1.5
- Author:
- Richard Holland
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected NCBITaxon
readName
(BufferedReader names) Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.readNode
(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
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Constructor Details
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SimpleNCBITaxonomyLoader
public SimpleNCBITaxonomyLoader()
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Method Details
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readNode
Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.- Specified by:
readNode
in interfaceNCBITaxonomyLoader
- Parameters:
nodes
- something that reads the nodes.dmp file- Returns:
- the next NCBITaxon object in the file, or null if the file has ended.
- Throws:
IOException
ParseException
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findTaxon
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readName
Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already. Note that this does not clear out existing names from the taxon, it only adds them. Use the code snippet below if you want to clear out the names first:for (Iterator i = taxon.getNameClasses().iterator(); i.hasNext(); ) { taxon.getNames((String)i.next()).clear(); }
- Specified by:
readName
in interfaceNCBITaxonomyLoader
- Parameters:
names
- something that reads the names.dmp file- Returns:
- the NCBITaxon object corresponding to the next entry in the file, or null if the file has ended.
- Throws:
IOException
ParseException
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