org.biojava.ontology.io

Class OboParser

java.lang.Object

org.biojava.ontology.io.OboParser

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

Constructor Summary

Constructors

Constructor and Description
OboParser()

Method Summary

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