Package org.biojavax.bio.taxa.io
Interface NCBITaxonomyLoader
- All Known Implementing Classes:
SimpleNCBITaxonomyLoader
public interface NCBITaxonomyLoader
Implementors are able to load taxonomy files and generate sets of NCBITaxon objects
that represent them. Taxon objects should be generated using RichObjectFactory.
- Since:
- 1.5
- Author:
- Richard Holland
-
Method Summary
Modifier and TypeMethodDescriptionreadName
(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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Method Details
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readNode
Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.- 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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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(); }
- 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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