org.biojava.ontology.io
Class OboParser

java.lang.Object
  extended by org.biojava.ontology.io.OboParser

public class OboParser
extends java.lang.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

Constructor Summary
OboParser()
           
 
Method Summary
 Ontology parseOBO(java.io.BufferedReader oboFile, java.lang.String ontoName, java.lang.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(java.io.BufferedReader oboFile,
                         java.lang.String ontoName,
                         java.lang.String ontoDescription)
                  throws ParseException,
                         java.io.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
java.io.IOException