public class OboParser
extends Object 

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

• Constructor Summary

  Constructors

  Constructor and Description
  OboParser ()

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  Ontology	parseOBO (BufferedReader oboFile, String ontoName, String ontoDescription) Parse a OBO file and return its content as a BioJava Ontology object

  • Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Constructor Detail

  • OboParser

    public OboParser()

• Method Detail

  • 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 parsed

    ontoName -

    ontoDescription -

    Returns:

    the ontology represented as a BioJava ontology file

    Throws:

    ParseException

    IOException