Package org.biojava.nbio.ontology.io
Class OboParser
- java.lang.Object
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- org.biojava.nbio.ontology.io.OboParser
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public class OboParser extends Object
Parses an OBO file.- Since:
- 1.7
Example
OboParser parser = new OboParser(); InputStream inStream = this.getClass().getResourceAsStream("/files/ontology/biosapiens.obo"); BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) ); try { Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology"); Set keys = ontology.getTerms(); Iterator iter = keys.iterator(); while (iter.hasNext()){ System.out.println(iter.next()); } } catch (Exception e){ e.printStackTrace(); }
- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description OboParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Ontology
parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription)
Parse a OBO file and return its content as a BioJava Ontology object
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Constructor Detail
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OboParser
public OboParser()
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Method Detail
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parseOBO
public Ontology parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription) throws ParseException, IOException
Parse a OBO file and return its content as a BioJava Ontology object- Parameters:
oboFile
- the file to be parsedontoName
-ontoDescription
-- Returns:
- the ontology represented as a BioJava ontology file
- Throws:
ParseException
IOException
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