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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
OboParser
public OboParser()
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